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.