Figure 6. Illustration of the Calculation of Energy Dispersion of Native and Non-Native Contacts for the Lattice Model.

(A) Zoom-in into contact matrix of one of the 103,346 compact lattice conformations, the cartoon. Even/even, odd/odd, diagonal, (i,i + 1), (i,i + 2) contacts do not exist in a 3 × 3 × 3 lattice (red). Every compact conformation has 28 contacts considered native for this conformation (green). There are also a total of 128 contacts that may appear in alternative conformations; they serve as non-native contacts for this conformation (shown in blue).

(B) Calculation of average energies and dispersion of all native and non-native contacts; illustrative example. Ten aligned sequences all folding into the same shown structure are presented. An example of residues making native (cyan) and non-native (red) contacts is shown. As an illustration, energy of the selected native and non-native contacts are shown for each sequence (this energy is calculated according to the identities of amino acids forming a contact using Miyazawa–Jernigan knowledge-based potential). Average energy of all ten aligned sequences of shown native and non-native contacts and its standard deviation are calculated for illustration here.