Protein sequences are represented as binary pattern of polar and nonpolar Aminoacids. This pattern is because of the appropriate arrangement of polar and nonpolar residues which can direct a polypeptide chain to fold into secondary structure and then which form a desired tertiarytertiary structure. The pattern helps to identify the side chains at polar and nonpolar position.
Binary patterns are of two types : class A and class B.Class A patterns are mostly found in alpha helices than in Beta strands where as class B patterns are mostly found in Beta strands than in alpha helices.
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