The coupling pattern of surrounding catalytic sites is extracted from the flanking sequences of kinase-specific phosphorylation sites. Let [XdZ] denote the coupling pattern of amino acids X and Z that are separated by d amino acids. Since the protein sequence is directional, the sign of d is determined by the relative positions of X and Z. For example, as shown in Figure 1, a coupling pattern [R3Q] occurs in the training set, another coupling pattern [Q-3R] also occurs. Herein, we would not consider the coupling pattern with minus symbol. Let N(XdZ) be the number of occurrences of the coupling pattern [XdZ] in training sequences and the conditional probability RXdZ is 1 where and Y ∈ {20 types of amino acid}. The coupling strength CXdZ between X and Z of the pattern [XdZ] is given by 2 where P(Z) is the probability of the occurrence of amino acid Y. If CXdZ ≥ 1, then X and Z are positively correlated with respect to the distance d, and they are negatively correlated if CXdZ < 1.
