Insights into Protein–DNA Interactions through Structure Network Analysis
Figure 1
A bipartite graph representation of the amino acid–nucleotide interactions in a protein–DNA complex.
In the bipartite graph representation of the protein–DNA complex, the amino acids and the nucleotides of the DNA form the two node sets. Shown in yellow are amino acid nodes, and blue, the nucleotides. The edges (between the nodes from one set to the other) are shown in red. These edges are defined based on a specific MEC. The MEC quantifies the minimum number of atomic contacts expected between an amino acid and a nucleotide to define an edge (Equation 1). The contacts are specifically evaluated between side chains of the amino acids and the phosphate, or the deoxyribose sugar or the base of nucleotides to form the P-p, P-S, and P-B clusters, respectively.