A reexamination of the propensities of amino acids towards a particular secondary structure: classification of amino acids based on their chemical structure
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The correlation between the primary and secondary structures of proteins was analysed using a large data set from the Protein Data Bank. Clear preferences of amino acids towards certain secondary structures classify amino acids into four groups: alpha-helix preferrers, strand preferrers, turn and bend preferrers, and His and Cys (the latter two amino acids show no clear preference for any secondary structure). Amino acids in the same group have similar structural characteristics at their C beta and C gamma atoms that predicts their preference for a particular secondary structure. All alpha-helix preferrers have neither polar heteroatoms on C beta and C gamma atoms, nor branching or aromatic group on the C beta atom. All strand preferrers have aromatic groups or branching groups on the C beta atom. All turn and bend preferrers have a polar heteroatom on the C beta or C gamma atoms or do not have a C beta atom at all. These new rules could be helpful in making predictions about non-natur...al amino acids.
Keywords:amino acid / protein / protein secondary structure / statistical correlation
Source:Journal of Molecular Modeling, 2008, 14, 8, 769-775
- Springer, New York