Co-Occurring Patterns of Amino Acid Physicochemical Properties in Proteins

It is well known that amino acids in peptides and proteins show individually distinct preferences for secondary structural conformations. While each amino acid is associated with multiple physicochemical properties, most existing statistical analysis methods treat amino acids separately and independently in calculating the frequencies of residues at each site of protein sequences. Such approaches remain at describing coarse-level tendencies of amino acid preferences for particular conformations. We propose a more advanced and refined method in which co-occurring patterns of two or three physicochemical attributes are examined to identify conformational preferences of amino acids at the sub-residue scale.