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© Oxford University Press

ø—{psi}conformational pattern clustering of protein amino acid residues using the potential function method

Motokazu Kamimura and Yoshimasa Takahashi 1

Department of Knowledge-based Information Engineering, Toyohashi University of Technology Tempaku, Toyohashi 441, Japan

1To whom reprint requests should be sent

This paper describes ø—{psi} conformational pattern clustering of protein amino acid residues. The method is based on the potential function method and mode seeking technique. ø—{psi} conformational pattern distribution maps and their three-dimensional potential surface maps were computed for 20 different kinds of amino acid residues, using 67 proteins (14 723 residues) taken from the Protein Data Bank. It was found that glycine residues of proteins have five major clusters in the ø—{psi} conformational space, and two or three major clusters were found for the other kinds of residues. Mode seeking on the potential surface of glycine residues identified their representative ø—{psi} conformational patterns: (82.64°, 9.84°), (–62.63°, –41.71°), (–85.33°, 176.78°), (91.88°, 178.14°) and (167.06°, –175.33°). The details of the method and the results are discussed with new classifications of ø—{psi} conformational patterns of amino acid residues of proteins.

; accepted on December 9, 1993

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