Figure 3

Knowledge-based protein-protein interacting scoring matrices: (A) sidechain-sidechain van-der Waals scoring matrix; (B) sidechain-backbone van-der Waals scoring matrix; (C) sidechain-sidechain special-bond scoring matrix; (D) sidechain- backbone special-bond matrix scoring. The sidechain-sidechain scoring matrices are symmetric and sidechain-backbone scoring matrices are nonsymmetric. For sidechain- sidechain van-der Waals scoring matrix, the scores are high (yellow blocks) if large-aliphatic residues (i.e. Val, Leu, Ile, and Met) interact to large-aliphatic residues or aromatic residues (i.e. Phe, Tyr, and Trp) interact to aromatic residue. In contrast, the scores are low (orange blocks) when nonpolar residues interact to polar residues. For sidechain-sidechain special- bond scoring matrix, the scores are high when an interacting resides (i.e. Cys to Cys) form a disulfide bond or basic residues (i.e. Arg, Lys, and His) interact to acidic residues (Asp and Glu). The scoring values are zero if nonpolar residues interact to other residues.