A 2-D graphical representation of proteins based on 2-D map of amino acids is outlined. The amino acid map was obtained by constructing the partial order on a selected pair of physico-chemical properties of amino acids. The plot of the difference between the (x,y) coordinates of two graphical representations of proteins allows visual inspection of protein alignment. The approach is illustrated on segments of a protein of the yeast Saccharomyces cerevisiae. (C) 2007 Elsevier B.V. All rights reserved.