DSSP new output format

From the July 1995 version onwards, the output format (new standard) has three new features (for details, see below).

• The Hbond columns are two characters wider.
• PDB chain break identifier is indicated by a star (*).
• The DSSP file header changed to alert the user to the format changes.

To obtain output in the pre-July 1995 format use the -c option. Example:

dssp -c myprotein.pdb myprotein.dssp

Wider Hbond Columns

The Hbond columns (energy and residue offset) are wider by two characters, in order to accommodate residue number offsets up to +/-99999. The format of the first block of columns (up to the Solvent Accessibility) is not affected by this change.

PDB chain break identifier

In addition to the chain break residue (!) detected as a discontinuity of backbone coordinates, DSSP now also detects a discontinuity in the PDB-supplied chain identifier, recorded as (*). The (*) is in the column between the Amino Acid Letter and the Secondary Structure Summary columns.

Examples

• Discontinuity in backbone coordinates (example from 1etu.pdb)

     35   39   Y  H  <5       0   0  110     -4,-1.4    -3,-0.2    -5,-0.3    -1,-0.2   0.906 360.0 360.0 -70.6 -52.6   74.0   40.9   29.8
     36   40   G     <<       0   0  101     -5,-1.1    -3,-0.1    -4,-0.6    -1,-0.1   0.383 360.0 360.0 -73.5 360.0   76.8   41.2   27.3
     37        !              0   0    0      0, 0.0     0, 0.0     0, 0.0     0, 0.0   0.000 360.0 360.0 360.0 360.0    0.0    0.0    0.0
     38   60   I              0   0  161      0, 0.0     2,-0.2     0, 0.0     0, 0.0   0.000 360.0 360.0 360.0 161.5  106.5   37.7   49.5
     39   61   T        -     0   0   91      2,-0.0     2,-0.4     0, 0.0     0, 0.0  -0.814 360.0-165.8-128.3 135.3  105.4   35.7   46.6
  

• Discontinuity in chain identifier and in backbone coordinates (example from 1tim.pdb)

    246  247 A K              0   0  161      1,-0.4   -25,-0.2   -29,-0.1   -26,-0.1  -0.879 360.0 360.0 178.1 167.1   53.2   14.3    7.1
    247  248 A H              0   0  200     -2,-0.2    -1,-0.4   -27,-0.1   -26,-0.2   0.741 360.0 360.0 -48.4 360.0   52.1   10.8    8.1
    248        !*             0   0    0      0, 0.0     0, 0.0     0, 0.0     0, 0.0   0.000 360.0 360.0 360.0 360.0    0.0    0.0    0.0
    249    1 B A              0   0  133      0, 0.0     2,-1.4     0, 0.0     0, 0.0   0.000 360.0 360.0 360.0-178.2   46.5   82.7    0.4
    250    2 B P        +     0   0   94      0, 0.0     2,-0.1     0, 0.0     0, 0.0  -0.822 360.0  58.6 -85.7  94.3   46.3   80.1    3.1
  

New header line

To reflect the change in format, a new header line is used (line starts with ====, text is in mixed case):

==== Secondary Structure Definition by the program DSSP, Version July 1995 ==== DATE=27-JUL-1995                      .

If the pre-July 1995 format is forced (using dssp -c ...) first line reverts to the pre-July 1995 style (line starts with ****, text is in upper case):

**** SECONDARY STRUCTURE DEFINITION BY THE PROGRAM DSSP, VERSION JULY 1995 **** DATE=27-JUL-1995                      .