DSSP

References

If you use the DSSP software or databank please cite the appropriate paper:

Current version	Joosten RP, te Beek TAH, Krieger E, Hekkelman ML, Hooft RWW, Schneider R, Sander C, Vriend A series of PDB related databases for everyday needs. Nuc. Acids Res. 2010; 39:D411-D419.
Original algorithm	Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983; 22:2577-2637.

Using DSSP data

DSSP provides an elaborate description of the secondary structure elements in a protein structure, including backbone hydrogen bonding and the topology of β-sheets. The most popular feature is the per-residue assignment of secondary structure with a single character code:

H = α-helix
B = residue in isolated β-bridge
E = extended strand, participates in β ladder
G = 3₁₀-helix
I = π-helix
P = κ-helix (poly-proline II helix)
T = hydrogen-bonded turn
S = bend

The full DSSP output is provided in two formats. The legacy DSSP format was origianlly designed for structures that were in PDB-formatted models. Now, 40 years later, the PDB format has become obsolete as it cannot capture the large structure models that modern structural biology methods can provide. The mmCIF format is the data format of choice for structural biology as it has no size limitations for structure models and it can hold extensive annotations and metadata. DSSP now writes its data straight to these mmCIF files by default. The legacy DSSP format can still be written but only for structure models that fit.

DSSP format

The output from DSSP contains secondary structure assignments and other information. Extract from 3kew.dssp (header):


==== Secondary Structure Definition by the program DSSP, NKI version 4.3                           ==== DATE=2023-06-08        .
REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637                                                              .
HEADER    TRANSFERASE                             26-OCT-09   3KEW                                                             .
COMPND    MOL_ID: 1; MOLECULE: DHHA1 domain protein; CHAIN: A, B; FRAGMENT: N-TERMINAL FRAGMENT, RESIDUES 1-231; SYNONYM: A... .
SOURCE    MOL_ID: 1; GENE: ALAS, CPF_0714; STRAIN: ATCC 13124; ORGANISM_SCIENTIFIC: Clostridium perfringens; ORGANISM_TAXID... .
AUTHOR    Y.Patskovsky; R.Toro; M.Gilmore; S.Miller; J.M.Sauder; S.C.Almo; S.K.Burley; New York SGX Research Center for Str... .
  458  3  0  0  0 TOTAL NUMBER OF RESIDUES, NUMBER OF CHAINS, NUMBER OF SS-BRIDGES(TOTAL,INTRACHAIN,INTERCHAIN)                .
 24682.5   ACCESSIBLE SURFACE OF PROTEIN (ANGSTROM**2)                                                                         .
  319 69.7   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(J)  , SAME NUMBER PER 100 RESIDUES                              .
    6  1.3   TOTAL NUMBER OF HYDROGEN BONDS IN     PARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES                              .
  144 31.4   TOTAL NUMBER OF HYDROGEN BONDS IN ANTIPARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES                              .
    0  0.0   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-5), SAME NUMBER PER 100 RESIDUES                              .
    2  0.4   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-4), SAME NUMBER PER 100 RESIDUES                              .
   12  2.6   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-3), SAME NUMBER PER 100 RESIDUES                              .
    0  0.0   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-2), SAME NUMBER PER 100 RESIDUES                              .
    0  0.0   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-1), SAME NUMBER PER 100 RESIDUES                              .
    0  0.0   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+0), SAME NUMBER PER 100 RESIDUES                              .
    0  0.0   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+1), SAME NUMBER PER 100 RESIDUES                              .
   50 10.9   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+2), SAME NUMBER PER 100 RESIDUES                              .
   34  7.4   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+3), SAME NUMBER PER 100 RESIDUES                              .
   84 18.3   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+4), SAME NUMBER PER 100 RESIDUES                              .
    2  0.4   TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+5), SAME NUMBER PER 100 RESIDUES                              .
  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30     *** HISTOGRAMS OF ***           .
  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  1  1  0  0  0  0  0  0  0  2  0  0  0  0  0    RESIDUES PER ALPHA HELIX         .
  0  2  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0    PARALLEL BRIDGES PER LADDER      .
  4  0  4  8  2  6  0  2  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0    ANTIPARALLEL BRIDGES PER LADDER  .
  2  2  2  0  0  2  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0    LADDERS PER SHEET                .

The first few lines are taken from the input model file, then some general statistics about the model and hydrogen bonding are given. The histograms describe the distribution of sizes of secondary structure elements. For instance, this structure has three helices, one short one consisting of 4 residues and two longer ones of 16 and 17 residues. Note that beta sheets are described as a collection of ladders, rather than strands. Ladders can be seen as two strands together with the hydrogen bonds as the rungs of the ladder. More formal definitions are given in the Kabsch and Sander paper.

The model statistics are followed by a detailed per-residue description. Extract from 3kew.dssp (continued):

....;....1....;....2....;....3....;....4....;....5....;....6....;....7..
  .-- sequential resnumber, including chain breaks as extra residues
  |    .-- original resname, not necessarily sequential, may contain letters for insertion codes
  |    | .-- one-letter chain ID
  |    | | .-- amino acid sequence in one letter code
  |    | | |  .-- secondary structure summary based on columns 19-38
  |    | | |  |.-- PPII (kappa) helix
  |    | | |  ||.-- 3-10 helix
  |    | | |  |||.-- alpha helix
  |    | | |  ||||.-- pi helix
  |    | | |  |||||.-- geometrical bend
  |    | | |  ||||||.-- chirality
  |    | | |  |||||||.-- beta bridge label
  |    | | |  ||||||||.-- beta bridge label
  |    | | |  |||||||||   .-- beta bridge partner resnum
  |    | | |  |||||||||   |   .-- beta bridge partner resnum
  |    | | |  |||||||||   |   |.-- beta sheet label
  |    | | |  |||||||||   |   ||   .-- solvent accessibility
  |    | | |  |||||||||   |   ||   |
#  RESIDUE AA STRUCTURE BP1 BP2  ACC     N-H-->O    O-->H-N    N-H-->O    O-->H-N    TCO  KAPPA ALPHA  PHI   PSI    X-CA   Y-CA   Z-CA
  1    1 A L              0   0  119      0, 0.0     2,-0.3     0, 0.0    33,-0.2   0.000 360.0 360.0 360.0 168.8    8.7    6.9   63.0
  2    2 A T  E     -a   34   0A  66     31,-2.0    33,-2.1     1,-0.1     2,-0.7  -0.456 360.0-169.6 -87.8 130.5    7.7    8.8   59.8
  3    3 A K  E >   -a   35   0A  66     -2,-0.3     3,-1.2    31,-0.2     4,-0.2  -0.850   8.5-179.0-111.3  94.7    7.6    7.5   56.2
  4    4 A L  G >> S+     0   0   23     31,-2.5     4,-2.9    -2,-0.7     3,-2.0   0.786  71.6  72.4 -65.6 -32.5    7.1   10.6   54.1
  5    5 A Y  G 34 S+     0   0    2     30,-0.8    -1,-0.3     1,-0.3    31,-0.1   0.709 101.0  46.1 -56.9 -26.7    7.0    8.7   50.7
  6    6 A Y  G <4 S+     0   0   39     -3,-1.2    -1,-0.3     2,-0.1    -2,-0.2   0.439 115.4  47.1 -93.5  -4.1    3.5    7.4   51.7
  7    7 A E  T <4 S-     0   0  138     -3,-2.0     2,-0.3     1,-0.2    -2,-0.2   0.825 135.2  -0.3 -99.6 -48.8    2.4   10.9   52.8
  8    8 A D    ><  -     0   0   57     -4,-2.9     3,-1.4     3,-0.1    -1,-0.2  -0.852  61.5-167.8-144.3 106.0    3.6   13.0   49.9

Below is a brief description of the data columns. More details are described in the Kabsch and Sander paper.

RESIDUE

Two columns of residue numbers. First column is DSSP's sequential residue number, starting at the first residue actually in the model set and including chain breaks; this number is used to refer to residues throughout. The second column gives the numbering as is used in the structure model 'residue number','insertion code' and 'chain identifier'; these are given for reference only.

AA

One letter amino acid code, non standard residues are marked as X. CYS in an SS-bridge are marked by a lower case letter. So when cysteines are bridged, then the first bridged cysteine in the sequence and its partner elsewhere in the sequence are marked a. The next bridged cysteine, that is not yet marked, and its partner are both marked b, etcetera. Unbridged cysteines remain marked as C.

STRUCTURE

The first column (under the S) gives aone-letter summary of secondary structure, intended to approximate crystallographers' intuition. This summary is based on the next 8 columns, which are the principal result of DSSP analysis of the atomic coordinates. More details in the Kabsch and Sander paper.

BP1 and BP2

Residue numbers of the first and (if available) second beta bridge partner. The letter marked the B-sheet that contains the bridges.

ACC

Water exposed surface in Ångström². Note: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. it also ignores HETATOMS, like a heme or metal ligands. Also, side chains may not have all atoms explicitly modeled.
Effects leading to smaller than expected values: in complexes, e.g. a dimer, 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.
Unknown or non-standard residues are named X on output and are not checked for the expected number of sidechain atoms.
All explicit water molecules, like other hetatoms, are ignored.

N-H-->O etc.

Hydrogen bonds; e.g. -3,-1.4 means that this residue (i) has its HN atom H-bonded to O of residue 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. Note:The marked H-bonds are the best and second best candidate. The second best and even the best (in rare occasions) may be unrealistically por H-bonds.

TCO

The cosine of angle between C=O of residue i and C=O of residue i-1. For α-helices, TCO is near +1, for β-sheets TCO is near -1. These values are descriptive and not used for structure definition.

KAPPA

Virtual bond angle (bend angle) defined by the three Cα atoms of residues i-2, i, and i+2. Used to define bends (structure code S).

ALPHA

Virtual torsion angle (dihedral angle) defined by the four Cα atoms of residues i-1, i, i+1, and i+2. Used to define chirality (structure code + or -).

PHI and PSI

The peptide backbone torsion angles as described in the IUPAC standard

X-CA, Y-CA, and Z-CA

Just a copy of the Cα atom coordinates in the structure model

DSSP data in mmCIF files

The mmCIF-formatted DSSP output caries the same information as the DSSP format but in a more scalable way and with a formal description caputered in an mmCIF dictionary. It is designed to be machine readable. Developers who create software to read these annotations can use our extension to the mmCIF dictionary on GitHub. Note: For sake of speed the solvent accessibility is not calculated by default when using mmCIF output. The command-line switch --calculate-accessibility can be used to switch this feature on.