Motifs and conformational analysis of amino acid residues adjoining beta-turns in proteins.
Using a data set of 250 non-homologous high-resolution globular proteins, a systematic analysis of the conformations that precede and succeed (positions i and i + 3) the various classical beta-turn types has been carried out. The collective conformation of a specific beta-turn type, including the flanking positions, termed motif, has been studied. In all the four turn types, the majority of examples are preceded and succeeded by extended conformation. Some of the other observations are: (1) In a type I beta-turn, Gly at position i + 3 has a higher favorability to occur with positive phi and does not prefer the major motif beta-alpha R-alpha R-beta. (2) The left-handed alpha-helical conformation (alpha L) is not preferred at both the flanking positions for type I' and II' beta-turns. (3) The beta--beta motif is favourable for all the turn types and the motif beta--alpha L very highly favourable for type I.
Ramakrishnan
C
C
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
Srinivasan
N
N
Nataraj
D V
DV
D000596:Amino Acids / Q000737:chemistry*; D003198:Computer Simulation; D016208:Databases, Factual; D008958:Models, Molecular; D017433:Protein Structure, Secondary
D000596:Amino Acids