About the Program:
PepDraw is a tool that was developed to facilitate the
study of the chemical structure and properties of peptides.
It allows users to draw the primary chemical structure of an
amino acid sequence and predict some chemical properties such
as mass, charge, and hydrophobicity. PepDraw was designed
to be a powerful yet user-friendly tool for peptide analysis.
It is especially useful for teaching students about the
structure and properties of the amino acids.
The latest (and greatest) version of pepdraw is now on the web.
A sequence may be entered by typing directly into the sequence
entry field or by clicking the buttons in the "Amino Acid Keypad."
The program will only read characters that code for the 20 natural
Properties are generated automatically upon changing the
information in the sequence entry field.
The sequence that was analyzed, displayed in single-letter
The number of valid amino acid characters entered by the user.
The mass or formula weight is the sum of monoisotopic masses
of all amino acid residues in the peptide. This is calculated
by adding the atomic masses of all side-chain atoms to the
mass of all backbone atoms plus the mass of water.
Isoelectric point (pI)
The isoelectric point is the pH at which the net charge of
a peptide is zero. The calculation of the pI assesses the partial
charge of the peptide at various pH values starting from 0 and
incrementing 0.01 pH units per step.
The net charge is the sum of positively (basic) and negatively
(acidic) charged residues at neutral pH.
Hydrophobicity (Wimley-White scale)*
Hydrophobicity here is the free energy associated with transitioning
a peptide from an aqueous environment to a hydrophobic environment
like octanol. The scale used is the Wimley-White scale, an
experimentally determined scale, where the hydrophobicity of
the peptide is the sum of Wimley-White hydrophobicities. The
units of measure is in Kcal per mol. Neutral pH is assumed.
Molar extinction coefficient
The molar extinction coefficient is a factor used to describe
how much light a molecule absorbs. In this case the light is
at a wavelength of 280 nm. The most strongly absorbing side
chains at this wavelength are tryptophan, tyrosine, and cysteine
when it forms disulfide pairs called cystines. The molar
extinction is calculated by first counting the number of
tryptophans (W), the number of tyrosines (Y), and the number
of disulfide bonding pairs (cystines). Then the following formula
is used to calculate the first extinction coefficient:
W*5500 + Y*1490 + cystines*125. This calculation assumes that
all cysteines pair into cystines. The second version assumes
that all cysteines are reduced and there are no cystines, thus
it is calculated as W*5500 + Y*1490.
Peptide structure image
The image is in PNG (portable network graphics) format. The
images are larger than they appear on-screen. Images can
be saved or copied by right-clicking.
Further Questions: Any further questions/concerns/inputs about the program can be emailed to Thomas Freeman at firstname.lastname@example.org or Hussain Badani at email@example.com.
* S.H. White, W.C. Wimley, Hydrophobic interactions of peptides with membrane interfaces, Biochimica et biophysica acta 1376 (1998) 339-352.