In this study, we are only interested in the descriptors frequently occurring in positive samples (DNA-binding proteins). Therefore, the discriminant weight of an amino acid pair is calculated as the quadratic sum of the discriminant weights of the corresponding descriptors with positive discriminant weight for this amino acid pair. The discriminant weights of all the 400 amino acid pairs in PSSM-DT are depicted in Figure 2A. According to this figure, the top four most discriminative amino acid pairs are (R, R), (R, P), (P, R) and (A, R), which indicate that the amino acid R (Arg) and A (Ala) are important for identifying the DNA-protein interaction. This conclusion is consistent with Szilágyi and Skolnick's study [34], in which they found that the percentage of Arg, Ala, Gly, Lys and Asp are useful for identification of DNA-binding proteins. Sieber and Allemann [72] found that R (348) can't directly interact with the nucleobases, but can determine the DNA binding specificity of the basic helix-loop-helix proteins (BHLH) E12 by directly interacting with both the phosphate backbone and the carboxylate of E(345) resulting in locking the side chain conformation of E(345). what's more, by comprehensively analyzing the three dimensional structures of protein-DNA complexes, Rohs and West et al. [73] demonstrated that the binding of R to narrow minor grooves can be applied to mode for protein-DNA recognition, indicating that R is an important component in protein-DNA binding activity. It has been previously reported that the DNA usually enveloped with negative electrostatic potential and the amino acid R shows positive charge [12], which explain the reason why the amino acid R is important for DNA-binding protein identification.