I've recently noticed that the Helix and Sheet records in PDB entries
differ from those generated by DSSP and would like to ask if anyone
can explain how the PDB makes the assignments. Until now I'd always
assumed that the PDB and DSSP records were the same.
As an example I've listed a few lines from 2V3U.pdb. There are
similar difference in both helix lengths and start/stop positions
that occur in 9 other entries I've looked at.
2V3U.pdb
HELIX 1 1 GLY A 31 GLY A 45 1 15
HELIX 2 2 ASN A 68 PHE A 76 1 9
HELIX 3 3 THR A 89 ASN A 94 1 6
and for the same structure the DSSP entry from the CMBI data base
http://swift.cmbi.ru.nl/gv/dssp/
REMARK 1 secondary structure assigned by dssp
HELIX 1 1 PHE A 32 LEU A 44 1 13
HELIX 2 2 GLY A 69 VAL A 75 1 7
HELIX 3 3 PRO A 90 GLU A 93 1 4
Its not a big deal, but makes comparing secondary structures a bit
more difficult.
--
Mark
