Based on a selected pair of physicochemical properties of amino acids, we propose a new 2D graphical representation of protein sequence, which may reflect the innate structure of the protein sequence. This graphical representation has no circuit or degeneracy, and the correspondence between the sequences and the graphical curves is one-to-one. Then, we introduce and compare two numerical characterizations of protein graphs as descriptors to analyze the nine DN5 protein sequences. (C) 2009 Elsevier B.V. All rights reserved.