Description of the DSSPcont program

DSSP was written by Wolfgang Kabsch and Chris Sander
DSSPcont was written by Claus A.F. Andersen, Arthur G. Palmer, Søren Brunak and Burkhard Rost

Function

Definition of secondary structure of proteins given a set of 3D coordinates in PDB format.

Description

The DSSP program defines secondary structure in eight categories, geometrical features and solvent exposure of proteins, given atomic coordinates in Protein Data Bank format. The DSSPcont program has extended the discrete DSSP assignments to a continuous assignment in the same eight categories.

Authors of the DSSP method

Wolfgang Kabsch and Chris Sander, MPI MF, Heidelberg, 1983.
Reference: Kabsch,W. and Sander,C. (1983) Biopolymers 22, p2577-2637

Authors of the DSSPcont method

Claus A.F. Andersen, Arthur G. Palmer, Søren Brunak and Burkhard Rost, CUBIC, New York 2001
Reference: Andersen CAF, Palmer AG, Brunak S, Rost B (2002) Structure 10, p175-184

Usage and command line options

dsspcont pdb_file|pdbid

Command line options:

pdb_file: Name of the flatfile containing the PDB entry.
pdbid: The 4 letter PDB identifier e.g. 101m

Examples

In this example the filename was used for the large photoreaction center (1prc) input file.

    unix% dsspcont 1prc.pdb > 1prc.dsspc

Output file is 1prc.dsspc

Output

The output from DSSPcont contains secondary structure assignments and other information, one line per residue. Simplified extract from PDB-ID: 1A53

...
HEADER    SYNTHASE                                19-FEB-98   1A53                                                             .
COMPND   2 MOLECULE: INDOLE-3-GLYCEROLPHOSPHATE SYNTHASE;                                                                      .
SOURCE   2 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS;                                                                       .
AUTHOR    M.HENNIG,B.DARIMONT,K.KIRSCHNER,J.N.JANSONIUS                                                                        .
  247  1  0  0  0 TOTAL NUMBER OF RESIDUES, NUMBER OF CHAINS, NUMBER OF SS-BRIDGES(TOTAL,INTRACHAIN,INTERCHAIN)                .
 10789.0   ACCESSIBLE SURFACE OF PROTEIN (ANGSTROM**2)                                                                         .
  184 74.5   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(J)  , SAME NUMBER PER 100 RESIDUES                              .
   35 14.2   TOTAL NUMBER OF HYDROGEN BONDS IN     PARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES                              .
...
   81 32.8   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+4), SAME NUMBER PER 100 RESIDUES                              .
    5  2.0   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+5), SAME NUMBER PER 100 RESIDUES                              .
...
    .-- sequential residue number, including chain breaks as extra residues
    |    .-- original PDB residue number, not nec. sequential, may contain letters
    |    |   .-- amino acid sequence in one letter code (where ! means chain break)
    |    |   |  .-- secondary structure summary (eight category discrete assignment) based on columns 19-38
    |    |   |  | 
    |    |   |  | .-- 3-turn-helix H-bond (I+3) or (I-3) forming 3_10-helices  | 		      > means H-bond downstream
    |    |   |  | |.-- 4-turn-helix H-bond (I+4) or (I-4) forming alpha-helices| turn-helix columns:  < means H-bond upstream
    |    |   |  | ||.-- 5-turn-helix H-bond (I+5) or (I-5) forming pi-helices  | 		      X means both H-bonds
    |    |   |  | |||.-- geometrical bend
    |    |   |  | ||||.-- chirality
    |    |   |  | |||||.-- beta bridge label 
    |    |   |  | ||||||.-- beta bridge label 
    |    |   |  | |||||||   .-- beta bridge partner residue number
    |    |   |  | |||||||   |   .-- beta bridge partner residue number
    |    |   |  | |||||||   |   |.-- beta sheet label 
    |    |   |  | |||||||   |   ||   .-- solvent accessibility
    |    |   |  | |||||||   |   ||   |    
    |    |   |  | |||||||   |   ||   |    .-- continuous assignment of 3_10 helix (DSSP 'G')
    |    |   |  | |||||||   |   ||   |    |   .-- continuous assignment of alpha-helix (DSSP 'H')
    |    |   |  | |||||||   |   ||   |    |   |   .-- continuous assignment of pi-helix (DSSP 'I')
    |    |   |  | |||||||   |   ||   |    |   |   |   .-- continuous assignment of a helix turn (DSSP 'T')
    |    |   |  | |||||||   |   ||   |    |   |   |   |   .-- continuous assignment of an extended beta-sheet (DSSP 'E')
    |    |   |  | |||||||   |   ||   |    |   |   |   |   |   .-- continuous assignment of a beta-bridge (DSSP 'B')
    |    |   |  | |||||||   |   ||   |    |   |   |   |   |   |   .-- continuous assignment of a bend (DSSP 'S')
    |    |   |  | |||||||   |   ||   |    |   |   |   |   |   |   |   .-- continuous assignment of other/loop (DSSP 'L')
    |    |   |  | |||||||   |   ||   |    |   |   |   |   |   |   |   |
  #  RESIDUE AA STRUCTURE BP1 BP2  ACC    G   H   I   T   E   B   S   L  
...
   64   65   D     >  -     0   0   81    0   0   0   0   0   0   0 100 
   65   66   P  H  > S+     0   0   15    0 100   0   0   0   0   0   0 
   66   67   I  H  > S+     0   0   22    0 100   0   0   0   0   0   0 
   67   68   E  H  > S+     0   0  121    0 100   0   0   0   0   0   0 
   68   69   Y  H  X S+     0   0    7    0 100   0   0   0   0   0   0 
   69   70   S  H  X S+     0   0    0    0 100   0   0   0   0   0   0 
   70   71   K  H  < S+     0   0   96    0 100   0   0   0   0   0   0 
   71   72   F  H >< S+     0   0   33    0 100   0   0   0   0   0   0 
   72   73   M  H >X S+     0   0    0    0 100   0   0   0   0   0   0 
   73   74   E  T 3< S+     0   0   49    0  53   0  47   0   0   0   0 
   74   75   R  T <4 S+     0   0  171    0  53   0  47   0   0   0   0 
   75   76   Y  T <4 S+     0   0   52    0  53   0  47   0   0   0   0 
   76   77   A     <  -     0   0    1    0   0   0   0  10   0   0  90 
   77   78   V  S    S-     0   0    0    0   0   0   0  10   0  90   0 
   78   79   G  E     -b   48   0A   0    0   0   0   0 100   0   0   0 
   79   80   L  E     -bc  49 106A   0    0   0   0   0 100   0   0   0 
   80   81   S  E     -bc  50 107A   0    0   0   0   0 100   0   0   0 
   81   82   I  E     -bc  51 108A   0    0   0   0   0 100   0   0   0 
   82   83   L  E     + c   0 109A   5    0   0   0   0 100   0   0   0 
   83   84   T        +     0   0    0    0   0   0   0   0   0   0 100 
   84   85   E        -     0   0    4    0   0   0   0   0   0   0 100 
   85   86   E     >  +     0   0  103    0  10   0   0   0   0   0  90 
   86   87   K  T  4 S+     0   0  124    0  10   0  64   0   0  26   0 
   87   88   Y  T  4 S+     0   0   43    0  10   0  64   0   0  26   0 
   88   89   F  T  4 S-     0   0   19    0  10   0  64   0   0  26   0 
   89   90   N     <  +     0   0   72    0   0   0   0   0  10   0  90 
...

For definitons, see above BIOPOLYMERS and STRUCTURE articles.

Each line contains the following residue information

`# RESIDUE`

two columns of residue numbers. First column is DSSP'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' (see protein data bank file record format manual), given for reference only.

`AA`

one letter amino acid code. NB lower case letters indicate Cystein (CYS) residue pairs, which are covalently bonded with an SS-bridge.

`S` (first column in STRUCTURE block)

compromise a summary of secondary structure (eight categories), intended to approximate crystallographers' intuition, based on columns 19-38, which are the principal result of DSSP analysis of the 3D atomic coordinates. These eight categories are:

3_10-helix (DSSP 'G')
alpha-helix (DSSP 'H')
pi-helix (DSSP 'I')
helix turn (DSSP 'T')
extended beta-sheet (DSSP 'E')
beta-bridge (DSSP 'B')
bend (DSSP 'S')
other/loop (DSSP ' ' i.e. a space. In the DSSPcont column 'L')

`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` (doner) and `O-->H-N` (acceptor) 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. There are two columns for each type of H-bond, to allow for bifurcated H-bonds.

`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

Warnings

The values for solvent exposure may not mean what you think!

effects leading to larger than expected values: solvent exposure calculation ignores unusual residues, like ACE, or residues with incomplete backbone, like ALA 1 of data set 1CPA. it also ignores HETATOMS, like a heme or metal ligands. Also, side chains may be incomplete (an error message is written).
effects leading to smaller than expected values: if you apply this program to protein data bank data sets containing oligomers, solvent exposure is for the entire assembly, not for the monomer. Also, atom OXT of c-terminal residues is treated like a side chain atom if it is listed as part of the last residue. also, peptide substrates, when listed as atoms rather than hetatoms, are treated as part of the protein, e.g. residues 499 s and 500 s in 1CPA.

Unknown or unusual residues are named X on output and are not checked for standard number of sidechain atoms. All explicit water molecules, like other hetatoms, are ignored.

Input file

Coordinate file in PDB format.

Adapted for DSSPcont by Claus A.F. Andersen