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Table 3 Validation results of our PDZ predictions.

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

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
  1. 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.