omega-Helices in proteins

Protein J. 2010 May;29(4):242-9. doi: 10.1007/s10930-010-9245-5.

Abstract

A modification of the alpha-helix, termed the omega-helix, has four residues in one turn of a helix. We searched the omega-helix in proteins by the HELFIT program which determines the helical parameters-pitch, residues per turn, radius, and handedness-and p = rmsd/(N - 1)(1/2) estimating helical regularity, where "rmsd" is the root mean square deviation from the best fit helix and "N" is helix length. A total of 1,496 regular alpha-helices 6-9 residues long with p < or = 0.10 A were identified from 866 protein chains. The statistical analysis provides a strong evidence that the frequency distribution of helices versus n indicates the bimodality of typical alpha-helix and omega-helix. Sixty-two right handed omega-helices identified (7.2% of proteins) show non-planarity of the peptide groups. There is amino acid preference of Asp and Cys. These observations and analyses insist that the omega-helices occur really in proteins.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acids / chemistry
  • Chi-Square Distribution
  • Computational Biology / methods*
  • Databases, Protein
  • Models, Molecular
  • Protein Structure, Secondary
  • Proteins / chemistry*

Substances

  • Amino Acids
  • Proteins