Figure 2. Dependance of alphabet size on interaction energies.

We want to determine the number of sequences of size comprised of three residue types (one example shown on top). (A) Three residues with equal frequencies implies A = 3 using Eq. (3), and 3^N possible sequences. The matrix shows the pairwise interaction energies between all the residue types. The blue and green residues, however, are identical energetically based on their interactions with the other residues. (B) The same system can be described using two residues, with modified frequencies. Now, A = 1.9, with only 1.9^N sequences.