Table 2. Expanding the set of residues that can match a single position in the input motif.
Predicted residues | Pairwise Distances in Å | Pairwise Potential difference | ||||||||
PDB: | a | b | c | ab | ac | bc | ab | ac | bc | Score |
1B0F | Ser195 | His57 | Ser214 | 5 | 6.8 | 4.7 | 53.7 | 105.7 | 51.9 | 0 |
1CFE (Ser214 can be Ser only) | Ser49 | His48 | Ser120 | 0.1 | −0.2 | 1.9 | 15.3 | 83.9 | 68.6 | 0.111 |
1CFE (Ser214 can be Ser or Tyr) | Ser49 | His48 | Tyr36 | 0.1 | 0.3 | −0.3 | 15.3 | 88.6 | 73.3 | 0.023 |
When the position Ser214 in the input motif (Ser195, His57, Ser214) can be matched by a Ser or Tyr, Tyr36 has a much better spatial orientation with respect to Ser49 and His48 as compared to Ser120 in the P14A protein (PDBid:1CFE). The distances are specified in the reference protein (PDBid:1B0F) in A. For the remaining, we show the deviation from the reference value. Potential differences are in units of kT/e (k is Boltzmann’s constant, T is the temperature in K and e is the charge of an electron). They are absolute values and not shown as deviations.