An illustration of physical reasons for differences in designability between two structures. The balls schematically represent amino acids. Suppose that the interaction between the “red” amino acid and the “blue” amino acid is favorable and gives E = -1. The configuration on the left yields lower energy -4, compared with right structures, where contribution from interactions between these amino acids is only -3. Thus, the 4-loop in the left structure contributes more to the stability of the structure overall, allowing more freedom to select the remaining part of the sequence to obtain overall stabilization of the structure. Similar considerations apply to 3-loops, 5-loops, etc.
