@text
Kinemage Supplement to Branden & Tooze "Introduction to Protein Structure"
Chapter 12 -  RECOGNITION OF FOREIGN MOLECULES BY THE IMMUNE SYSTEM

		Contents of file C12IMMUN.KIN:
Kin.1- Immunoglobulin domains - CL, VL, light chain, and FAB (Fig. 12.8, 12.9)
Kin.2- Lysozyme/antibody complex - overview and a binding detail (Fig. 12.15,12.16)
Kin.3- HLA-A2, an MHC antigen - Calphas, SS, and domains (Fig. 12.20a, 12.21)

	Kinemage 1 shows the domain organization of the FAB part of an immunoglobulin, and the internal organization of the domains.  View1 is a constant domain (CL), colored as in Fig. 12.8a, with the rear beta sheet in skyblue and the front sheet in seagreen; the strands are all antiparallel and have a Greek key topology.  The highly-conserved disulfide bond that crosses the inside of the barrel is in yellow.  The connection in pink is homologous to the region that is enlarged to form CDR2 in variable domains.
	View2 is a similar view of a variable domain (VL); the blue and green beta strands are in equivalent positions and have equivalent connections as in the constant domain.  The pink region of CDR2 is longer and has two additional short strands.  Along with the CDR1 and CDR3 loops and the 3 CDR's on VH, it makes up the hypervariable region that changes sequence and conformation in various antibody molecules to provide complementary binding for an extremely wide variety of antigens.
	View3 shows both domains of the light chain, which are joined by a somewhat flexible linker.  Turn on "Heavy ch" and turn off "labels" to see all 4 domains of this FAB fragment.  The two variable domains associate tightly, with their green sheets back-to-back and their CDR's close together, and the two constant domains associate tightly with their two blue sheets back-to-back.  In an intact IgG, the second half of the heavy chains from two FAB's associate to form a 4-domain FC region made up of CH2 and CH3 domains.

	Kinemage 2 shows a complex of the enzyme lysozyme with an anti-lysozyme antibody (the FAB portion of Hy/Hel-10).  Lysozyme is in greentint, FAB in white and yellowtint, with SS bridges.  This is a different anti-lysozyme antibody than the one illustrated in Fig. 12.15 and 12.16, and it binds to a completely separate region on lysozyme (Gln 121 from the other interface is shown for comparison), but the general nature of the binding is quite similar.  As can be seen in View1, the interface is quite extensive and fairly flat, and lysozyme sits over almost all of the surface made by the tops of the two variable domains.  	In addition to the usual aromatic, hydrophobic, and Hbond interactions, this particular complex buries and complements several charged residues.  Choose View3 and turn on "binding sc" to see the set of heavy-chain sidechains that bind Lys 97 of lysozyme.  The lysine is sandwiched between two aromatic rings and makes a charged Hbond to Asp 32, which in turn is Hbonded to an Asn.

	Kinemage 3 shows the Calpha backbone of the HLA-A2 molecule, a class 1 major-histocompatibility-complex (MHC) antigen involved in T-cell activation.  It consists of 2 chains, a single-domain light chain called beta2-microglobulin (pinktint), and a heavy chain of 3 domains, alpha1 (yellowtint), alpha2 (greentint), and alpha3 (bluetint).  B2m and a3 are related to immunoglobulin constant domains, and are paired at bottom of the molecule (in View1, like Fig. 12.20a), near the cell surface.  A1 and a2 are the similar halves of the antigen-presenting top portion, which consists of a "floor" of an 8-stranded antiparallel beta sheet with two long alpha-helices on top separated by a crevice in which the antigen peptide binds (orange line in View2, from the top, like Fig. 12.21).  Each of a1 and a2 has a simple topology of 4 up&down beta strands (called a "W") followed by a long helix across the top of the sheet.  MHC proteins are highly polymorphic, with the different classes binding different sets of peptides that have been cleaved from foreign antigenic proteins.  T-cell receptors recognize those peptides by binding to the top surface of the complex formed by the peptide bound into the cleft of a particular MHC molecule.

@kinemage 1
@caption (B&T Fig. 12.8, 12.9)
Immunoglobulin domains - CL constant domain (View1) and VL variable domain (View2), with rear beta sheet in skyblue, front beta sheet in seagreen,disulfide in yellow, and CDR loops or homologous region in pink.  Choose View3 to see the entire light chain, and turn on "Heavy ch" to see the entire FAB fragment.  (from PDB file 2FB4)
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@group {Heavy ch} off 
@subgroup {VH} dominant 
@vectorlist {ca-ca} color= gray 
{ca glu h 1}P 56.019 52.32 19.417
{ca val h 2}52.829 51.682 21.334
{ca gln h 3}49.937 53.678 19.865
{ca leu h 4}46.423 53.884 21.416
{ca val h 5}43.663 55.651 19.383
{ca gln h 6}40.229 56.3 20.973
{ca ser h 7}37.071 56.651 18.917
{ca gly h 8}33.299 56.871 19.29
{ca gly h 9}32.792 59.983 21.378
{ca gly h 10}29.79 62.217 20.931
{ca val h 11}27.046 64.49 22.226
{ca val h 12}23.982 62.769 23.689
{ca gln h 13}21.061 63.46 25.959
{ca pro h 14}20.542 61.831 29.403
{ca gly h 15}19.61 58.182 29.434
{ca arg h 16}21.092 57.466 25.998
{ca ser h 17}24.06 55.271 24.976
{ca leu h 18}27.489 55.368 23.403
{ca arg h 19}30.24 52.915 22.606
{ca leu h 20}33.894 53.843 22.693
{ca ser h 21}36.662 51.922 21.017
{ca cys h 22}40.425 51.969 21.474
{ca ser h 23}42.472 50.509 18.715
{ca ser h 24}46.069 49.583 19.39
{ca ser h 25}49.396 48.791 17.66
{ca gly h 26}53.126 48.422 18.528
{ca phe h 27}52.679 45.712 21.225
{ca ile h 28}51.274 42.245 21.969
{ca phe h 29}47.887 43.485 22.996
{ca ser h 30}46.699 40.279 24.657
{ca ser h 31}49.491 40.487 27.261
{ca tyr h 32}48.475 43.592 29.08
{ca ala h 33}45.609 44.871 31.201
{ca met h 34}43.856 47.903 29.661
{ca tyr h 35}42.253 50.955 31.311
{ca trp h 36}39.591 53.567 30.687
{ca val h 37}40.149 56.926 32.458
{ca arg h 38}38.121 60.087 32.052
{ca gln h 39}38.486 63.811 32.652
{ca ala h 40}35.549 66.164 33.234
{ca pro h 41}36.158 69.693 32.052
{ca gly h 42}38.04 71.602 34.693
{ca lys h 43}38.445 68.543 36.869
{ca gly h 44}41.063 65.859 37.531
{ca leu h 45}41.71 62.336 36.191
{ca glu h 46}39.083 59.765 37.241
{ca trp h 47}39.661 56.013 36.639
{ca val h 48}36.679 54.25 35.015
{ca ala h 49}37.595 50.605 34.493
{ca ile h 50}40.257 47.938 34.044
{ca ile h 51}40.139 44.631 32.195
{ca trp h 52}42.637 41.764 32.532
{ca asp h 53}44.835 40.582 29.672
{ca asp h 54}42.526 37.625 28.876
{ca gly h 55}39.352 39.508 29.863
{ca ser h 56}38.69 37.021 32.642
{ca asp h 57}37.838 39.785 35.038
{ca gln h 58}36.969 43.465 34.954
{ca his h 59}36.67 46.144 37.675
{ca tyr h 60}34.738 49.419 37.679
{ca ala h 61}34.542 52.777 39.469
{ca asp h 62}31.523 52.877 41.826
{ca ser h 63}29.909 55.742 39.821
{ca val h 64}29.746 53.643 36.695
{ca lys h 65}29.146 50.113 37.813
{ca gly h 66}26.258 48.55 35.983
{ca arg h 67}25.926 51.279 33.347
{ca phe h 68}29.343 50.742 31.723
{ca thr h 69}30.845 47.535 30.3
{ca ile h 70}34.528 47.105 29.476
{ca ser h 71}35.409 44.358 27.064
{ca arg h 72}38.15 43.548 24.595
{ca asn h 73}38.884 41.714 21.409
{ca asp h 74}42.44 40.34 21.515
{ca ser h 75}41.881 39.122 18.025
{ca lys h 76}41.444 42.617 16.725
{ca asn h 77}43.668 44.344 19.348
{ca thr h 78}40.685 46.598 20.396
{ca leu h 79}39.261 47.738 23.688
{ca phe h 80}35.582 48.744 24.067
{ca leu h 81}33.557 50.814 26.498
{ca gln h 82}29.753 50.335 26.286
{ca met h 83}28.206 53.265 28.057
{ca asp h 84}24.536 52.876 28.908
{ca ser h 85}22.036 55.22 30.625
{ca leu h 86}24.462 58.089 30.416
{ca arg h 87}24.288 60.954 32.925
{ca pro h 88}25.416 64.593 32.599
{ca glu h 89}28.112 63.852 35.157
{ca asp h 90}29.637 61.456 32.686
{ca thr h 91}30.711 64.33 30.478
{ca gly h 92}34.47 64.233 29.926
{ca val h 93}37.405 63.267 27.748
{ca tyr h 94}37.859 59.482 27.723
{ca phe h 95}41.328 57.967 27.545
{ca cys h 96}42.348 54.401 27.154
{ca ala h 97}45.663 53.336 28.625
{ca arg h 98}47.863 50.264 28.784
{ca asp h 99}48.771 48.695 32.133
{ca gly h 100}52.535 48.363 32.093
{ca gly h 101}52.741 45.159 34.136
{ca his h 101a} 51.857 41.51 33.918
{ca gly h 101b} 48.263 41.482 32.772
{ca phe h 101c} 46.471 42.413 36.028
{ca cys h 101d} 46.541 44.362 39.285
{ca ser h 102}46.349 42.814 42.743
{ca ser h 103}47.516 42.965 46.364
{ca ala h 104}50.798 41.646 44.994
{ca ser h 104a} 51.424 44.18 42.274
{ca cys h 104b} 49.988 46.964 40.061
{ca phe h 104c} 52.173 48.754 37.579
{ca gly h 104d} 49.554 51.259 36.48
{ca pro h 105}48.936 53.132 33.198
{ca asp h 106}52.054 53.458 31.128
{ca tyr h 107}51.073 54.558 27.702
{ca trp h 108}47.928 56.625 27.071
{ca gly h 109}45.774 57.446 24.05
{ca gln h 110}44.743 60.926 22.909
{ca gly h 111}41.198 61.044 24.311
{ca thr h 112}37.712 61.029 22.852
{ca pro h 113}35.231 63.65 24.22
{ca val h 114}31.828 62.722 25.609
{ca thr h 115}29.145 65.343 26.23
{ca val h 116}25.906 64.409 28.01
{ca ser h 117}23.496 67.32 28.356
{ca ser h 118}19.828 68.098 28.821
@vectorlist {ss} color= gold 
{ca cys h 22}P 40.425 51.969 21.474
{cb cys h 22}40.847 51.978 22.951
{sg cys h 22}42.611 52.068 23.299
{sg cys h 96}42.88 53.671 24.547
{cb cys h 96}42.051 53.329 26.084
{ca cys h 96}42.348 54.401 27.154
{ca cys h 101d} P 46.541 44.362 39.285
{cb cys h 101d} 45.967 45.786 39.249
{sg cys h 101d} 46.915 46.919 38.202
{sg cys h 104b} 47.582 48.41 39.462
{cb cys h 104b} 48.727 47.641 40.639
{ca cys h 104b} 49.988 46.964 40.061
@subgroup {CH1} dominant 
@vectorlist {Calphas} color= gray 
{ca ser h 118}P 19.828 68.098 28.821
{ca ala h 119}20.23 70.628 26.018
{ca ser h 120}19.362 69.866 22.444
{ca thr h 121}21.09 71.102 19.32
{ca lys h 122}20.422 74.814 18.836
{ca gly h 123}21.899 76.957 16.055
{ca pro h 124}23.228 80.385 17.132
{ca ser h 125}21.722 83.798 16.906
{ca val h 126}24.253 86.098 15.251
{ca phe h 127}24.513 89.802 16.171
{ca pro h 128}26.954 92.349 14.845
{ca leu h 129}29.031 94.268 17.415
{ca ala h 130}29.343 97.547 15.572
{ca pro h 131}32.498 99.676 15.691
{ca ser h 132}31.99 102.638 18.051
{ca ser h 133}32.264 106.291 16.93
{ca lys h 134}33.845 107.028 20.277
{ca ser h 135}37.525 107.34 19.582
{ca thr h 136}40.213 105.511 21.5
{ca ser h 137}43.815 106.513 22.237
{ca gly h 138}45.717 104.767 19.438
{ca gly h 139}45.126 103.397 15.934
{ca thr h 140}42.364 101.086 17.121
{ca ala h 141}38.766 100.461 16.213
{ca ala h 142}37.175 97.284 17.478
{ca leu h 143}34.329 95.483 15.797
{ca gly h 144}32.978 91.933 16.193
{ca cys h 145}30.195 89.353 16.192
{ca leu h 146}28.159 87.916 19.029
{ca val h 147}27.384 84.245 18.555
{ca lys h 148}24.734 83.71 21.048
{ca asp h 149}22.962 80.685 22.64
{ca tyr h 150}24.137 77.67 20.613
{ca phe h 151}24.549 73.936 21.369
{ca pro h 152}26.773 72.135 21.16
{ca gln h 153}30.319 73.38 20.666
{ca pro h 154}32.055 74.134 18.564
{ca val h 155}31.315 76.968 16.15
{ca thr h 156}33.529 78.233 13.371
{ca val h 157}33.895 81.98 12.85
{ca ser h 158}35.98 83.55 10.14
{ca trp h 159}36.098 87.124 8.708
{ca asn h 160}35.654 88.247 5.136
{ca ser h 161}35.427 84.644 4.289
{ca gly h 162}38.712 83.969 5.986
{ca ala h 163}40.446 86.494 3.75
{ca leu h 164}40.938 88.445 7.001
{ca thr h 165}43.107 86.959 9.653
{ca ser h 166}45. 90.002 10.781
{ca gly h 167}43.913 91.19 14.232
{ca val h 168}41.073 88.787 14.731
{ca his h 169}40.538 87.563 18.268
{ca thr h 170}37.816 84.941 18.894
{ca phe h 171}37.286 84.383 22.596
{ca pro h 172}36.51 81.202 24.439
{ca ala h 173}32.774 80.652 24.677
{ca val h 174}30.775 81.081 27.925
{ca leu h 175}28.588 78.134 29.099
{ca gln h 176}25.525 79.84 30.387
{ca ser h 177}23.125 78.593 33.066
{ca ser h 178}20.829 77.695 30.16
{ca gly h 179}23.067 74.941 29.064
{ca leu h 180}23.729 76.989 25.942
{ca tyr h 181}26.951 78.663 24.802
{ca ser h 182}27.803 82.135 23.591
{ca leu h 183}31.04 83.473 22.131
{ca ser h 184}32.485 86.703 20.775
{ca ser h 185}34.91 87.264 17.925
{ca val h 186}36.509 90.698 17.514
{ca val h 187}38.691 92.411 14.973
{ca thr h 188}40.812 95.338 15.993
{ca val h 189}41.314 97.449 12.864
{ca pro h 190}43.033 100.838 12.242
{ca ser h 191}40.237 103.323 12.543
{ca ser h 192}41.114 104.859 9.157
{ca ser h 193}39.759 101.757 7.352
{ca leu h 194}36.488 101.668 9.176
{ca gly h 195}34.108 102.846 6.569
{ca thr h 196}36.703 102.565 3.773
{ca gln h 197}36.256 98.766 3.972
{ca thr h 198}33.651 95.986 4.558
{ca tyr h 199}33.638 93.442 7.367
{ca ile h 200}31.45 90.381 7.487
{ca cys h 201}31.77 87.532 9.954
{ca asn h 202}30.985 84.062 8.573
{ca val h 203}29.509 81.796 11.219
{ca asn h 204}29.226 78.062 10.734
{ca his h 205}27.572 75.818 13.254
{ca lys h 206}28.089 72.347 11.775
{ca pro h 207}25.948 70.364 14.318
{ca ser h 208}22.827 72.349 13.373
{ca asn h 209}23.931 73.177 9.874
{ca thr h 210}23.372 76.874 10.681
{ca lys h 211}25.467 79.08 8.373
{ca val h 212}25.149 82.844 8.876
{ca asp h 213}27.043 85.835 7.479
{ca lys h 214}26.627 89.049 9.366
{ca arg h 215}27.764 92.37 7.806
{ca val h 216}29.287 94.556 10.519
{ca glu h 217}28.779 98.193 9.84
{ca pro h 218}29.437 101.556 11.548
{ca lys h 219}26.287 103.022 13.075
{ca ser h 220}24.717 105.969 11.209
{ca cys h 221}26.501 108.437 13.497
@vectorlist {ss} color= yellow 
{ca cys h 145}P 30.195 89.353 16.192
{cb cys h 145}30.05 88.403 14.992
{sg cys h 145}29.812 89.26 13.43
{sg cys h 201}29.914 87.749 12.042
{cb cys h 201}31.62 87.684 11.467
{ca cys h 201}31.77 87.532 9.954
@group {Light ch} 
@subgroup {VL} dominant 
@vectorlist {loops} color= white 
{ca gln l 1}P 37.58 54.759 49.388
{ca ser l 2}37.742 57.18 46.535
{ca val l 3}40.586 59.749 46.332
{ca leu l 4}44.265 60.491 46.942
{ca gln l 6}P 47.173 66.484 46.748
{ca pro l 7}47.691 70.182 47.45
{ca pro l 8}45.854 72.161 44.696
{ca ser l 9}48.917 74.177 43.91
{ca ala l 10}52.649 74.367 44.336
{ca ser l 11}54.83 77.265 43.26
{ca gly l 12}58.321 78.569 43.183
{ca thr l 13}60.883 80.574 41.268
{ca pro l 14}62.925 78.989 38.457
{ca gly l 15}65.738 76.837 39.84
{ca gln l 16}64.161 76.303 43.245
{ca gly l 67}P 53.74 54.692 54.922
{ca ala l 68}50.6 56.075 53.414
{ca gly l 76}P 65.365 72.931 39.915
{ca leu l 77}62.035 74.218 38.69
{ca gln l 78}62.11 75.162 34.983
{ca ser l 79}59.472 76.95 32.806
{ca glu l 80}58.496 73.632 31.17
{ca asp l 81}57.361 72.351 34.534
{ca glu l 82}54.243 74.446 34.566
{ca thr l 106}P 53.277 77.806 38.611
{ca val l 107}56.751 79.112 37.8
{ca leu l 108}56.772 82.265 39.797
{ca gly l 109}57.552 85.677 38.525
@vectorlist {sheet 1} color= sky master= {sheet 1} 
{ca leu l 4}P 44.265 60.491 46.942
{ca thr l 5}44.828 63.965 48.378
{ca gln l 6}47.173 66.484 46.748
{ca gln l 16}P 64.161 76.303 43.245
{ca arg l 17}63.286 72.907 44.609
{ca val l 18}59.545 72.311 44.526
{ca thr l 19}57.942 69.203 45.96
{ca ile l 20}54.38 67.887 45.744
{ca ser l 21}52.762 65.671 48.366
{ca cys l 22}50.102 62.935 47.96
{ca ser l 23}48.337 61.66 51.033
{ca gly l 24}46.574 58.321 51.001
{ca arg l 60}P 65.472 66.447 38.215
{ca phe l 61}62.32 64.465 38.908
{ca ser l 62}62.467 62.135 41.857
{ca gly l 63}59.907 60.139 43.777
{ca ser l 64}59.586 59.028 47.335
{ca lys l 65}57.154 56.947 49.397
{ca ser l 66}56.687 56.109 53.072
{ca gly l 67}53.74 54.692 54.922
{ca ala l 68}P 50.6 56.075 53.414
{ca ser l 69}52.268 59.119 51.929
{ca ala l 70}54.271 59.847 48.805
{ca ser l 71}55.92 62.802 47.219
{ca leu l 72}57.232 64.11 43.904
{ca ala l 73}60.395 66.32 43.912
{ca ile l 74}61.267 68.773 41.133
{ca gly l 75}64.798 69.707 41.717
{ca gly l 76}65.365 72.931 39.915
@vectorlist {sheet 2} color= sea master= {sheet 2} 
{ca thr l 31}P 53.309 51.447 44.673
{ca val l 32}52.723 55.049 43.494
{ca asn l 33}52.969 56.525 39.99
{ca trp l 34}53.17 60.216 39.059
{ca tyr l 35}51.761 61.74 35.87
{ca gln l 36}52.348 65.079 34.278
{ca gln l 37}49.433 66.479 32.315
{ca leu l 38}48.318 69.505 30.359
{ca pro l 39}44.528 69.703 30.977
{ca glu l 82}P 54.243 74.446 34.566
{ca thr l 83}51.614 71.736 34.353
{ca asp l 84}49.248 69.531 36.327
{ca tyr l 85}50.642 66.604 38.305
{ca tyr l 86}48.73 63.522 39.506
{ca cys l 87}49.816 60.717 41.799
{ca ala l 88}48.126 57.312 41.462
{ca ala l 89}47.838 53.896 43.136
{ca trp l 90}45.811 50.705 43.26
{ca asp l 91}43.578 50.231 46.249
{ca val l 92}43.607 46.525 47.329
{ca asn l 95}P 39.84 46.879 43.833
{ca ala l 96}40.213 50.208 42.086
{ca tyr l 97}42.882 52.365 40.55
{ca val l 98}42.836 55.687 42.378
{ca phe l 99}44.004 59.101 41.119
{ca gly l 100}45.141 61.984 43.241
{ca thr l 101}43.064 65.213 43.165
{ca gly l 102}46.005 66.821 41.425
{ca thr l 103}48.382 69.784 41.69
{ca lys l 104}49.003 72.766 39.49
{ca val l 105}52.511 74.221 39.438
{ca thr l 106}53.277 77.806 38.611
@vectorlist {CDR} color= pink master= {CDR's} 
{ca gly l 24}P 46.574 58.321 51.001
{ca thr l 25}45.456 55.464 53.274
{ca ser l 26}46.619 52.026 54.343
{ca ser l 27}44.668 50.387 51.572
{ca asn l 27a} 46.246 52.226 48.627
{ca ile l 27b} 49.615 54.004 49.172
{ca gly l 28}50.148 51.989 52.327
{ca ser l 29}49.7 48.784 50.339
{ca ser l 30}50.763 49.429 46.763
{ca thr l 31}53.309 51.447 44.673
{ca pro l 39}P 44.528 69.703 30.977
{ca gly l 40}42.336 67.635 28.64
{ca met l 41}45.415 66.316 26.876
{ca ala l 42}47.027 62.898 27.343
{ca pro l 43}49.024 62.529 30.542
{ca lys l 44}52.536 61.174 30.515
{ca leu l 45}54.109 58.794 33.091
{ca leu l 46}56.874 60.612 35.012
{ca ile l 47}57.516 58.212 37.89
{ca tyr l 48}56.514 54.539 38.283
{ca arg l 49}56.722 52.175 41.213
{ca asp l 50}57.395 54.942 43.805
{ca ala l 51}60.766 56.057 42.565
{ca met l 52}61.536 54.793 39.097
{ca arg l 53}61.818 56.987 36.031
{ca pro l 54}61.07 56.09 32.41
{ca ser l 55}63.751 56.972 29.89
{ca gly l 56}63.313 60.473 28.536
{ca val l 57}62.238 61.838 31.887
{ca pro l 58}64.729 64.377 33.258
{ca asp l 59}66.946 63.541 36.225
{ca arg l 60}65.472 66.447 38.215
{ca val l 92}P 43.607 46.525 47.329
{ca ser l 93}40.332 46.769 49.429
{ca leu l 94}38.248 48.598 46.767
{ca asn l 95}39.84 46.879 43.833
@vectorlist {ss} color= yellow master= {SS} 
{ca cys l 22}P 50.102 62.935 47.96
{cb cys l 22}50.634 62.048 46.799
{sg cys l 22}49.578 60.677 46.251
{sg cys l 87}48.929 61.216 44.43
{cb cys l 87}50.236 60.75 43.279
{ca cys l 87}49.816 60.717 41.799
@labellist {CDR lbl} color=hotpink master= {labels}
{ CDR 1} 49.7 48.784 50.339
{ CDR 3} 40.332 46.769 49.429
{CDR 2}54.762 52.601 41.812
@labellist {N lbl} color=blue master= {labels}
{ N} 37.58 54.759 49.388
@subgroup {CL} dominant 
@vectorlist {loops} color= white 
{ca gly l 109}P 57.552 85.677 38.525
{ca gln l 110}56.621 86.547 34.96
{ca pro l 111}55.817 90.19 34.404
{ca lys l 112}52.385 91.371 35.344
{ca ala l 113}50.446 92.422 32.239
{ca asn l 114}47.531 94.93 32.485
{ca pro l 122}P 23.488 95.854 22.693
{ca ser l 123}22.97 95.515 18.99
{ca ser l 124}19.928 97.246 17.458
{ca glu l 125}18.913 93.941 15.908
{ca glu l 126}19.051 92.23 19.25
{ca leu l 127}17.021 95.041 20.802
{ca gln l 128}14.373 94.311 18.18
{ca ala l 129}14.339 90.732 19.339
{ca asn l 130}13.448 92.242 22.715
{ca lys l 131}16.708 91.202 24.372
{ca phe l 141}P 46.535 89.963 31.06
{ca tyr l 142}48.894 88.208 33.447
{ca pro l 143}48.32 86.803 35.993
{ca gly l 144}44.969 85.158 35.213
{ca ala l 145}43.033 86.635 38.125
{ca gln l 169}P 46.47 81.986 25.227
{ca ser l 170}49.502 80.781 23.26
{ca asn l 171}50.655 84.237 24.253
{ca asn l 172}51.176 83.031 27.828
{ca lys l 173}48.699 85.73 28.723
{ca thr l 183}P 15.883 93.993 28.909
{ca pro l 184}15.872 96.745 26.313
{ca glu l 185}13.92 98.751 28.851
{ca gln l 186}16.522 98.387 31.624
{ca trp l 187}19.126 99.246 29.016
{ca lys l 188}17.272 102.335 27.994
{ca ser l 189}16.305 103.431 31.455
{ca his l 190}19.882 104.418 32.417
{ca arg l 191}22.264 107.005 31.02
{ca glu l 200}P 46.314 93.326 40.737
{ca gly l 201}45.108 96.465 42.53
{ca pro l 210}P 22.328 104.057 24.54
{ca thr l 211}23.495 107.121 22.478
{ca glu l 212}23.443 105.749 18.977
{ca cys l 213}23.561 109.134 17.24
{ca ser l 214}22.355 111.173 20.197
@vectorlist {sheet 1} color= sky master= {sheet 1} 
{ca asn l 114}P 47.531 94.93 32.485
{ca pro l 115}44.305 93.939 30.737
{ca thr l 116}42.787 95.429 27.555
{ca val l 117}39.094 96.111 28.117
{ca thr l 118}36.73 96.262 25.159
{ca leu l 119}33.057 97.01 25.777
{ca phe l 120}30.068 96.566 23.369
{ca pro l 121}26.519 97.792 23.986
{ca pro l 122}23.488 95.854 22.693
{ca lys l 131}P 16.708 91.202 24.372
{ca ala l 132}19.972 92.981 25.365
{ca thr l 133}23.457 91.769 25.883
{ca leu l 134}26.376 93.929 26.908
{ca val l 135}29.769 92.357 26.212
{ca cys l 136}32.983 93.104 28.097
{ca leu l 137}36.037 91.501 26.567
{ca ile l 138}39.285 91.38 28.586
{ca ser l 139}42.579 90.348 26.905
{ca asp l 140}46.342 90.117 27.281
{ca phe l 141}46.535 89.963 31.06
{ca gly l 160}P 22.296 88.84 34.631
{ca val l 161}26.098 88.679 34.612
{ca glu l 162}27.912 85.658 33.091
{ca thr l 163}31.731 85.752 33.409
{ca thr l 164}34.155 83.187 31.949
{ca lys l 165}37.084 81.818 33.855
{ca pro l 166}40.264 83.184 32.361
{ca ser l 167}42.015 81.026 29.843
{ca lys l 168}45.582 81.073 28.778
{ca gln l 169}46.47 81.986 25.227
{ca lys l 173}P 48.699 85.73 28.723
{ca tyr l 174}45.029 85.313 29.601
{ca ala l 175}41.593 86.173 28.18
{ca ala l 176}38.13 86.423 29.639
{ca ser l 177}34.648 87.589 28.68
{ca ser l 178}31.752 88.932 30.687
{ca tyr l 179}28.152 89.182 29.507
{ca leu l 180}25.418 91.255 31.
{ca ser l 181}21.873 90.365 30.145
{ca leu l 182}19.134 92.939 30.338
{ca thr l 183}15.883 93.993 28.909
@vectorlist {sheet 2} color= sea master= {sheet 2} 
{ca ala l 145}P 43.033 86.635 38.125
{ca val l 146}40.499 89.386 37.458
{ca thr l 147}37.408 90.83 39.039
{ca val l 148}34.72 92.135 36.75
{ca ala l 149}31.938 94.396 37.973
{ca trp l 150}29.043 95.918 36.114
{ca lys l 151}27.709 99.323 36.991
{ca ala l 152}24.692 101.302 35.738
{ca asp l 153}24.866 105.064 36.24
{ca arg l 191}P 22.264 107.005 31.02
{ca ser l 192}25.378 104.866 31.192
{ca tyr l 193}26.672 101.354 31.647
{ca ser l 194}30.167 100.409 32.83
{ca cys l 195}32.339 97.374 32.853
{ca gln l 196}34.991 97.631 35.49
{ca val l 197}37.925 95.256 35.656
{ca thr l 198}40.229 95.014 38.646
{ca his l 199}43.551 93.315 38.154
{ca glu l 200}46.314 93.326 40.737
{ca gly l 201}P 45.108 96.465 42.53
{ca ser l 202}44.549 98.323 39.274
{ca thr l 203}40.941 99.065 38.033
{ca val l 204}40.081 99.869 34.435
{ca glu l 205}36.615 101.067 33.48
{ca lys l 206}34.941 101.328 30.078
{ca thr l 207}31.592 103.074 29.54
{ca val l 208}28.813 102.768 26.859
{ca ala l 209}25.502 104.686 26.479
{ca pro l 210}22.328 104.057 24.54
@vectorlist {CDR-like} color= pink 
{ca asp l 153}P 24.866 105.064 36.24
{ca gly l 154}26.226 105.345 39.765
{ca ser l 155}25.332 101.813 40.844
{ca pro l 156}26.3 98.128 40.879
{ca val l 157}24.387 95.868 38.485
{ca lys l 158}22.551 93.071 40.35
{ca ala l 159}22.087 90.006 38.214
{ca gly l 160}22.296 88.84 34.631
@vectorlist {ss} color= yellow master= {SS} 
{ca cys l 136}P 32.983 93.104 28.097
{cb cys l 136}32.894 93.46 29.575
{sg cys l 136}34.284 94.419 30.202
{sg cys l 195}33.63 95.053 31.984
{cb cys l 195}32.662 96.531 31.613
{ca cys l 195}32.339 97.374 32.853
@labellist {C lbl} color=red master= {labels}
{ C} 22.355 111.173 20.197
@kinemage 2
@caption (B&T Fig. 12.15, 12.16)
Complex of lysozyme with an anti-lysozyme antibody (FAB portion of Hy/Hel-10).  Lysozyme is in greentint, FAB in white and yellowtint, with SS bridges.  Choose View3 and turn on "binding sc" to see sidechains that bind Lys 97 of lysozyme.  (from PDB file 3HFM)
@onewidth 
@zoom 0.94
@zslab 130
@center 21.285 34.368 46.308
@matrix
.861171 -.357865 -.360996 -.508301 -.611749 -.60613 -.003926 .705476 -.708723
@2zoom 1.45
@2zslab 170
@2center 19.016 22.138 62.562
@2matrix
.89157 -.322639 -.317819 -.450791 -.564825 -.691202 .043497 .759524 -.649023
@3zoom 3.3
@3zslab 190
@3center 22.985 19.865 63.074
@3matrix
-.621699 -.565063 .542397 .774676 -.545817 .319313 .115618 .618698 .777074
@group {FAB} 
@subgroup dominant {light ch} 
@vectorlist {ca-ca} color= white master= {Calphas}
{ca asp l 1}P 9.822 19.54 43.611
{ca ile l 2}8.185 22.322 45.717
{ca val l 3}8.059 26.04 44.9
{ca leu l 4}8.071 29.244 46.882
{ca thr l 5}6.917 32.484 45.22
{ca gln l 6}8.659 35.602 46.481
{ca ser l 7}6.718 38.811 46.071
{ca pro l 8}7.52 41.604 45.518
{ca ala l 9}10.411 41.496 43.034
{ca thr l 10}12.176 44.677 44.185
{ca leu l 11}11.693 47.245 46.917
{ca ser l 12}13.219 50.704 47.017
{ca val l 13}12.773 52.03 50.588
{ca thr l 14}13.392 55.144 52.56
{ca pro l 15}15.562 54.846 55.634
{ca gly l 16}13.248 54.462 58.601
{ca asn l 17}10.222 53.024 56.809
{ca ser l 18}8.829 49.535 57.413
{ca val l 19}8.677 46.944 54.651
{ca ser l 20}7.528 43.312 54.383
{ca leu l 21}8.475 40.482 52.042
{ca ser l 22}6.222 37.496 51.295
{ca cys l 23}7.043 33.906 50.284
{ca arg l 24}4.356 31.47 49.125
{ca ala l 25}5.149 27.8 49.157
{ca ser l 26}2.923 25.609 46.962
{ca gln l 27}2.545 23.183 49.845
{ca ser l 28}1.605 23.03 53.482
{ca ile l 29}5.286 22.885 54.505
{ca gly l 30}4.2 24.126 57.931
{ca asn l 31}6.713 26.227 59.838
{ca asn l 32}9.97 25.292 58.073
{ca leu l 33}10.526 28.401 55.947
{ca his l 34}13.814 30.143 56.743
{ca trp l 35}15.128 33.424 55.52
{ca tyr l 36}18.623 34.391 54.493
{ca gln l 37}20.176 37.67 53.35
{ca gln l 38}22.814 37.964 50.619
{ca lys l 39}24.464 41.386 50.682
{ca ser l 40}26.389 42.398 47.548
{ca his l 41}29.627 40.468 47.243
{ca glu l 42}29.081 37.658 49.703
{ca ser l 43}27.711 34.365 50.774
{ca pro l 44}24.306 34.486 52.431
{ca arg l 45}23.66 34.445 56.173
{ca leu l 46}20.691 33.058 58.113
{ca leu l 47}18.36 35.703 59.529
{ca ile l 48}15.405 33.757 60.903
{ca lys l 49}15.02 29.978 61.409
{ca tyr l 50}11.871 27.821 61.25
{ca ala l 51}9.487 30.802 60.774
{ca ser l 52}9.689 33.307 63.599
{ca gln l 53}12.748 31.923 65.423
{ca ser l 54}15.255 34.791 65.182
{ca ile l 55}18.935 33.777 64.888
{ca ser l 56}21.248 35.433 67.465
{ca gly l 57}23.205 38.522 66.554
{ca ile l 58}20.586 39.781 64.104
{ca pro l 59}18.642 43.035 64.428
{ca ser l 60}15.398 43.277 66.366
{ca arg l 61}14.07 44.96 63.247
{ca phe l 62}13.749 41.527 61.684
{ca ser l 63}10.509 39.712 62.411
{ca gly l 64}9.029 36.632 60.783
{ca ser l 65}5.705 34.901 61.155
{ca gly l 66}3.453 32.416 59.449
{ca ser l 67}3.081 28.712 59.007
{ca gly l 68}0.963 26.934 56.415
{ca thr l 69}1.517 28.44 52.955
{ca asp l 70}1.579 32.166 53.533
{ca phe l 71}4.876 33.224 55.066
{ca thr l 72}6.274 36.726 55.678
{ca leu l 73}9.371 38.483 57.044
{ca ser l 74}9.163 42.13 58.114
{ca ile l 75}11.968 44.676 58.291
{ca asn l 76}10.905 47.376 60.75
{ca ser l 77}12.543 50.797 60.577
{ca val l 78}14.877 49.867 57.69
{ca glu l 79}18.519 50.815 57.649
{ca thr l 80}20.944 51.561 54.847
{ca glu l 81}22.811 48.471 55.928
{ca asp l 82}19.71 46.521 54.863
{ca phe l 83}20.316 46.752 51.136
{ca gly l 84}20.843 43.218 49.85
{ca met l 85}18.66 40.361 48.723
{ca tyr l 86}16.37 38.098 50.667
{ca phe l 87}15.499 34.53 49.692
{ca cys l 88}13.399 31.934 51.537
{ca gln l 89}14.112 28.172 51.753
{ca gln l 90}11.83 25.359 52.91
{ca ser l 91}13.505 22.301 54.468
{ca asn l 92}10.217 20.515 54.896
{ca ser l 93}10.667 18.356 51.828
{ca trp l 94}13.485 17.129 49.637
{ca pro l 95}14.758 18.826 47.678
{ca tyr l 96}15.169 21.938 49.798
{ca thr l 97}14.087 24.749 47.398
{ca phe l 98}14.961 28.465 47.425
{ca gly l 99}12.939 31.524 46.464
{ca gly l 100}13.038 34.026 43.647
{ca gly l 101}14.724 36.587 45.927
{ca thr l 102}13.837 40.222 46.66
{ca lys l 103}16.263 43.119 46.174
{ca leu l 104}15.544 45.765 48.8
{ca glu l 105}16.955 49.126 47.736
{ca ile l 106}17.623 52.127 49.956
{ca lys l 107}16.149 55.438 48.841
{ca arg l 108}19.035 57.876 48.779
{ca ala l 109}18.61 61.543 47.816
{ca asp l 110}18.794 62.604 44.116
{ca ala l 111}22.446 62.801 43.132
{ca ala l 112}24.081 63.437 39.771
{ca pro l 113}26.524 61.605 37.567
{ca thr l 114}30.184 62.576 37.271
{ca val l 115}30.974 61.857 33.636
{ca ser l 116}34.454 61.046 32.407
{ca ile l 117}35.982 60.187 29.032
{ca phe l 118}39.247 58.474 28.03
{ca pro l 119}40.388 58.031 24.41
{ca pro l 120}41.628 54.691 23.109
{ca ser l 121}44.884 54.087 25.017
{ca ser l 122}48.09 54.329 22.945
{ca glu l 123}49.193 50.758 23.14
{ca gln l 124}45.649 49.67 22.227
{ca leu l 125}45.8 51.459 18.887
{ca thr l 126}48.901 49.444 17.995
{ca ser l 127}46.834 46.262 18.059
{ca gly l 128}44.419 48.035 15.721
{ca gly l 129}42.067 48.397 18.664
{ca ala l 130}40.541 51.631 19.98
{ca ser l 131}38.361 51.836 23.067
{ca val l 132}36.711 55.114 24.028
{ca val l 133}35.497 54.758 27.621
{ca cys l 134}32.9 56.701 29.569
{ca phe l 135}32.74 56.716 33.348
{ca leu l 136}29.421 57.954 34.753
{ca asn l 137}30.104 57.387 38.444
{ca asn l 138}28.002 57.801 41.528
{ca phe l 139}24.377 58.466 40.731
{ca tyr l 140}20.915 57.622 41.961
{ca pro l 141}18.305 56.837 40.871
{ca lys l 142}19.297 53.754 38.948
{ca asp l 143}17.784 55.278 35.769
{ca ile l 144}19.8 57.17 33.185
{ca asn l 145}20.378 57.198 29.411
{ca val l 146}23.782 57.61 27.876
{ca lys l 147}24.347 58.36 24.2
{ca trp l 148}27.56 58.507 22.225
{ca lys l 149}28.327 60.862 19.366
{ca ile l 150}31.325 60.379 17.06
{ca asp l 151}31.759 63.801 15.522
{ca gly l 152}28.27 65.25 15.09
{ca ser l 153}25.777 62.489 15.814
{ca glu l 154}24.753 59.321 17.555
{ca arg l 155}26.072 55.766 17.467
{ca gln l 156}24.427 52.349 17.989
{ca asn l 157}25.41 48.757 18.753
{ca gly l 158}29.193 49.163 19.141
{ca val l 159}28.162 50.341 22.64
{ca leu l 160}29.011 48.508 25.83
{ca asn l 161}27.601 49.517 29.178
{ca ser l 162}28.003 47.908 32.61
{ca trp l 163}26.155 48.998 35.729
{ca thr l 164}26.881 48.193 39.346
{ca asp l 165}24.86 47.104 42.346
{ca gln l 166}23.935 49.886 44.784
{ca asp l 167}26.998 51.037 46.765
{ca ser l 168}27.924 49.907 50.287
{ca lys l 169}28.45 53.595 51.047
{ca asp l 170}25.668 56.06 50.197
{ca ser l 171}23.219 54.018 48.118
{ca thr l 172}24.929 55.655 45.146
{ca tyr l 173}25.271 53.922 41.776
{ca ser l 174}27.854 54.174 39.007
{ca met l 175}27.815 52.609 35.526
{ca ser l 176}30.35 52.349 32.688
{ca ser l 177}30.044 52.438 28.888
{ca thr l 178}32.656 51.374 26.379
{ca leu l 179}32.692 52.156 22.706
{ca thr l 180}34.8 49.826 20.613
{ca leu l 181}35.797 50.305 17.036
{ca thr l 182}38.746 49.474 14.832
{ca lys l 183}41.651 51.823 14.235
{ca asp l 184}40.618 52.908 10.713
{ca glu l 185}37.063 53.873 11.716
{ca tyr l 186}38.506 55.506 14.766
{ca glu l 187}40.278 58.395 13.002
{ca arg l 188}37.801 59.064 10.163
{ca his l 189}36.493 61.342 12.808
{ca asn l 190}37.936 63.449 15.581
{ca ser l 191}35.092 64.283 17.942
{ca tyr l 192}33.845 61.7 20.403
{ca thr l 193}31.129 62.633 22.877
{ca cys l 194}29.608 60.799 25.816
{ca glu l 195}26.47 62.682 26.759
{ca ala l 196}24.208 61.458 29.48
{ca thr l 197}20.879 62.713 30.716
{ca his l 198}19.725 62.004 34.247
{ca lys l 199}16.911 63.018 36.58
{ca thr l 200}19.402 65.268 38.375
{ca ser l 201}19.221 67.919 35.605
{ca thr l 202}17.241 69.19 32.623
{ca ser l 203}20.356 69.344 30.509
{ca pro l 204}22.957 66.769 29.616
{ca ile l 205}26.312 66.406 31.307
{ca val l 206}28.558 66.612 28.185
{ca lys l 207}32.042 65.117 28.389
{ca ser l 208}33.949 65.303 25.122
{ca phe l 209}37.356 65.5 23.553
{ca asn l 210}38.586 65.52 19.921
{ca arg l 211}41.519 63.342 18.761
{ca asn l 212}44.099 66.117 19.191
{ca glu l 213}46.549 63.221 19.524
{ca cys l 214}49.955 62.2 20.718
@vectorlist {SS} color= yellow master= {SS}
{ca cys l 23}P 7.043 33.906 50.284
{cb cys l 23}8.324 33.547 51.007
{sg cys l 23}9.014 31.905 50.74
{sg cys l 88}10.917 32.28 50.149
{cb cys l 88}11.918 32.161 51.632
{ca cys l 88}13.399 31.934 51.537
{ca cys l 134}P 32.9 56.701 29.569
{cb cys l 134}31.664 57.156 28.802
{sg cys l 134}31.149 58.788 29.438
{sg cys l 194}29.679 59.362 28.187
{cb cys l 194}30.571 60.066 26.76
{ca cys l 194}29.608 60.799 25.816
@subgroup dominant {heavy ch} 
@vectorlist {ca-ca} color= yellowtint master= {Calphas}
{ca asp h 1}P 35.745 30.294 65.089
{ca val h 2}34.445 27.829 62.487
{ca gln h 3}35.558 28.485 58.907
{ca leu h 4}34.852 26.655 55.665
{ca gln h 5}36.845 27.534 52.527
{ca glu h 6}35.869 25.916 49.224
{ca ser h 7}38.546 25.091 46.676
{ca gly h 8}39.012 23.638 43.216
{ca pro h 9}39.391 24.68 39.585
{ca ser h 10}38.132 27.66 37.66
{ca leu h 11}37.308 25.743 34.542
{ca val h 12}36.797 22.375 32.993
{ca lys h 13}35.624 21.234 29.608
{ca pro h 14}32.053 20.247 29.028
{ca ser h 15}31.301 16.612 29.705
{ca gln h 16}34.457 16.41 31.766
{ca thr h 17}34.138 16.249 35.579
{ca leu h 18}34.55 18.946 38.171
{ca ser h 19}35.848 18.27 41.621
{ca leu h 20}35.878 20.863 44.367
{ca thr h 21}36.605 20.67 48.08
{ca cys h 22}35.646 22.565 51.197
{ca ser h 23}38.369 22.343 53.792
{ca val h 24}36.653 22.824 57.145
{ca thr h 25}39.006 24.104 59.827
{ca gly h 26}38.593 25.245 63.427
{ca asp h 27}35.435 23.272 64.228
{ca ser h 28}35.176 19.502 64.026
{ca ile h 29}33.436 17.63 61.18
{ca thr h 30}32.967 14.302 62.857
{ca ser h 31}29.249 14.467 62.162
{ca asp h 32}27.816 17.974 61.721
{ca tyr h 33}25.669 17.628 58.581
{ca trp h 34}27.301 19.413 55.611
{ca ser h 35}26.113 20.517 52.172
{ca trp h 36}26.757 21.961 48.738
{ca ile h 37}24.77 24.869 47.246
{ca arg h 38}25.141 26.514 43.83
{ca lys h 39}24.214 30.074 42.861
{ca phe h 40}23.523 30.516 39.135
{ca pro h 41}23.973 33.663 37.011
{ca gly h 42}20.319 34.656 37.29
{ca asn h 43}21.159 35.038 40.994
{ca arg h 44}18.952 32.103 41.979
{ca leu h 45}20.316 29.622 44.445
{ca glu h 46}19.974 25.872 44.173
{ca tyr h 47}20.77 23.309 46.849
{ca met h 48}22.872 20.396 45.626
{ca gly h 49}22.537 17.662 48.344
{ca tyr h 50}24.237 16.964 51.71
{ca val h 51}26.183 14.632 54.017
{ca ser h 52}24.59 13.734 57.347
{ca tyr h 53}26.347 11.889 60.183
{ca ser h 54}26.736 8.26 59.116
{ca gly h 55}27.348 8.742 55.403
{ca ser h 56}23.691 9.17 54.598
{ca thr h 57}23.572 11.315 51.435
{ca tyr h 58}20.651 12.991 49.663
{ca tyr h 59}20.806 14.801 46.301
{ca asn h 60}18.666 17.21 44.332
{ca pro h 61}17.083 15.272 41.473
{ca ser h 62}17.468 18.423 39.336
{ca leu h 63}21.136 17.402 39.522
{ca lys h 64}20.829 14.026 37.682
{ca ser h 65}23.106 11.412 39.242
{ca arg h 66}26.127 13.387 38.145
{ca ile h 67}26.938 14.209 41.763
{ca ser h 68}28.702 12.283 44.51
{ca ile h 69}29.348 14.208 47.751
{ca thr h 70}31.897 12.536 50.057
{ca arg h 71}34.199 13.201 53.027
{ca asp h 72}37.632 12.708 54.576
{ca thr h 73}37.623 12.851 58.402
{ca ser h 74}41.35 12.424 59.003
{ca lys h 75}41.897 15.282 56.59
{ca asn h 76}38.88 17.031 58.15
{ca gln h 77}37.531 17.979 54.671
{ca tyr h 78}34.723 16.907 52.384
{ca tyr h 79}34.39 17.158 48.624
{ca leu h 80}31.997 17.55 45.738
{ca asp h 81}32.116 15.817 42.394
{ca leu h 82}29.91 16.814 39.489
{ca asn h 83}30.393 14.335 36.686
{ca ser h 84}29.348 14.958 33.103
{ca val h 85}29.675 18.727 33.476
{ca thr h 86}27.942 21.073 31.011
{ca thr h 87}27.267 24.726 30.2
{ca glu h 88}24.364 25.242 32.626
{ca asp h 89}26.618 23.913 35.361
{ca thr h 90}28.277 27.355 35.097
{ca ala h 91}27.687 28.962 38.44
{ca thr h 92}29.266 29.461 41.82
{ca tyr h 93}29.335 26.509 44.151
{ca tyr h 94}29.412 26.987 47.917
{ca cys h 95}29.592 24.554 50.858
{ca ala h 96}27.462 24.903 53.997
{ca asn h 97}26.367 23.078 57.152
{ca trp h 98}22.818 21.784 57.589
{ca asp h 99}21.045 25.122 57.874
{ca gly h 100}23.481 27.77 56.59
{ca asp h 101}24.685 28.827 59.953
{ca tyr h 102}28.082 29.042 58.258
{ca trp h 103}29.177 29.44 54.609
{ca gly h 104}32.22 30.049 52.396
{ca gln h 105}33.457 32.73 49.984
{ca gly h 106}32.143 30.728 47.017
{ca thr h 107}34.239 29.733 43.988
{ca leu h 108}33.334 30.544 40.4
{ca val h 109}33.261 27.677 37.937
{ca thr h 110}33.08 27.774 34.185
{ca val h 111}32.066 25.083 31.799
{ca ser h 112}33.105 26.287 28.355
{ca ala h 113}34.854 24.697 25.389
{ca ala h 114}36.49 28.037 24.671
{ca lys h 115}39.875 28.48 26.346
{ca thr h 116}41.809 30.491 28.833
{ca thr h 117}43.393 33.685 27.553
{ca pro h 118}45.355 36.131 29.661
{ca pro h 119}43.999 39.63 29.85
{ca ser h 120}45.248 42.662 27.958
{ca val h 121}45.455 45.449 30.534
{ca tyr h 122}45.073 48.908 28.981
{ca pro h 123}45.467 52.22 30.811
{ca leu h 124}42.748 54.886 30.812
{ca ala h 125}44.58 58.203 30.954
{ca pro h 126}42.755 61.401 31.765
{ca gly h 127}42.338 63.963 29.02
{ca ser h 128}43.075 67.648 29.66
{ca ala h 129}39.306 68.174 29.723
{ca ala h 130}38.023 69.495 33.081
{ca gln h 131}35.339 68.533 35.62
{ca thr h 132}32.684 69.804 38.025
{ca asn h 133}35.074 69.854 40.991
{ca ser h 134}38.835 69.383 40.52
{ca met h 135}38.843 65.667 41.397
{ca val h 136}40.997 63.511 39.139
{ca thr h 137}39.511 60.218 38.061
{ca leu h 138}41.723 57.598 36.46
{ca gly h 139}40.811 54.204 35.039
{ca cys h 140}42.243 51.011 33.607
{ca leu h 141}40.97 48.5 31.07
{ca val h 142}41.14 44.72 31.144
{ca lys h 143}40.163 43.426 27.741
{ca gly h 144}40.287 39.902 26.39
{ca tyr h 145}40.634 37.292 29.095
{ca phe h 146}39.265 33.87 29.996
{ca pro h 147}37.894 32.806 32.321
{ca glu h 148}36.778 35.146 35.056
{ca pro h 149}37.18 36.455 37.604
{ca val h 150}40.092 38.872 37.888
{ca thr h 151}41.58 40.919 40.658
{ca val h 152}42.021 44.562 39.876
{ca thr h 153}43.466 46.476 42.788
{ca trp h 154}44.819 49.991 42.622
{ca asn h 155}48.368 50.261 43.844
{ca ser h 156}48.085 46.988 45.742
{ca gly h 157}45.24 47.596 48.194
{ca ser h 158}46.823 50.968 48.995
{ca leu h 159}44.272 52.897 46.929
{ca ser h 160}41.114 51.811 48.705
{ca ser h 161}39.842 55.322 49.185
{ca gly h 162}37.524 55.355 46.213
{ca val h 163}37.412 53.019 43.225
{ca his h 164}34.693 51.342 41.148
{ca thr h 165}35.17 47.913 39.482
{ca phe h 166}32.202 47.331 37.165
{ca pro h 167}31.134 43.733 36.606
{ca ala h 168}32.313 42.47 33.182
{ca val h 169}30.501 41.955 29.871
{ca leu h 170}31.158 39.008 27.551
{ca gln h 171}32.164 39.576 23.924
{ca ser h 172}30.657 36.461 22.428
{ca asp h 173}32.969 33.956 24.14
{ca leu h 174}35.445 36.432 25.696
{ca tyr h 175}35.334 38.999 28.437
{ca thr h 176}36.086 42.634 29.159
{ca leu h 177}35.564 44.81 32.254
{ca ser h 178}36.972 48.098 33.595
{ca ser h 179}37.966 49.918 36.786
{ca ser h 180}38.254 53.553 37.79
{ca val h 181}39.753 55.44 40.678
{ca thr h 182}39.014 58.979 41.806
{ca val h 183}41.803 60.973 43.454
{ca pro h 184}42.831 64.446 44.641
{ca ser h 185}43.114 66.736 41.631
{ca ser h 186}46.819 67.004 41.006
{ca pro h 187}47.606 65.186 43.272
{ca arg h 188}47.83 63.641 39.781
{ca pro h 189}51.209 63.191 38.096
{ca ser h 190}52.616 63.708 41.599
{ca glu h 191}51.707 60.464 43.422
{ca thr h 192}51.568 58.061 40.541
{ca val h 193}48.99 55.322 40.696
{ca thr h 194}48.719 51.953 39.045
{ca cys h 195}46.063 49.372 38.346
{ca asn h 196}47.264 46.05 39.724
{ca val h 197}45.218 43.431 37.892
{ca ala h 198}45.293 39.662 38.262
{ca his h 199}44.047 36.758 36.171
{ca pro h 200}43.986 34.074 38.886
{ca ala h 201}43.7 31.165 36.459
{ca ser h 202}45.701 32.527 33.526
{ca ser h 203}48.532 32.739 36.021
{ca thr h 204}49.507 36.213 34.955
{ca lys h 205}50.142 39.174 37.253
{ca val h 206}50.186 42.403 35.269
{ca asp h 207}51.672 45.569 36.646
{ca lys h 208}50.191 48.555 34.83
{ca lys h 209}50.839 52.197 34.567
{ca ile h 210}48.59 55.209 34.802
{ca val h 211}50.757 58.213 35.425
{ca pro h 212}48.221 60.903 34.389
{ca arg h 213}50.021 61.547 31.133
{ca asp h 214}49.271 62.773 27.669
{ca cys h 215}50.552 62.223 24.191
@vectorlist {SS} color= gold master= {SS}
{ca cys h 22}P 35.646 22.565 51.197
{cb cys h 22}34.152 22.66 51.346
{sg cys h 22}33.623 23.915 52.537
{sg cys h 95}32.254 24.94 51.46
{cb cys h 95}30.901 23.82 51.079
{ca cys h 95}29.592 24.554 50.858
{ca cys h 140}P 42.243 51.011 33.607
{cb cys h 140}43.069 50.323 34.692
{sg cys h 140}44.462 49.366 34.119
{sg cys h 195}45.904 49.378 35.551
{cb cys h 195}45.104 49.384 37.159
{ca cys h 195}46.063 49.372 38.346
@vectorlist off {binding sc} color= cyan master= {binding sc}
{ca asp h 32}P 27.816 17.974 61.721
{cb asp h 32}28.457 19.31 62.01
{cg asp h 32}27.461 20.459 61.889
{od1 asp h 32}26.271 20.218 61.625
{cg asp h 32}P 27.461 20.459 61.889
{od2 asp h 32}27.895 21.619 62.065
{ca tyr h 33}P 25.669 17.628 58.581
{cb tyr h 33}24.147 17.571 58.549
{cg tyr h 33}23.427 16.644 59.48
{cd1 tyr h 33}24.01 16.04 60.591
{ce1 tyr h 33}23.279 15.194 61.411
{cz tyr h 33}21.937 14.939 61.129
{oh tyr h 33}21.163 14.112 61.904
{cg tyr h 33}P 23.427 16.644 59.48
{cd2 tyr h 33}22.077 16.373 59.222
{ce2 tyr h 33}21.332 15.528 60.03
{cz tyr h 33}21.937 14.939 61.129
{ca tyr h 50}P 24.237 16.964 51.71
{cb tyr h 50}23.443 17.733 52.755
{cg tyr h 50}22.214 17.089 53.312
{cd1 tyr h 50}22.28 16.011 54.185
{ce1 tyr h 50}21.127 15.422 54.691
{cz tyr h 50}19.88 15.925 54.319
{oh tyr h 50}18.721 15.374 54.794
{cg tyr h 50}P 22.214 17.089 53.312
{cd2 tyr h 50}20.956 17.569 52.956
{ce2 tyr h 50}19.786 16.998 53.449
{cz tyr h 50}19.88 15.925 54.319
{ca asn h 97}P 26.367 23.078 57.152
{cb asn h 97}27.258 23.385 58.319
{cg asn h 97}27.124 24.646 59.122
{od1 asn h 97}26.504 25.68 58.816
{cg asn h 97}P 27.124 24.646 59.122
{nd2 asn h 97}27.772 24.605 60.306
{ca trp h 98}P 22.818 21.784 57.589
{cb trp h 98}22.436 21.547 59.071
{cg trp h 98}21.011 21.042 59.073
{cd1 trp h 98}20.013 21.192 59.985
{ne1 trp h 98}18.872 20.548 59.554
{ce2 trp h 98}19.121 19.972 58.344
{ce2 trp h 98}P 19.121 19.972 58.344
{ne1 trp h 98}18.872 20.548 59.554
{cg trp h 98}P 21.011 21.042 59.073
{cd2 trp h 98}20.46 20.258 57.997
{ce2 trp h 98}19.121 19.972 58.344
{cz2 trp h 98}18.29 19.231 57.525
{ch2 trp h 98}18.855 18.785 56.341
{cd2 trp h 98}P 20.46 20.258 57.997
{ce3 trp h 98}20.995 19.793 56.799
{cz3 trp h 98}20.169 19.059 55.987
{ch2 trp h 98}18.855 18.785 56.341
@vectorlist off {at O} color=red master= {binding sc}
{od1 asp h 32}P U 26.171 20.218 61.625
U 26.371 20.218 61.625
P U 26.271 20.118 61.625
U 26.271 20.318 61.625
P U 26.271 20.218 61.525
U 26.271 20.218 61.725
{od2 asp h 32}P U 27.795 21.619 62.065
U 27.995 21.619 62.065
P U 27.895 21.519 62.065
U 27.895 21.719 62.065
P U 27.895 21.619 61.965
U 27.895 21.619 62.165
@vectorlist off {at N} color=sky master= {binding sc}
{nd2 asn h 97}P U 27.672 24.605 60.306
U 27.872 24.605 60.306
P U 27.772 24.505 60.306
U 27.772 24.705 60.306
P U 27.772 24.605 60.206
U 27.772 24.605 60.406
@vectorlist off {Hbonds} color=purple master= {binding sc}
{nz lys y 97}P U 23.622 19.933 62.793
{od1 asp h 32}U 25.634 20.15 61.906
{od2 asp h 32}P U 27.87 22.222 61.71
{nd2 asn h 97}U 27.797 24.002 60.661
@group {lysozyme} 
@vectorlist {Calphas} color= greentint
{ca lys y 1}P 5.401 19.65 82.325
{ca val y 2}3.502 16.538 81.354
{ca phe y 3}1.546 16.917 78.138
{ca gly y 4}-1.91 15.479 77.462
{ca arg y 5}-1.889 13.421 74.248
{ca cys y 6}-3.953 16.022 72.35
{ca glu y 7}-2.077 18.954 73.91
{ca leu y 8}1.284 17.878 72.562
{ca ala y 9}-0.376 16.612 69.391
{ca ala y 10}-1.283 20.209 68.536
{ca ala y 11}1.859 21.915 69.811
{ca met y 12}3.773 19.566 67.538
{ca lys y 13}1.59 20.55 64.594
{ca arg y 14}2.271 24.164 65.604
{ca his y 15}5.954 23.316 65.459
{ca gly y 16}5.635 22.029 61.917
{ca leu y 17}6.209 18.311 62.434
{ca asp y 18}3.076 17.042 60.664
{ca asn y 19}4.628 15.331 57.613
{ca tyr y 20}7.936 16.819 58.618
{ca arg y 21}10.002 15.155 55.95
{ca gly y 22}7.673 12.224 55.415
{ca tyr y 23}6.463 11.483 58.923
{ca ser y 24}2.856 12.004 59.868
{ca leu y 25}2.235 13.922 63.106
{ca gly y 26}1.164 10.656 64.728
{ca asn y 27}4.768 9.374 64.717
{ca trp y 28}5.804 12.251 66.978
{ca val y 29}2.978 12.095 69.494
{ca cys y 30}3.589 8.373 69.629
{ca ala y 31}7.368 8.313 69.92
{ca ala y 32}7.158 10.716 72.877
{ca lys y 33}4.512 8.685 74.621
{ca phe y 34}6.558 5.495 74.744
{ca glu y 35}9.887 7.359 74.997
{ca ser y 36}9.246 9.816 77.858
{ca asn y 37}5.615 9.47 78.85
{ca phe y 38}4.977 12.959 77.474
{ca asn y 39}7.189 14.228 80.291
{ca thr y 40}9.496 17.091 79.344
{ca gln y 41}11.554 16.267 82.453
{ca ala y 42}12.216 12.574 81.888
{ca thr y 43}15.879 11.612 82.062
{ca asn y 44}17.527 8.2 81.862
{ca arg y 45}21.248 7.632 81.83
{ca asn y 46}22.785 5.288 79.294
{ca thr y 47}25.14 2.961 81.154
{ca asp y 48}27.573 4.157 78.529
{ca gly y 49}28.006 7.307 80.599
{ca ser y 50}25.418 9.129 78.504
{ca thr y 51}22.102 10.642 79.538
{ca asp y 52}18.716 11.155 77.834
{ca tyr y 53}16.744 14.417 77.845
{ca gly y 54}13.108 15.418 77.449
{ca ile y 55}10.159 14.486 75.274
{ca leu y 56}12.007 12.653 72.445
{ca gln y 57}14.889 11.828 74.821
{ca ile y 58}17.728 13.36 72.814
{ca asn y 59}21.054 11.681 73.743
{ca ser y 60}24.127 13.082 75.518
{ca arg y 61}26.504 11.705 72.873
{ca trp y 62}25.876 13.115 69.474
{ca trp y 63}23.253 15.739 70.413
{ca cys y 64}23.636 17.956 73.487
{ca asn y 65}26.224 18.812 76.121
{ca asp y 66}25.777 17.696 79.705
{ca gly y 67}29.443 18.171 80.597
{ca arg y 68}29.326 14.585 81.895
{ca thr y 69}30.149 13.061 78.543
{ca pro y 70}33.436 13.608 76.716
{ca gly y 71}32.966 12.05 73.249
{ca ser y 72}30.372 14.766 73.271
{ca arg y 73}29.598 16.054 69.801
{ca asn y 74}26.831 18.631 69.973
{ca leu y 75}25.344 18.303 66.479
{ca cys y 76}22.425 20.34 67.852
{ca asn y 77}24.595 23.02 69.555
{ca ile y 78}22.145 23.012 72.498
{ca pro y 79}23.048 22.638 76.165
{ca cys y 80}20.97 19.616 77.163
{ca ser y 81}19.398 21.554 80.042
{ca ala y 82}17.601 23.351 77.218
{ca leu y 83}15.847 20.022 76.47
{ca leu y 84}14.365 19.666 79.984
{ca ser y 85}12.334 22.893 79.626
{ca ser y 86}8.653 23.756 79.515
{ca asp y 87}9.408 24.856 75.965
{ca ile y 88}9.974 22.085 73.426
{ca thr y 89}11.221 24.506 70.755
{ca ala y 90}14.656 23.304 71.642
{ca ser y 91}13.718 19.631 71.503
{ca val y 92}11.695 19.826 68.323
{ca asn y 93}14.358 21.807 66.494
{ca cys y 94}16.987 19.153 67.249
{ca ala y 95}14.48 16.404 66.379
{ca lys y 96}13.825 18.105 63.051
{ca lys y 97}17.607 17.655 62.763
{ca ile y 98}18.24 14.038 63.774
{ca val y 99}15.388 12.729 61.666
{ca ser y 100}17.115 14.256 58.654
{ca asp y 101}19.671 11.415 58.187
{ca gly y 102}18.267 8.248 56.542
{ca asn y 103}17.6 6.637 59.919
{ca gly y 104}14.822 9.202 60.207
{ca met y 105}12.674 7.923 63.065
{ca asn y 106}14.675 4.678 63.387
{ca ala y 107}16.83 6.832 65.632
{ca trp y 108}13.953 6.507 68.078
{ca val y 109}13.82 3.017 69.554
{ca ala y 110}10.438 3.103 71.273
{ca trp y 111}9.282 4.342 67.879
{ca arg y 112}11.113 1.484 66.219
{ca asn y 113}9.977 -1.118 68.778
{ca arg y 114}6.479 -0.03 69.815
{ca cys y 115}5.416 2.889 67.582
{ca lys y 116}6.608 2.18 64.053
{ca gly y 117}4.132 0.689 61.594
{ca thr y 118}1.083 0.888 63.847
{ca asp y 119}-1.945 2.908 62.615
{ca val y 120}-0.348 6.058 64.099
{ca gln y 121}-3.341 8.119 63.004
{ca ala y 122}-4.491 6.735 66.34
{ca trp y 123}-2.283 9.095 68.292
{ca ile y 124}-3.927 12.131 66.627
{ca arg y 125}-7.602 11.057 66.734
{ca gly y 126}-10.045 12.855 69.057
{ca cys y 127}-7.794 15.897 69.095
{ca arg y 128}-8.688 19.461 68.251
{ca leu y 129}-5.824 20.309 65.926
@subgroup dominant {Gln 121}
@vectorlist {Gln 121} color=sky 
{ca gln y 121}P -3.341 8.119 63.004
{cb gln y 121}-4.385 7.812 61.958
{cg gln y 121}-4.131 8.415 60.589
{cd gln y 121}-5.43 8.854 59.941
{oe1 gln y 121}-6.21 8.044 59.445
{cd gln y 121}P -5.43 8.854 59.941
{ne2 gln y 121}-5.636 10.174 59.973
@subgroup dominant {Lys 97}
@vectorlist {Lys 97} color=sea
{ca lys y 97}P 17.607 17.655 62.763
{cb lys y 97}18.571 18.424 63.682
{cg lys y 97}19.998 17.902 63.642
{cd lys y 97}20.868 18.708 62.693
{ce lys y 97}22.324 18.542 63.101
{nz lys y 97}22.985 19.865 63.074
@vectorlist {at N} color=sky
{nz lys y 97}P U 22.885 19.865 63.074
U 23.085 19.865 63.074
P U 22.985 19.765 63.074
U 22.985 19.965 63.074
P U 22.985 19.865 62.974
U 22.985 19.865 63.174
@kinemage 3
@caption (B&T Fig. 12.20a, 12.21)
Human lymphocyte antigen (HLA) A2 structure - Calphas and SS for the light chain beta2 microglobulin (pinktint) and the heavy chain, composed of domains alpha1 (yellowtint), alpha2 (greentint) and alpha3 (bluetint).  View1 is from the side (like Fig. 12.20) and View2 from the top (like Fig. 12.21), with an orange line marking the position where antigen peptides bind.  (from PDB file 1HLA)
@onewidth 
@zoom 1.00 
@zslab 150 
@center 50.632 35.223 85.331 
@matrix 
-.616927 .359943 .699887 .551667 -.436468 .710745 .561306 .824583 .070701
@2zoom 1.06
@2zslab 80
@2center 54.847 26.978 99.435
@2matrix
-.755358 -.022542 .654925 -.272673 -.897971 -.345395 .595889 -.439477 .672143
@group {HLA a} 
@subgroup dominant {domain a1}
@vectorlist {dom a1} color= yellowtint 
{ca gly a 1}P 50.608 50.107 101.03
{ca ser a 2}49.509 48.255 100.516
{ca his a 3}51.941 45.133 99.736
{ca ser a 4}51.863 41.155 99.362
{ca met a 5}54.284 38.235 98.788
{ca arg a 6}52.642 35.204 97.269
{ca tyr a 7}53.73 31.719 96.427
{ca phe a 8}52.461 30.097 93.519
{ca phe a 9}53.452 26.829 92.353
{ca thr a 10}52.654 24.304 89.769
{ca ser a 11}53.338 20.503 89.337
{ca val a 12}52.623 18.209 86.765
{ca ser a 13}53.47 14.032 86.749
{ca arg a 14}54.237 12.06 83.49
{ca pro a 15}55.796 8.396 82.749
{ca gly a 16}58.939 6.349 82.258
{ca arg a 17}60.617 9.609 82.444
{ca gly a 18}60.771 12.295 84.964
{ca glu a 19}60.646 13.373 88.216
{ca pro a 20}58.04 15.95 88.324
{ca arg a 21}58.181 19.291 87.03
{ca phe a 22}58.167 21.959 89.562
{ca ile a 23}58.343 25.547 89.456
{ca ala a 24}57.732 28.121 92.088
{ca val a 25}57.316 31.384 91.472
{ca gly a 26}56.791 33.841 94.084
{ca tyr a 27}56.123 37.437 93.151
{ca val a 28}56.058 40.236 95.751
{ca asp a 29}53.795 43.286 94.601
{ca asp a 30}53.837 42.256 90.991
{ca thr a 31}57.126 40.305 90.185
{ca gln a 32}59.907 38.538 91.699
{ca phe a 33}60.617 35.594 90.239
{ca val a 34}62.22 33.154 91.666
{ca arg a 35}61.936 30.639 89.42
{ca phe a 36}62.85 27.455 89.639
{ca asp a 37}61.938 25.593 86.484
{ca ser a 38}63.62 22.425 87.302
{ca asp a 39}64.263 20.883 83.987
{ca ala a 40}66.552 23.25 85.223
{ca ala a 41}69.821 23.766 84.028
{ca ser a 42}71.395 24.306 87.113
{ca gln a 43}69.47 23.072 89.887
{ca arg a 44}69.896 26.154 91.35
{ca met a 45}67.174 28.58 92.796
{ca glu a 46}67.437 31.585 90.897
{ca pro a 47}67.245 34.904 92.165
{ca arg a 48}65.912 37.181 89.154
{ca ala a 49}64.782 40.496 90.51
{ca pro a 50}67.863 42.916 91.623
{ca trp a 51}67.314 43.88 95.513
{ca ile a 52}67.558 40.162 96.443
{ca glu a 53}70.855 39.424 94.522
{ca gln a 54}72.04 41.749 97.102
{ca glu a 55}71.062 38.765 99.172
{ca gly a 56}73.456 36.211 99.822
{ca pro a 57}74.342 32.874 101.043
{ca glu a 58}72.551 31.229 102.871
{ca tyr a 59}69.144 32.972 102.235
{ca trp a 60}69.215 32.114 99.349
{ca asp a 61}70.526 28.29 99.841
{ca gly a 62}68.152 27.835 102.72
{ca glu a 63}65.946 28.676 99.67
{ca thr a 64}67.019 25.736 97.472
{ca arg a 65}66.197 23.728 99.626
{ca lys a 66}63.017 24.743 101.279
{ca val a 67}61.766 24.616 97.777
{ca lys a 68}63.067 21.46 96.352
{ca ala a 69}62.315 19.42 99.365
{ca his a 70}59.073 21.057 98.734
{ca ser a 71}58.698 19.556 95.35
{ca gln a 72}58.949 16.265 96.47
{ca thr a 73}56.213 16.532 98.885
{ca his a 74}53.913 17.801 96.024
{ca arg a 75}55.004 14.777 93.831
{ca val a 76}53.834 12.368 96.223
{ca asp a 77}50.64 13.95 96.368
{ca leu a 78}50.107 12.856 92.826
{ca gly a 79}50.526 9.196 93.954
{ca thr a 80}48.788 9.923 97.168
{ca leu a 81}46.022 11.567 94.872
{ca arg a 82}44.893 9.578 91.749
{ca gly a 83}45.151 7.03 94.723
{ca tyr a 84}43.32 8.413 96.432
{ca tyr a 85}40.661 9.316 94.522
{ca asn a 86}41.298 6.718 91.776
{ca gln a 87}42.689 8.538 88.059
{ca ser a 88}45.306 6.459 85.96
{ca glu a 89}49.637 6.046 85.613
{ca ala a 90}48.803 6.832 82.219
@subgroup dominant {domain a2}
@vectorlist {dom a2} color=greentint 
{ca ala a 90}P 48.803 6.832 82.219
{ca gly a 91}48.378 10.167 80.401
{ca ser a 92}48.287 11.487 83.897
{ca his a 93}47.878 15.326 84.755
{ca thr a 94}48.651 18.515 87.508
{ca val a 95}48.976 20.129 91.334
{ca gln a 96}48.926 23.918 92.316
{ca arg a 97}49.415 25.69 95.722
{ca met a 98}48.73 29.574 97.221
{ca tyr a 99}50.953 30.792 100.001
{ca gly a 100}50.339 34.572 100.363
{ca cys a 101}50.999 37.466 102.541
{ca asp a 102}49.24 40.234 102.615
{ca val a 103}49.994 43.026 104.642
{ca gly a 104}48.553 46.458 104.519
{ca ser a 105}49.343 49.682 105.858
{ca asp a 106}50.393 50.384 109.33
{ca trp a 107}51.782 47.967 107.34
{ca arg a 108}50.9 44.637 109.241
{ca phe a 109}48.042 41.856 108.661
{ca leu a 110}44.95 41.181 106.465
{ca arg a 111}46.143 37.998 106.6
{ca gly a 112}47.73 35.7 104.798
{ca tyr a 113}46.191 33.396 102.427
{ca his a 114}47.158 29.281 101.572
{ca gln a 115}45.224 27.464 98.656
{ca tyr a 116}45.249 24.171 96.407
{ca ala a 117}43.992 22.729 93.486
{ca tyr a 118}44.745 19.657 91.819
{ca asp a 119}43.669 19.787 88.219
{ca gly a 120}41.438 22.708 89.367
{ca lys a 121}39.948 23.825 92.594
{ca asp a 122}39.777 21.652 95.183
{ca tyr a 123}41.32 20.148 97.916
{ca ile a 124}41.782 22.595 100.789
{ca ala a 125}42.088 26.168 101.576
{ca leu a 126}42.604 27.561 104.947
{ca lys a 127}40.181 30.003 105.976
{ca glu a 128}40.262 33.21 107.123
{ca asp a 129}41.39 34.63 109.885
{ca leu a 130}41.097 31.67 110.953
{ca arg a 131}43.639 30.016 110.603
{ca ser a 132}42.008 26.961 111.241
{ca trp a 133}40.256 25.199 108.241
{ca thr a 134}37.914 24.263 104.795
{ca ala a 135}37.493 21.618 101.894
{ca ala a 136}36.363 20.967 98.33
{ca asp a 137}35.513 17.876 96.322
{ca met a 138}36.064 15.091 99.243
{ca ala a 139}38.871 13.313 98.99
{ca ala a 140}39.96 15.999 99.795
{ca gln a 141}38.534 16.139 103.205
{ca thr a 142}39.949 12.926 104.409
{ca thr a 143}43.139 15.356 104.116
{ca lys a 144}40.964 17.656 106.926
{ca his a 145}42.819 16.243 109.475
{ca lys a 146}45.7 15.159 108.493
{ca trp a 147}45.826 17.966 108.418
{ca glu a 148}45.112 19.103 111.592
{ca ala a 149}44.728 17.103 114.581
{ca ala a 150}47.639 18.817 115.801
{ca his a 151}49.629 20.357 113.234
{ca val a 152}49.332 21.729 109.904
{ca ala a 153}46.962 24.537 109.912
{ca glu a 154}48.412 25.729 113.302
{ca gln a 155}51.644 25.802 112.036
{ca leu a 156}51.289 27.593 109.108
{ca arg a 157}49.899 30.444 111.213
{ca ala a 158}52.626 31.291 113.66
{ca tyr a 159}54.396 32.038 110.451
{ca leu a 160}51.922 34.158 109.455
{ca glu a 161}52.358 37.51 110.976
{ca gly a 162}55.135 35.3 111.67
{ca thr a 163}58.196 35.356 109.444
{ca cys a 164}56.539 36.706 106.183
{ca val a 165}55.767 39.958 107.297
{ca glu a 166}59.416 39.98 108.327
{ca trp a 167}60.314 38.938 104.828
{ca leu a 168}58.108 41.544 103.071
{ca arg a 169}60.103 44.273 104.937
{ca arg a 170}63.457 43.312 103.595
{ca tyr a 171}61.792 42.258 100.422
{ca leu a 172}60.038 45.64 100.18
{ca glu a 173}62.041 48.286 101.659
{ca asn a 174}65.527 46.943 100.941
{ca gly a 175}64.253 46.74 97.379
{ca lys a 176}61.611 49.476 97.485
{ca glu a 177}62.859 51.755 95.174
{ca thr a 178}62.033 49.889 92.096
{ca leu a 179}59.33 47.829 93.601
{ca gln a 180}57.442 49.993 95.914
{ca arg a 181}57.904 53.314 95.071
@vectorlist {SS} color=yellow master= {SS}
{ca cys a 101}P 50.999 37.466 102.541
{ca cys a 164}56.539 36.706 106.183
@subgroup dominant {domain a3}
@vectorlist {dom a3} color=bluetint 
{ca arg a 181}P 57.904 53.314 95.071
{ca thr a 182}54.881 54.041 92.576
{ca asp a 183}54.228 54.975 88.915
{ca ala a 184}51.344 56.438 87.373
{ca pro a 185}50.21 56.046 84.108
{ca lys a 186}49.395 58.507 81.43
{ca thr a 187}48.066 57.681 78.105
{ca his a 188}46.764 58.784 74.852
{ca met a 189}43.866 58.904 72.903
{ca thr a 190}43.602 57.838 69.448
{ca his a 191}40.9 57.574 66.952
{ca his a 192}40.614 55.415 64.199
{ca ala a 193}37.305 54.569 62.013
{ca val a 194}35.032 51.832 62.226
{ca ser a 195}33.292 52.6 58.708
{ca asp a 196}31.861 56.08 57.672
{ca his a 197}30.31 57.795 60.494
{ca glu a 198}31.477 55.683 62.791
{ca ala a 199}34.634 56.253 65.272
{ca thr a 200}36.339 54.377 67.752
{ca leu a 201}38.451 56.099 70.033
{ca arg a 202}40.982 54.212 72.331
{ca cys a 203}42.202 54.877 76.187
{ca trp a 204}45.748 53.477 76.811
{ca ala a 205}47.702 54.016 79.464
{ca leu a 206}50.649 52.442 79.734
{ca ser a 207}52.607 52.041 82.595
{ca phe a 208}51.842 50.733 86.437
{ca tyr a 209}52.518 49.676 89.396
{ca pro a 210}49.815 47.902 90.392
{ca ala a 211}48.299 46.445 87.866
{ca glu a 212}45.102 47.635 88.924
{ca ile a 213}43.006 50.021 87.643
{ca thr a 214}39.986 51.159 86.485
{ca leu a 215}39.485 52.365 83.134
{ca thr a 216}36.015 53.591 83.294
{ca trp a 217}34.532 55.884 80.375
{ca gln a 218}31.948 58.404 80.745
{ca arg a 219}29.533 59.826 78.331
{ca asp a 220}27.439 62.924 78.751
{ca gly a 221}28.277 62.957 82.468
{ca glu a 222}26.923 59.628 82.472
{ca asp a 223}28.096 56.37 81.738
{ca gln a 224}28.195 54.4 78.851
{ca thr a 225}29.301 51.068 79.581
{ca gln a 226}27.31 49.257 77.139
{ca asp a 227}28.396 49.474 73.551
{ca thr a 228}32.27 49.368 73.816
{ca glu a 229}35.398 46.65 74.667
{ca leu a 230}38.293 47. 77.105
{ca val a 231}40.961 44.533 77.753
{ca glu a 232}42.01 42.786 80.712
{ca thr a 233}45.135 43.81 81.583
{ca arg a 234}48.393 42.67 79.94
{ca pro a 235}52.34 42.591 81.47
{ca ala a 236}55.532 44.064 79.546
{ca gly a 237}59.079 42.631 79.954
{ca asp a 238}59.614 45.766 81.709
{ca gly a 239}57.081 45.859 85.214
{ca thr a 240}55. 48.15 83.066
{ca phe a 241}51.109 47.039 82.359
{ca gln a 242}48.81 48.453 79.759
{ca lys a 243}45.045 49.001 79.374
{ca trp a 244}43.221 49.918 76.114
{ca ala a 245}39.466 50.623 76.058
{ca ala a 246}37.064 51.456 73.17
{ca val a 247}33.714 52.841 71.764
{ca val a 248}32.343 53.088 68.335
{ca val a 249}31.28 56.366 67.943
{ca pro a 250}29.153 57.806 65.386
{ca ser a 251}31.969 60.197 64.385
{ca gly a 252}29.868 63.096 63.606
{ca gln a 253}30.522 63.828 67.125
{ca glu a 254}32.838 62.523 68.986
{ca gln a 255}33.012 64.401 72.002
{ca arg a 256}30.806 64.088 74.837
{ca tyr a 257}32.819 61.273 75.921
{ca thr a 258}35.627 61.473 78.483
{ca cys a 259}37.384 58.343 80.167
{ca his a 260}38.419 57.57 83.614
{ca val a 261}41.36 55.979 84.969
{ca gln a 262}42.341 54.927 88.59
{ca his a 263}45.644 54.38 89.186
{ca glu a 264}47.085 55.094 92.228
{ca gly a 265}49.335 57.484 91.901
{ca leu a 266}48.049 60.699 90.707
{ca pro a 267}44.61 61.994 91.856
{ca lys a 268}43.087 61.353 89.75
{ca pro a 269}41.504 61.823 86.129
{ca leu a 270}38.937 63.601 84.791
@vectorlist {SS} color=yellow master= {SS}
{ca cys a 203}P 42.202 54.877 76.187
{ca cys a 259}37.384 58.343 80.167
@group dominant {HLA b2m} 
@vectorlist {Calphas} color=pinktint 
{ca ile m 1}P 39.691 20.717 83.505
{ca gln m 2}40.157 22.703 80.572
{ca arg m 3}39.86 25.932 79.609
{ca thr m 4}40.575 27.599 76.524
{ca pro m 5}42.864 30.53 76.59
{ca lys m 6}43.601 33.815 75.837
{ca ile m 7}45.758 35.269 73.399
{ca gln m 8}46.809 38.836 73.398
{ca val m 9}49.428 40.927 71.84
{ca tyr m 10}51.487 43.603 72.827
{ca ser m 11}53.982 46.524 71.849
{ca arg m 12}57.224 49.241 73.149
{ca his m 13}55.299 51.176 70.818
{ca pro m 14}55.49 52.161 67.17
{ca ala m 15}57.333 55.005 66.045
{ca glu m 16}57.608 52.942 62.622
{ca asn m 17}60.297 51.037 60.964
{ca gly m 18}63.156 51.975 62.284
{ca lys m 19}62.665 50.832 65.004
{ca ser m 20}63.816 47.898 67.735
{ca asn m 21}60.769 47.061 69.848
{ca phe m 22}59.779 44.219 71.372
{ca leu m 23}56.265 42.324 70.485
{ca asn m 24}54.7 39.52 72.538
{ca cys m 25}51.742 37.257 72.753
{ca tyr m 26}50.049 36.978 76.282
{ca val m 27}48.292 33.678 77.114
{ca ser m 28}45.617 32.817 79.766
{ca gly m 29}42.851 30.89 81.173
{ca phe m 30}44.671 28.175 79.952
{ca his m 31}44.697 25.006 81.805
{ca pro m 32}46.353 22.019 81.055
{ca ser m 33}49.206 23.687 82.65
{ca asp m 34}51.15 23.218 79.311
{ca ile m 35}50.325 25.289 76.197
{ca glu m 36}52.494 25.332 73.017
{ca val m 37}53.166 29.281 72.17
{ca asp m 38}55.819 29.784 69.276
{ca leu m 39}55.781 33.446 67.281
{ca leu m 40}56.056 33.925 63.497
{ca lys m 41}57.408 36.808 60.998
{ca asn m 42}56.015 36.353 57.626
{ca gly m 43}54.017 33.627 58.356
{ca glu m 44}56.854 31.359 59.331
{ca arg m 45}59.656 31.265 62.497
{ca ile m 46}61.789 33.195 64.95
{ca glu m 47}63.745 32.177 67.915
{ca lys m 48}64.598 34.706 70.577
{ca val m 49}61.571 33.93 71.948
{ca glu m 50}61.791 34.342 75.612
{ca his m 51}58.973 32.702 77.603
{ca ser m 52}58.297 33.706 80.996
{ca asp m 53}57.647 31.766 83.792
{ca leu m 54}54.3 29.895 84.645
{ca ser m 55}51.838 31.942 86.225
{ca phe m 56}48.836 31.509 88.183
{ca ser m 57}45.652 33.767 88.266
{ca lys m 58}42.438 33.428 90.535
{ca asp m 59}41.176 30.999 88.454
{ca trp m 60}44.199 29.057 88.909
{ca ser m 61}44.372 29.457 85.093
{ca phe m 62}47.926 30.276 83.984
{ca tyr m 63}49.619 33.261 82.27
{ca leu m 64}52.769 33.239 80.403
{ca leu m 65}54.38 35.837 78.369
{ca tyr m 66}56.144 34.659 75.306
{ca tyr m 67}58.494 37.714 73.948
{ca thr m 68}61.261 38.449 71.053
{ca glu m 69}62.903 41.934 69.143
{ca phe m 70}62.199 43.892 66.807
{ca thr m 71}62.741 46.294 64.124
{ca pro m 72}59.201 46.732 62.65
{ca thr m 73}58.647 47.558 59.071
{ca glu m 74}56.065 47.577 56.335
{ca lys m 75}55.42 44.125 54.862
{ca asp m 76}57.029 41.801 57.39
{ca glu m 77}54.079 40.838 59.518
{ca tyr m 78}53.511 39.254 62.603
{ca ala m 79}51.724 36.427 64.674
{ca cys m 80}51.711 33.861 67.602
{ca arg m 81}50.53 30.276 67.09
{ca val m 82}49.363 28.154 69.537
{ca asn m 83}47.773 25.328 70.255
{ca his m 84}46.999 23.518 72.743
{ca val m 85}44.919 21.195 73.108
{ca thr m 86}41.99 22.206 72.51
{ca leu m 87}41.771 23.992 69.989
{ca ser m 88}41.511 22.338 67.312
{ca gln m 89}43.309 22.482 65.975
{ca pro m 90}45.107 25.454 65.759
{ca lys m 91}45.972 28.427 66.479
{ca ile m 92}46.71 32. 64.727
{ca val m 93}46.42 36.046 65.275
{ca lys m 94}47.478 38.877 63.986
{ca trp m 95}49.101 42.303 64.711
{ca asp m 96}47.934 45.991 65.193
{ca arg m 97}46.728 49.434 66.627
@vectorlist {SS} color=yellow master= {SS}
{ca cys m 25}P 51.742 37.257 72.753
{ca cys m 80}51.711 33.861 67.602
@group {pept site} dominant 
@vectorlist {Drawn} color=orange 
{3rd point} P 46.673 12.719 101.715
{avg of 3 pts} 62.787 34.005 105.238