Relative Occurrence of Amino Acid-Nucleotide Contacts Assessed by Voronoi-Delaunay Tessellation of Protein-DNA Interfaces

The data for 1109 protein-DNA complexes in PDB were analyzed for direct contacts between particular amino acid residues and nucleotides by rigorous space partitioning (Voronoi-Delaunay tessellation). When the actual occurrence of each kind of residue-nucleotide contact in the interface was related to its chance expectation, the most abundant contacts (made by Arg or Lys as well as by Ser or Thr) proved indiscriminate to heterocyclic bases, whereas a number of other, rarer contacts were clearly nonrandom, being significantly overrepresented or underrepresented in the sample of interfaces. Especially remarkable was the high overrepresentation of G/C contacts with negatively charged Asp/Glu. The nonrandom combinations showed no distinctions between purines and pyrimidines. This first step in formal analysis provides some hints concerning the accessibility of the “protein-DNA recognition code.”