title: omega-Helices in proteins.
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.
authors.affiliation: Department of Biophysics and Bioinformatics, National University of Mongolia, Ulaanbaatar, Mongolia.
authors.forename: Purevjav
authors.initials: P
authors.lastname: Enkhbayar
authors.forename: Bazartseren
authors.initials: B
authors.lastname: Boldgiv
authors.forename: Norio
authors.initials: N
authors.lastname: Matsushima
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry; D016009:Chi-Square Distribution; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
chemical_list: D000596:Amino Acids; D011506:Proteins