What are “six types” and “twenty types” in the context of amino acids?
A. In “twenty types” the statistics are calculated considering each of the twenty naturally occurring amino acids as distinct. “Six types” is based on the observation that amino acids may be grouped by their physical properties into aliphatic (AVLIMC), aromatic (FWYH), polar (STNQ), positive (KR), negative (DE), and “special” (GP) types. Such grouping of amino acids avoids penalizing residue positions with conservative substitutions such as Val to Leu and results in better statistics for calculation of CoC (see methods section).
