Based on nucleotide triplet codon, a graphical representation of protein sequences is outlined. A numerical characterization including the location, number and distribution information of all the 20 kinds of amino acids is proposed. The similarity/dissimilarity analysis of ND5 protein sequences of nine species is done, and our approach is compared to other approaches recently proposed based on the coefficient of correlation of the results of these approaches with the results calculated by ClustalW. It shows that our approach has better correlations with ClustalW for all nine species than other approaches, which gives an intuition of better performance.