In this paper, we converted a protein sequence into three-letter sequence based on hydropathy profile of amino acid and defined the three curves to represent different hydropathy features. We then selected conditional probability as a new invariant for the protein sequences. To illustrate the proposed method, we made a comparison of the sequences belonging to eight ND6 (NADH dehydrogenase subunit 6) proteins from http://www.ncbi.nlm.nih.gov/: human