The classic results by Biro, Blalock and Root-Bernstein link genetic code nucleotide patterns to amino acid properties, protein structure and interaction. This study explores the use of the Miyazawa-Jernigan residue contact potential in analyses of protein interaction and recognition between sense and complementary (antisense) peptides. We show that Miyazawa-Jernigan residue contact energies, derived from 3D data, define the recognition rules of peptide-peptide interaction based on the complementary coding of DNA and RNA sequences. The model is strongly correlated with several other chemoinformatic scales often used for the determination of protein antigenic sites and transmembrane regions (Parker et al. r = 0.94; Rose et al. r = ?0.92; Manavalan-Ponnuswamy r = ?0.92; Cornette et al. r = ?0.91; Kolaskar-Tongaonkar r = ?0.91; Grantham r = 0.90; White-Wimley (octanol) r = ?0.88; Kyte-Doolittle r = ?0.85). The algorithms presented have important biomedical and proteomic applications related to modulation of the peptide-receptor function and epitope-paratope interaction, the design of lead compounds and the development of new immunochemical assays and diagnostic procedures.