The structure of the β-sheet motif and the associated dihedral angles of the strands are indicated and labelled i, j and k for the three different strands (b), where residues i, j and k are opposite one another, as are residues i−1, j+1 and k−1.
The residue and dihedral indexing defines three antiparallel strands indicated in Fig. 1b and labelled i, j and k for the three different strands, where residues i, j and k are opposite one another, as are residues i−1, j+1 and k−1.
where σij is the distance between the Cα's of residues i and j in the reference structure, rij is the same distance but in the instantaneous configuration and εij is the strength of the pairwise interaction33.
Cooperativity correlation between two residues i and j, C ij, describes both rigid and flexible couplings.
For example, the energy function frequently identifies very weak H-bonds, such as those between residues i and i+3 within α-helices (results not shown).
In order to define ECO, we assume four residues i, k, m, and j along a primary sequence.
Two residues, i and j, are defined to be in contact (Cij = 1), if the distance between their COP's is less than or equal to 6.5Å, and not in contact (Cij = 0), otherwise.
The position-specific mutation scores at residues i and j and their neighboring residues are used.
r ij is the distance between residues i and j with i < j.
