We use the occurrence frequency of 20 amino acids and take the new numerical characteristic of 2D graphical representation based on three physicochemical properties indexes as pseudo amino acid components. After a protein sequence is converted into a 23 dimensional vectors. Finally, based on the Euclidean distance, the similarities of ND5 proteins of nine species are used to demonstrate the effectiveness and rationality of our method. And correlation analysis has been provided to compare both our results and the results basing on the other graphical representation with the Clustal W's results in order to show the utility of our method. (C) 2013 Elsevier B. V. All rights reserved.