dssp Module

Reads output from DSSP program.

DSSP is a program for classifying secondary structures and solvent accessibility from protein structures. This module contains functions that process the output.

These functions have been tested on output from the DSSP webserver (http://swift.cmbi.ru.nl/gv/dssp/) using the version available as of May-24-2013.

This module was written by Jesse Bloom.

List of functions

  • MaxASA : Maximum accessible surface area for amino acids.
  • ReadDSSP : reads secondary structures and RSA from DSSP output.

Documentation for individual functions

Documentation for individual functions is provided in their definitions below.

dssp.MaxASA(scale)

Returns the maximum accessible surface area for amino acids.

This function returns the maximum accessible surface area (ASA) for the amino acids in units of square angstroms. These ASAs are necessary for calculating the relative solvent accessibility of a residue.

There are a large variety of estimates for the exact ASA for each amino acid. The calling variable scale specifies which scale to use. Allowed values are the following strings:

The returned variable is a dictionary asa keyed by each upper-case one-letter amino-acid code, with the values being the ASA for that residue.

Example:

>>> asa = MaxASA('Tien2013')
>>> len(asa) == 20
True
>>> asa == {'A':129.0, 'R':274.0, 'N':195.0, 'D':193.0, 'C':167.0, 'E':223.0, 'Q':225.0, 'G':104.0, 'H':224.0, 'I':197.0, 'L':201.0, 'K':236.0, 'M':224.0, 'F':240.0, 'P':159.0, 'S':155.0, 'T':172.0, 'W':285.0, 'Y':263.0, 'V':174.0}
True
dssp.ReadDSSP(infile, asa_scale, chain=None)

Reads secondary structure and ASA from DSSP output.

DSSP is a program that calculates secondary structure and absolute solvent accessibility (ASA) on a per-residue basis from a PDB protein structure file.

These functions have been tested on output from the DSSP webserver (http://swift.cmbi.ru.nl/gv/dssp/) using the version available as of May-24-2013.

NOTE that this function currently does not process DSSP output from PDB structures where the residue numbers have letter suffixes (such as residue 25A). It will raise an error if such residue numbers exist in the DSSP output.

CALLLING VARIABLES:

  • infile : name of a text file containing the output of a DSSP analysis.
  • asa_scale : calculation of relative solvent accessiblity (RSA) from the absolute solvent accessibility (ASA) returned by DSSP requires normalization by the maximum solvent accessibility of each residue. asa_scale specifies those maximum values. It should be a string that is passable to MaxASA as its single calling paramter – those maximum ASAs are used to normalize the DSSP ASAs to RSAs.
  • chain is an optional variable. If the PDB structure used to run DSSP has only one chain, then this variable can just have its default value of None. Otherwise it should provide a letter specifying the protein chain from which we read the ASA values. If there are multiple chains, this variable must be set to a value matching one of those chains.

RETURN VARIABLE:

The return variable is a dictionary dssp. For each residue number in the original PDB analyzed by DSSP, there is an integer key in dssp. The value for each of these residues is in turn a dictionary which has the following string keys:

  • ASA : the value is absolute solvent accessibility in square angstroms.

  • RSA : the value is the relative solvent accessiblity.

  • SS : the DSSP secondary structure code, which can be the following letters:

    • G : 3-10 helix
    • H : alpha helix
    • I : pi helix
    • B : beta bridge
    • E : beta bulge
    • T : turn
    • S : high curvature
    • _ : loop

  • SS_CLASS : the larger secondary structure classes, which are defined by the following strings based on SS:

    • helix : a SS value of G, H, or I
    • strand : a SS value of B or E
    • loop : any of the other SS values.