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Proteins. 2005 Sep 1;60(4):679-89.

Main-chain conformational tendencies of amino acids.

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1
Serono Reproductive Biology Institute, One Technology Place, Rockland, Massachusetts, USA.

Abstract

A Ramachandran plot is a visual representation of the main-chain conformational tendencies of an amino acid. Despite forty years of research, the shape of Ramachandran plots is still a matter of debate. The issue in making a Ramachandran plot based on experimental data is deciding whether sparse data represent genuine conformations. We present here a simple solution to settle the ambiguities of the sparse data, and explain how we verified the accuracies of our plots using an independent dataset. To obtain our results, we then measured the pair-wise distances of main-chain conformational tendencies among amino acids, and showed that the conformational relationships of amino acids are well preserved in a two-dimensional map, leading to the conclusion that the conformational diversity space of amino acids is largely two dimensional. We further noticed that amino acids in early and late evolutionary stages are located in different zones in the two-dimensional map. In addition to these conclusions, we here present an amino acid substitution table derived from experimental data.

PMID:
16021632
DOI:
10.1002/prot.20530
[Indexed for MEDLINE]
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