Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps

Table 3 Validation results of our PDZ predictions.

PDZ site in 2H2C	Structure-based nomenclature [53]	Ligand position	Uncertainty coefficient	Distance (Å)	Specificity change
Phe34	β1:β2-7	-3	0.16	15.0	Significant
Ala37	β2-2	-3	0.20	6.4	Significant
Ser39	β2-4	-1	0.16	9.5	Significant
Ser57	β3-4	-3	0.18	7.2	Observed
Asp58	β3-5	-3	0.21	9.1	Observed
Leu60	β3:α1-1	-1	0.24	7.0	Significant

The six sites validated in Tonikian et al. [13] that were not filtered in our calculation are shown, along with their highest-scoring peptide PWM positions. Significant changes of the predicted PWM positions after mutating the PDZ sites were reported for four cases, while in the remaining two cases some changes were also observed.

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