Residue-residue interactions within single structures

Figure 9 shows how the number of interacting residue pairs (i.e., those pairs of residues with at least one side-chain to side-chain contact) behaves as a function of the sequence length. The behaviour is approximately linear, and there are interacting pairs per residue. Figure 10 shows how the number of favourable interacting residues pairs (i.e., where ) behaves as a function of the total number of interacting pairs. The behaviour is also approximately linear, and only about half of the interactions in proteins are favourable (i.e., contributing a negative pseudoenergy term).