The York Research Database

The polypeptide of a protein molecule can be considered as a chain of Calpha atoms linked by pseudobonds between the Calpha 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 Calpha 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 Calpha 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. (C) 1994 Wiley-Liss, Inc.