Amino acid distance matrices and classifications for different protein secondary structure
نویسندگان
چکیده
The property of an amino acid is different according to the variation of protein secondary structure. Each central amino acid corresponds to several conditional probability distributions of amino acid on the specific positions surrounding it. Based on this property, we get amino acid distance matrices for helix, sheet, coil and turn conformation. It is observed that, for different protein secondary structure, the discrepancy of amino acid distance is evident. Some obvious differences between the distance matrix and blocks substitution matrix(BLOSUM) are found which can tell the difference of amino acid property between in certain protein secondary structure and the whole protein database. The classification of amino acid alphabets for different protein secondary structure is performed. It provides a clue for observing the similarity of amino acid in different protein secondary structure. PACS number(s): 87.10.+e,02.50.-r
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