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Secondary Structure Files

Secondary structure assignments in the file ss.txt are calculated from the experimental coordinates using DSSP (W. Kabsch, C.Sander (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22:2577-637).

An 'X' in the sequence indicates a residue of unknown identity.

A blank in the ss.txt file stands for a loop or other irregular structure.

The codes used in the ss.txt file are:

  • H = alpha helix
  • B = residue in isolated beta-bridge
  • E = extended strand, participates in beta ladder
  • G = 3-helix (3/10 helix)
  • I = 5 helix (pi helix)
  • T = hydrogen bonded turn
  • S = bend

The file ss_dis.txt includes notation of regions that have not been experimentally observed in addition to the secondary structure.

Here, X's indicate differences between residues that exist in the originally studied molecule (the SEQRES records of the PDB file) but not in the observed structure (the coordinate records of the PDB file).

REMARK 465 in the PDB format file also lists discrepancies between the SEQRES and the coordinate section. Format descriptions are available from wwpdb.org.