In a case where a residue i-1 harbors an amide that is incompletely exchanged, the amide of the sequential residue i will encode the weighted sum of two frequencies, each corresponding to the Cα attached to the N H and N D, respectively (Supplementary Figure 18).
The probability that residue i was emitted by state k is the sum of the probabilities of all the state paths that use state k to generate residue i (that is, πi = k in the state path π), normalized by the sum over all possible state paths.
Finally, the distances from the δ-methyl protons of a Leu residue (i) to those of Leu i+2, which approximately correspond to the diameter of the helix in the central hydrophobic segment, are on average 10 Å.
Therefore, the complexes are ordered according to the following score σ: where #interactions i is the number of directed interactions from residue i to the ligand.
Occasionally β-turns are stabilized with a hydrogen bond between the N-H of residue i and the C = O of residue i+3.
For residue i, the AIC score for model m is given by equation 15 [17], [17].
The (i,j) entry of the matrix exponential T t) = exp(Qt) defines the probability of replacing residue i with residue j in time t≥0.
S ab is only summed over the optimal alignment for residue i from active site a with residue j from active site b.
Sidechain attractive interactions, or salt bridges, between residues on the same side of the helix (i.e., from residue i to residue i+4 or i+8, approximately [43]) are assumed to enhance the stability of peptide α-helices [40], [41], [42].
Of these, due to the periodicity of the α-helix (residue i and residue i+4 will be located on same side of the α-helix), the only other residue that could stabilize the bridging water appeared to be Asp-57 from helix α2 (which corresponds to Gly-285 in MnmE).
