@text
"PROTEIN-DNA  INTERACTIONS  --  LAMBDA  REPRESSOR"

In this kinemage, you can visualize the DNA-binding portion of lambda repressor protein (containing the helix-turn-helix motif) as it is associated to a double strand of DNA.  Note that in order to bind DNA effectively, lambda repressor must associate as a dimer (identical subunits A and B).  Each subunit is highlighted in a different color, while the helix-turn-helix portions are shown in darker shades.  Structure derived from PDB file, 1LMB.
@kinemage 1
@caption
Calpha trace of the N-domains of dimeric lambda repressor.  The subunits are displayed in yellowtint & pinktint, with the helix-turn-helix portions in gold & magenta, respectively.  Click on the DNA button to add the DNA double-helix backbone to the display.  View2 gives a good perspective down the central axis of the DNA.
@onewidth
@viewid {Side} 
@zoom 1.0
@matrix 
-.566114 -.479873 -.670251 .749582 .038637 -.660781 .342988 -.876488 .337831
@2viewid {Top}
@2zoom 1.4
@2zslab 260
@2matrix 
.594571 .603803 -.530949 .704786 -.709209 -.017282 -.386988 -.363931 -.847228 
@group {LRP sub A} 
@vectorlist {Alpha-C's} color=pinktint
{pro A 6}P 4.917 -12.878 21.502
{leu A 7}7.171 -14.734 19.108
{thr A 8}6.414 -18.341 18.088
{gln A 9}7.434 -21.207 20.413
{glu A 10}10.09 -22.093 17.832
{gln A 11}11.194 -18.465 17.478
{leu A 12}11.715 -18.403 21.262
{glu A 13}13.803 -21.578 20.875
{asp A 14}16.165 -20.176 18.196
{ala A 15}16.942 -17.153 20.373
{arg A 16}17.718 -19.297 23.411
{arg A 17}20.008 -21.42 21.245
{leu A 18}21.776 -18.444 19.615
{lys A 19}22.289 -16.658 22.921
{ala A 20}23.703 -19.833 24.488
{ile A 21}26.38 -19.901 21.747
{tyr A 22}27.191 -16.218 22.345
{glu A 23}27.475 -16.967 26.083
{lys A 24}29.83 -19.922 25.434
{lys A 25}32.006 -18.101 22.858
{lys A 26}32.166 -14.507 24.112
{asn A 27}35.515 -14.665 25.987
{glu A 28}37.252 -16.775 23.285
{leu A 29}36.121 -14.472 20.47
{gly A 30}36.102 -11.655 22.995
{leu A 31}32.791 -9.958 22.191
{ser A 32}29.905 -8.157 23.855
{gly A 53}P 13.698 -13.524 21.764
{ile A 54}12.044 -10.116 21.604
{asn A 55}12.523 -9.401 17.866
{ala A 56}12.578 -12.122 15.182
{leu A 57}15.764 -13.373 13.614
{asn A 58}15.732 -13.414 9.796
{ala A 59}18.04 -14.747 7.078
{tyr A 60}20.378 -11.751 6.685
{asn A 61}20.709 -11.174 10.469
{ala A 62}20.979 -14.912 11.181
{ala A 63}23.608 -15.256 8.446
{leu A 64}25.61 -12.321 9.91
{leu A 65}25.472 -13.813 13.409
{ala A 66}26.622 -17.262 12.252
{lys A 67}29.79 -15.696 10.771
{ile A 68}30.543 -13.442 13.757
{leu A 69}30.158 -16.328 16.213
{lys A 70}32.033 -18.781 13.922
{val A 71}28.93 -20.987 13.894
{ser A 72}26.66 -22.375 11.158
{val A 73}23.022 -21.138 11.101
{glu A 74}21.825 -24.746 11.637
{glu A 75}23.388 -24.732 15.136
{phe A 76}20.933 -22.093 16.361
{ser A 77}18.152 -21.929 13.774
{pro A 78}17.263 -25.055 11.819
{ser A 79}14.273 -23.289 10.201
{ile A 80}16.057 -20.211 8.896
{ala A 81}18.799 -22.561 7.676
{arg A 82}16.212 -24.416 5.562
{glu A 83}14.915 -21.09 4.331
{ile A 84}18.416 -20.046 3.214
{tyr A 85}19.029 -23.385 1.487
{glu A 86}15.88 -22.76 -0.541
{met A 87}16.859 -19.352 -1.892
{tyr A 88}20.178 -20.719 -3.14
{glu A 89}18.25 -23.434 -4.981
{ala A 90}17.194 -20.458 -7.135
{val A 91}20.709 -19.008 -7.562
{ser A 92}22.349 -22.403 -8.001
@vectorlist {hlx-t-hlx} color=magenta
{ser A 32}P 29.905 -8.157 23.855
{gln A 33}26.433 -7.167 22.601
{glu A 34}27.95 -3.807 21.764
{ser A 35}30.775 -5.127 19.541
{val A 36}28.611 -7.889 18.031
{ala A 37}26.29 -4.996 17.205
{asp A 38}28.639 -2.611 15.353
{lys A 39}29.817 -5.511 13.17
{met A 40}26.224 -6.137 12.247
{gly A 41}25.718 -2.405 11.853
{met A 42}23.108 -1.945 14.578
{gly A 43}23.049 -0.9 18.248
{gln A 44}23.566 -3.195 21.251
{ser A 45}19.858 -2.982 22.163
{gly A 46}18.963 -4.336 18.703
{val A 47}21.163 -7.387 19.285
{gly A 48}19.817 -7.82 22.835
{ala A 49}16.296 -7.841 21.382
{leu A 50}17.334 -10.7 19.068
{phe A 51}19.257 -12.741 21.627
{asn A 52}16.421 -12.39 24.146
{gly A 53}13.698 -13.524 21.764
@group {LRP sub B} 
@vectorlist {Alpha-C's} color=yellowtint
{ser B 1}P 4.538 4.776 9.386
{thr B 2}3.128 5.037 5.858
{lys B 3}5.989 6.453 3.869
{lys B 4}7.501 4.68 0.832
{lys B 5}11.182 5.078 -0.04
{pro B 6}12.365 5.669 -3.602
{leu B 7}14.211 2.824 -5.345
{thr B 8}17.924 2.763 -6.075
{gln B 9}19.233 2.989 -9.637
{glu B 10}20.342 -0.66 -9.437
{gln B 11}17.076 -1.773 -7.745
{leu B 12}15.168 -0.11 -10.583
{glu B 13}17.307 -1.924 -13.164
{asp B 14}16.785 -5.374 -11.603
{ala B 15}13.045 -4.618 -11.797
{arg B 16}13.284 -3.67 -15.495
{arg B 17}15.316 -6.851 -16.071
{leu B 18}12.563 -8.789 -14.184
{lys B 19}9.659 -7.477 -16.299
{ala B 20}11.752 -8.033 -19.433
{ile B 21}12.101 -11.696 -18.436
{tyr B 22}8.398 -11.999 -17.564
{glu B 23}7.623 -10.432 -20.937
{lys B 24}9.656 -12.919 -22.983
{lys B 25}8.435 -15.998 -21.051
{lys B 26}4.812 -15.008 -20.43
{asn B 27}3.295 -16.878 -23.371
{glu B 28}5.68 -19.86 -23.268
{leu B 29}4.916 -20.369 -19.541
{gly B 30}1.43 -18.925 -20.065
{leu B 31}0.964 -16.562 -17.142
{ser B 32}-0.463 -13.297 -15.94
{gly B 53}P 9.952 -0.337 -9.756
{ile B 54}7.446 0.818 -7.118
{asn B 55}8.444 -1.745 -4.422
{ala B 56}11.938 -3.312 -4.206
{leu B 57}12.531 -7.058 -4.434
{asn B 58}14.134 -8.975 -1.579
{ala B 59}15.829 -12.39 -1.533
{tyr B 60}12.626 -14.342 -0.809
{asn B 61}10.6 -12.727 -3.579
{ala B 62}13.504 -12.754 -6.012
{ala B 63}13.932 -16.513 -5.351
{leu B 64}10.162 -17.07 -5.551
{leu B 65}10.004 -15.07 -8.81
{ala B 66}12.983 -17.001 -10.298
{lys B 67}11.518 -20.424 -9.557
{ile B 68}8.165 -19.248 -11.016
{leu B 69}9.785 -17.943 -14.23
{lys B 70}11.962 -21.07 -14.429
{val B 71}15.056 -18.857 -14.441
{ser B 72}17.971 -17.97 -12.15
{val B 73}18.137 -14.658 -10.252
{glu B 74}21.664 -13.641 -11.386
{glu B 75}19.718 -13.098 -14.606
{phe B 76}17.615 -10.294 -13.136
{ser B 77}19.639 -9.456 -10.018
{pro B 78}23.389 -9.971 -9.699
{ser B 79}23.525 -8.123 -6.343
{ile B 80}20.69 -10.081 -4.724
{ala B 81}22.162 -13.29 -6.138
{arg B 82}25.515 -12.349 -4.559
{glu B 83}23.586 -11.559 -1.345
{ile B 84}21.998 -15.036 -1.294
{tyr B 85}25.42 -16.623 -2.006
{glu B 86}26.719 -14.665 0.992
{met B 87}23.969 -15.998 3.305
{tyr B 88}24.466 -19.578 2.086
{glu B 89}28.158 -19.51 3.083
{ala B 90}26.807 -19.324 6.662
{val B 91}25.058 -22.684 6.257
{ser B 92}27.897 -24.299 4.342
@vectorlist {hlx-t-hlx} color=gold
{ser B 32}P -0.463 -13.297 -15.94
{gln B 33}0.382 -11.085 -12.942
{glu B 34}-3.066 -12.404 -11.95
{ser B 35}-1.681 -15.971 -11.665
{val B 36}1.97 -15.173 -10.879
{ala B 37}0.391 -13.407 -7.864
{asp B 38}-1.641 -16.355 -6.497
{lys B 39}1.514 -18.499 -6.662
{met B 40}3.155 -15.943 -4.337
{gly B 41}0.26 -15.153 -2.012
{met B 42}-0.3 -11.517 -3.055
{gly B 43}-2.536 -9.525 -5.397
{gln B 44}-1.924 -8.288 -8.919
{ser B 45}-0.917 -4.852 -7.534
{gly B 46}1.75 -6.315 -5.26
{val B 47}3.194 -8.198 -8.246
{gly B 48}2.547 -5.058 -10.298
{ala B 49}4.666 -2.955 -7.91
{leu B 50}7.514 -5.436 -8.229
{phe B 51}7.579 -5.532 -12.036
{asn B 52}7.386 -1.711 -12.258
{gly B 53}9.952 -0.337 -9.756
@group {DNA} off
@subgroup {Strand 1} dominant
@vectorlist {mc} color=greentint
{c4* a 1 1}P 32.187 -1.67 32.865
{p a 1 2}32.632 -4.068 29.822
{c4* a 1 2}29.73 -6.418 29.964
{p t 1 3}27.177 -8.391 27.554
{c4* t 1 3}24.159 -8.157 29.753
{p a 1 4}20.618 -9.559 28.83
{c4* a 1 4}18.105 -7.47 30.887
{p c 1 5}14.104 -7.752 30.397
{c4* c 1 5}13.049 -4.137 31.298
{p c 1 6}9.322 -3.182 30.369
{c4* c 1 6}9.808 0.687 29.919
{p a 1 7}6.127 1.45 28.768
{c4* a 1 7}6.891 4.268 26.414
{p c 1 8}5.438 7.009 23.924
{c4* c 1 8}7.879 7.044 21.137
{p t 1 9}6.933 8.824 17.849
{c4* t 1 9}9.56 7.676 15.17
{p g 1 10}9.949 8.865 11.808
{c4* g 1 10}12.476 6.577 9.979
{p g 1 11}13.191 6.267 6.189
{c4* g 1 11}12.088 2.433 6.126
{p c 1 12}12.21 0.667 3.043
{c4* c 1 12}11.246 -2.797 4.513
{p g 1 13}10.567 -6.329 2.792
{c4* g 1 13}6.901 -6.528 2.992
{p g 1 14}4.914 -8.837 0.564
{c4* g 1 14}2.238 -6.996 0.16
{p t 1 15}-1.398 -7.999 -0.906
{c4* t 1 15}-4.12 -5.931 0.866
{p g 1 16}-7.591 -6.879 -0.536
{c4* g 1 16}-9.11 -3.457 -1.299
{p a 1 17}-12.254 -2.763 -3.642
{c4* a 1 17}-11.48 0.852 -4.616
{p t 1 18}-13.562 2.811 -7.38
{c4* t 1 18}-10.999 4.02 -9.677
{p a 1 19}-11.125 6.233 -12.976
{c4* a 1 19}-7.521 6.405 -14.179
{p t 1 20}-7.048 7.807 -17.769
{c4* t 1 20}-4.299 5.271 -19.091
@vectorlist {sug} color=greentint
{c4* a 1 1}P 32.187 -1.67 32.865
{c1* a 1 1}30.557 -3.168 33.72
{c4* a 1 2}P 29.73 -6.418 29.964
{c1* a 1 2}27.74 -5.388 30.614
{c4* t 1 3}P 24.159 -8.157 29.753
{c1* t 1 3}23.08 -6.109 29.759
{c4* a 1 4}P 18.105 -7.47 30.887
{c1* a 1 4}17.865 -5.449 29.748
{c4* c 1 5}P 13.049 -4.137 31.298
{c1* c 1 5}13.808 -2.515 29.845
{c4* c 1 6}P 9.808 0.687 29.919
{c1* c 1 6}10.615 0.88 27.713
{c4* a 1 7}P 6.891 4.268 26.414
{c1* a 1 7}8.193 4.048 24.493
{c4* c 1 8}P 7.879 7.044 21.137
{c1* c 1 8}8.407 5.14 20.083
{c4* t 1 9}P 9.56 7.676 15.17
{c1* t 1 9}9.322 5.408 14.663
{c4* g 1 10}P 12.476 6.577 9.979
{c1* g 1 10}10.79 5.03 9.494
{c4* g 1 11}P 12.088 2.433 6.126
{c1* g 1 11}9.76 2.144 6.075
{c4* c 1 12}P 11.246 -2.797 4.513
{c1* c 1 12}8.926 -2.673 4.251
{c4* g 1 13}P 6.901 -6.528 2.992
{c1* g 1 13}5.406 -5.003 2.08
{c4* g 1 14}P 2.238 -6.996 0.16
{c1* g 1 14}1.516 -4.831 0.747
{c4* t 1 15}P -4.12 -5.931 0.866
{c1* t 1 15}-4.339 -3.951 -0.399
{c4* g 1 16}P -9.11 -3.457 -1.299
{c1* g 1 16}-8.232 -2.295 -3.123
{c4* a 1 17}P -11.48 0.852 -4.616
{c1* a 1 17}-9.974 0.694 -6.417
{c4* t 1 18}P -10.999 4.02 -9.677
{c1* t 1 18}-9.3 2.845 -10.497
{c4* a 1 19}P -7.521 6.405 -14.179
{c1* a 1 19}-7.424 4.405 -15.432
{c4* t 1 20}P -4.299 5.271 -19.091
{c1* t 1 20}-5.18 3.202 -19.781
@subgroup {Strand 2} dominant
@vectorlist {mc} color=bluetint
{c4* t 2 1}-10.271 -10.39 -19.724
{p a 2 2}-6.677 -11.662 -18.322
{c4* a 2 2}-3.957 -9.69 -19.957
{p t 2 3}-0.737 -9.14 -17.626
{c4* t 2 3}-0.239 -5.161 -17.809
{p a 2 4}2.483 -3.292 -16.863
{c4* a 2 4}1.102 0.131 -16.196
{p t 2 5}2.865 3.285 -14.714
{c4* t 2 5}-0.074 4.625 -12.594
{p c 2 6}0.932 7.449 -10.224
{c4* c 2 6}-2.553 7.236 -8.731
{p a 2 7}-3.077 9.683 -5.75
{c4* a 2 7}-5.605 8.288 -3.294
{p c 2 8}-5.593 9.525 0.547
{c4* c 2 8}-5.38 5.827 1.801
{p c 2 9}-5.014 5.766 5.733
{c4* c 2 9}-3.833 2.206 6.286
{p g 2 10}-4.03 1.67 9.751
{c4* g 2 10}-2.9 -1.986 9.802
{p c 2 11}-2.214 -4.639 12.572
{c4* c 2 11}1.328 -5.546 11.557
{p c 2 12}3.501 -7.834 13.694
{c4* c 2 12}7.054 -6.673 12.486
{p a 2 13}9.948 -8.143 14.264
{c4* a 2 13}12.368 -6.109 12.321
{p g 2 14}16.384 -5.855 13.09
{c4* g 2 14}16.67 -2.027 13.575
{p t 2 15}19.56 0.131 15.176
{c4* t 2 15}17.604 3.34 15.905
{p g 2 16}20.357 5.484 17.706
{c4* g 2 16}18.292 7.346 20.288
{p g 2 17}20.04 9.538 22.938
{c4* g 2 17}17.624 8.803 25.764
{p t 2 18}18.317 9.978 29.52
{c4* t 2 18}16.533 6.989 31.19
{p a 2 19}16.377 6.219 34.974
{c4* a 2 19}15.586 2.426 35.31
{p t 2 20}16.253 0.302 38.592
{c4* t 2 20}17.84 -2.872 37.384
@vectorlist {sug} color=bluetint
{c4* t 2 1}P -10.271 -10.39 -19.724{c1* t 2 1}-9.258 -8.459 -20.407 {c4* a 2 2}P -3.957
-9.69 -19.957 {c1* a 2 2}-4.463 -7.868 -18.584 {c4* t 2 3}P -0.239
-5.161 -17.809 {c1* t 2 3}-1.976 -4.061 -16.766 {c4* a 2 4}P 1.102
0.131 -16.196 {c1* a 2 4}-0.24 0.11 -14.287 {c4* t 2 5}P -0.074
4.625 -12.594 {c1* t 2 5}-0.659 3.113 -10.942 {c4* c 2 6}P -2.553
7.236 -8.731 {c1* c 2 6}-2.975 5.738 -7.044 {c4* a 2 7}P -5.605
8.288 -3.294 {c1* a 2 7}-4.24 6.666 -2.314 {c4* c 2 8}P -5.38
5.827 1.801 {c1* c 2 8}-3.579 4.46 1.715 {c4* c 2 9}P -3.833
2.206 6.286 {c1* c 2 9}-1.556 1.979 5.824 {c4* g 2 10}P -2.9
-1.986 9.802 {c1* g 2 10}-0.673 -1.649 9.483 {c4* c 2 11}P 1.328
-5.546 11.557 {c1* c 2 11}2.913 -3.848 11.848 {c4* c 2 12}P 7.054
-6.673 12.486 {c1* c 2 12}7.261 -4.666 13.683 {c4* a 2 13}P 12.368
-6.109 12.321 {c1* a 2 13}12.436 -4.226 13.728 {c4* g 2 14}P 16.67
-2.027 13.575 {c1* g 2 14}15.505 -1.313 15.432 {c4* t 2 15}P 17.604
3.34 15.905 {c1* t 2 15}16.561 3.209 17.974 {c4* g 2 16}P 18.292
7.346 20.288 {c1* g 2 16}18.185 5.772 22.014 {c4* g 2 17}P 17.624
8.803 25.764 {c1* g 2 17}17.544 6.631 26.687 {c4* t 2 18}P 16.533
6.989 31.19 {c1* t 2 18}17.71 4.982 31.076 {c4* a 2 19}P 15.586
2.426 35.31 {c1* a 2 19}17.777 1.574 35.139 {c4* t 2 20}P 17.84
@subgroup {base pairs} dominant
@vectorlist {c1'-c1'} color=white
{c1* a 1 2}P 27.74 -5.388 30.614
{c1* t 2 20}19.909 -2.508 36.62
{c1* t 1 3}P 23.08 -6.109 29.759
{c1* a 2 19}17.777 1.574 35.139
{c1* a 1 4}P 17.865 -5.449 29.748
{c1* t 2 18}17.71 4.982 31.076
{c1* c 1 5}P 13.808 -2.515 29.845
{c1* g 2 17}17.544 6.631 26.687
{c1* c 1 6}P 10.615 0.88 27.713
{c1* g 2 16}18.185 5.772 22.014
{c1* a 1 7}P 8.193 4.048 24.493
{c1* t 2 15}16.561 3.209 17.974
{c1* c 1 8}P 8.407 5.14 20.083
{c1* g 2 14}15.505 -1.313 15.432
{c1* t 1 9}P 9.322 5.408 14.663
{c1* a 2 13}12.436 -4.226 13.728
{c1* g 1 10}P 10.79 5.03 9.494
{c1* c 2 12}7.261 -4.666 13.683
{c1* g 1 11}P 9.76 2.144 6.075
{c1* c 2 11}2.913 -3.848 11.848
{c1* c 1 12}P 8.926 -2.673 4.251
{c1* g 2 10}-0.673 -1.649 9.483
{c1* g 1 13}P 5.406 -5.003 2.08
{c1* c 2 9}-1.556 1.979 5.824
{c1* g 1 14}P 1.516 -4.831 0.747
{c1* c 2 8}-3.579 4.46 1.715
{c1* t 1 15}P -4.339 -3.951 -0.399
{c1* a 2 7}-4.24 6.666 -2.314
{c1* g 1 16}P -8.232 -2.295 -3.123
{c1* c 2 6}-2.975 5.738 -7.044
{c1* a 1 17}P -9.974 0.694 -6.417
{c1* t 2 5}-0.659 3.113 -10.942
{c1* t 1 18}P -9.3 2.845 -10.497
{c1* a 2 4}-0.24 0.11 -14.287
{c1* a 1 19}P -7.424 4.405 -15.432
{c1* t 2 3}-1.976 -4.061 -16.766
{c1* t 1 20}P -5.18 3.202 -19.781
{c1* a 2 2}-4.463 -7.868 -18.584
<end of file>