Main-chain conformational tendencies of amino acids. Proteins

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 inmaking aRamachand-ran plot based on experimental data is deciding whether sparse data represent genuine conforma-tions. 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 indepen-dent dataset. To obtain our results, we then mea-sured the pair-wise distances of main-chain confor-mational tendencies amongaminoacids, and showed that the conformational relationships of amino ac-ids are well preserved in a two-dimensional map, leading to the conclusion that the conformational diversity space of amino acids is largely two dimen-sional. 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