It is well known that there are some similarities among various naturally occurring amino acids. The standard amino acids have been grouped by their general properties and the chemical structures of their side chains. In this paper we divided the molecular weight of amino acid into two parts: backbone molecular weight Mb and side chain molecular weight Ms. We naturally grouped the amino acids into two sets according to the rate of Ms / Mb. We developed a method to construct a syntheses table to reflect the relevant physicochemical properties based on the PAM250 matrix and successfully established an elegant table of the twenty amino acids. Our work proved that PAM250 matrix could be used not only in finding reasonable alignments but also in grouping similar amino acid.