The dssp command assigns amino acid residues to helices and strands by identifying hydrogen-bonding patterns in protein atomic coordinates. H-bonds and virtual hydrogens from the dssp calculation are not shown on the structure, but see also: hbonds, addh
The dssp command implements the algorithm for Defining the Secondary Structure of Proteins described in:
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Kabsch W, Sander C. Biopolymers. 1983 Dec;22(12):2577-637.Per-residue helix and strand assignments are used for drawing protein cartoons, and may be used by matchmaker, depending on its settings. In PDB format, secondary structure assignments are described in HELIX and SHEET records, and analogous information is included in mmCIF files. However, not all input files include this information. The dssp calculation is run:
The calculation applies to all protein/peptide chains in models containing the specified atoms. The coordinates of protein backbone atoms (N, CA, C, O, and optionally H) are used to identify hydrogen bonds, which in turn define which residues are in helices and strands. If an amide hydrogen is not present, one is (virtually) placed 1.01 Å from N along the bisector of (1) the vector opposite the bisector of C-N-CA, and (2) the vector opposite the C-O vector from the previous amino acid.
The energyCutoff c specifies the least favorable (maximum) estimated energy required to classify an interaction as a hydrogen bond. The default is –0.5 kcal/mol, as recommended by Kabsch and Sander, who add that “A good H-bond has about –3 kcal/mol binding energy.”
The minHelixLen N and minStrandLen M specify the mininum number of residues in a helix or strand, respectively, and both default to 3. Single-residue strands should not be allowed, as there are bridges in many structures that would confuse the algorithm for identifying sheets.
The report option (default false) indicates whether to report detailed results in the Log, including helix and strand residue ranges and whether ladder (strand-pair) relationships are parallel or antiparallel. The last section lists each protein residue followed by various symbols. The notation is similar to that used by Kabsch and Sander, but is in a vertical instead of horizontal format. There are 6 single-character fields after the residue specifier, each preceded by a single space; if a field is blank, none of the values apply:
| Field | Possible contents and meaning |
|---|---|
| 1. Secondary structure type
(before filtering by minimum length) |
G = 3/10-helix
H = α-helix I = 5-helix E = β-strand |
| 2. 3-turn status
(interactions between residues 3 apart in sequence) |
> = backbone CO of this residue makes H-bond (i, i+3)
< = backbone NH of this residue makes H-bond (i-3, i) X = both of the above 3 = not participating but bracketed |
| 3. 4-turn status
(interactions between residues 4 apart in sequence) |
> = backbone CO of this residue makes H-bond (i, i+4)
< = backbone NH of this residue makes H-bond (i-4, i) X = both of the above 4 = not participating but bracketed |
| 4. 5-turn status
(interactions between residues 5 apart in sequence) |
> = backbone CO of this residue makes H-bond (i, i+5)
< = backbone NH of this residue makes H-bond (i-5, i) X = both of the above 5 = not participating but bracketed |
| 5. Pairing direction |
p = parallel
A = antiparallel + = both (parallel on one side, antiparallel on the other) |
| 6. Sheet membership | A single-character name for the β-sheet in which the residue participates. Sheets are named sequentially from N- to C-terminus. |