We present a new detection method of amino acid residues, which play the role of the protein function. The principle of the method is that proteins with the same function have similar amino acid residues at the similar three dimensional positions. Thus we assume that maximal amino acid residues existing the similar three dimensional positions of proteins are their function site residues. The method first constructs the graph describing relations of three dimensional positions of all possible pairs of amino acid residues in two proteins and then extracts its maximal complete subgraph, which means the maximal amino acid residues at the similar three dimensional positions by the algorithm of Carraghan. The method was tested using electron transport proteins; azurin and plastocyanin, and was obtained 6 reasonable amino acid residues as the function site residues of those proteins. Also the method was applied to acid proteases; porcine pepsin and Rhizopus chinensis acid protease. In this investigation, we restricted the formation of amino acid pairs only the same ones. The result gave 11 amino acid residues, consisting some active site residues, as the function residues of acid proteases. Those results indicate the effectiveness of this new method.
