Analysis of C alpha geometry in protein structures.
The polypeptide of a protein molecule can be considered as a chain of C alpha atoms linked by pseudobonds between the C alpha atoms of successive amino acid residues. This paper presents an analysis of the angle and dihedral angles made by these pseudobonds in protein structures determined at high resolution by X-ray crystallography. This analysis reveals a strong correlation between C alpha geometry and the protein fold. The regular features of protein secondary structure such as alpha-helix and beta-sheet are very clearly defined. In addition, it is possible to identify with some confidence the discrete populations of particular conformations of beta-turn. Comparison with the traditional Ramachandran type of plot demonstrates that an analysis of protein structure on the basis of C alpha geometry provides a richer description of protein conformation. In addition, the characteristics of this geometry could be a useful guide in model building of protein structure.
Oldfield
T J
TJ
Department of Chemistry, University of York, Heslington, United Kingdom.
Hubbard
R E
RE
D018360:Crystallography, X-Ray; D016208:Databases, Factual; D008956:Models, Chemical; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary
D010455:Peptides