daemon@ig.UUCP (10/27/87)
From: Sunil Maulik <MAULIK@BIONET-20.ARPA>
DSSP - DEFINE SECONDARY STRUCTURES OF PROTEINS
This program written by Kabsch and Sander defines secondary structures
of proteins from the patterns of hydrogen bonds and geometrical
features of the backbone structure. The program runs on a Protein
Data Bank file and the output contains up to 128 characters in one
line.
OUTPUT
The following notes are reproduced from the original program.
# RESIDUE - Two columns of residue numbers. First column is
DSSP(3)'s sequential residue number, starting at the first
residue actually in the data set and including chain breaks; this
number is used to refer to residues throughout. Second column
gives crystallographers' residue sequence number, insertion code
and chain identifier, given for reference only and not used
further.
AA - One letter amino acid code, lower case for SS-bridge CYS.
STRUCTURE - See ANNOT(3) and reference below.
BP1 BP2 - Residue number of first and second bridge partner followed
by one letter sheet label.
ACC - Number of water molecules in contact with this residue *10.
Or residue water exposed surface in angstrom**2.
N-H-->O etc. - Hydrogen bonds. e.g. -3,-1.4 means: if this residue
is residue I then N-H of I is H-bonded to C=O of I-3 with an
electrostatic H-bond energy of -1.4 kcal/mol.
TCO - Cosine of angle between C=O of residue I and C=O of residue
I-1. For alpha-helices, TCO is near +1, for beta-sheets TCO is
near -1. Not used for structure definition.
KAPPA - Virtual bond angle (bend angle) defined by the three C-alpha
atoms of residues I-2, I, I+2. Used to define bend (structure
code 'S').
ALPHA - Virtual torsion angle (dihedral angle) defined by the four
C-alpha atoms of residues I-1, I, I+1, I+2. Used to define
chirality (structure code '+' OR '-').
PHI PSI - IUPAC peptide backbone torsion angles.
X-CA Y-CA Z-CA - Echo of C-alpha atom coordinates.
REFERENCE
Kabsch, W. and Sander, C.; Dictionary of protein secondary structure:
Pattern recognition of hydrogen-bonded and geometrical features.
Biopolymers 22, 2577-2637 (1983).
For more help on the DSSP program, including an annotated example of
program use and the Brookhaven Protein Databank, enter HELP DSSP at the
@ sign. To run the program, simply enter DSSP at the @ sign.
For more information on the contributed software available on BIONET, enter
HELP SOFTWARE at the @ prompt. For a guide to the BIONET sytem, enter HELP
ME at the @ prompt.
Sincerely,
Sunil Maulik ARPAnet: Maulik@bionet-20.arpa
Senior Scientific Consultant BITnet: Maulik%bionet-20.arpa@wiscvm.bitnet
BIONET
(415)-324-4363
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