Identification, classification, and analysis of beta-bulges in proteins

Protein Sci. 1993 Oct;2(10):1574-90. doi: 10.1002/pro.5560021004.


A beta-bulge is a region of irregularity in a beta-sheet involving two beta-strands. It usually involves two or more residues in the bulged strand opposite to a single residue on the adjacent strand. These irregularities in beta-sheets were identified and classified automatically, extending the definition of beta-bulges given by Richardson et al. (Richardson, J.S., Getzoff, E.D., & Richardson, D.C., 1978, Proc. Natl. Acad. Sci. USA 75, 2574-2578). A set of 182 protein chains (170 proteins) was used, and a total of 362 bulges were extracted. Five types of beta-bulges were found: classic, G1, wide, bent, and special. Their characteristic amino acid preferences were found for most classes of bulges. Basically, bulges occur frequently in proteins; on average there are more than two bulges per protein. In general, beta-bulges produce two main changes in the structure of a beta-sheet: (1) disrupt the normal alternation of side-chain direction; (2) accentuate the twist of the sheet, altering the direction of the surrounding strands.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Aspartic Acid Endopeptidases / chemistry
  • Hydrogen Bonding
  • Immunoglobulins / chemistry
  • Molecular Sequence Data
  • Proline / chemistry
  • Protein Structure, Secondary*
  • Proteins / chemistry*
  • Proteins / classification
  • Sequence Homology, Amino Acid


  • Immunoglobulins
  • Proteins
  • Proline
  • Aspartic Acid Endopeptidases