Observed secondary structure content for 721 proteins

Contact: Burkhard Rost (rost@EMBL-Heidelberg.de)
Date: May, 1996

• Question:
  Can protein structures be classified successfully based on the simple feature secondary structure content ?
• Method:
  Update of the figure given in Rost & Sander, 1994 (Abstract).
  A crude classification of protein structures has been based on the simple feature secondary structure content (Levitt & Chothia, 1976, Nature, 261, 552-558; Zhang & Chou, 1992, Prot Sci, 1, 401-408; Rost & Sander, 1994). The separation suggested by Zhang & Chou is as follows: (1) all-alpha: > 5% strand and > 45% helix; (2) all-beta: > 45% strand and > 5% helix; (3) alpha/beta: > 20% strand and > 30% helix; (4) rest.
• Result and conclusion:
  The points obviously cannot be clustered in a unique way. This suggests that the simple classification of protein structures based on secondary structure is of limited generality.
• Figure caption:
  Each point represents the observation (according to DSSP assignments) of the percentage of secondary structure for one protein out of a set of 721 proteins. This set comprises the largest sequence unique subset of PDB in May 1996 (i.e. no two proteins in that set have more than 25% pairwise identical residues).
  Fig. 1: Boxes separate the classification initially suggested by Levitt & Chothia (1976, Nature, 261, 552-558).
  Fig. 2: Same as previous, no boxes.
  Fig. 3: Percentage of helical vs. strand segments (as opposed to residues in helices and strands!).

Fig. 1 (click on picture for full scale)

Fig. 2 (click on picture for full scale)

Fig. 3 (click on picture for full scale)