Putting into Practice Domain-Linear Motif Interaction Predictions for Exploration of Protein Networks
Figure 4
Atomic distance-based selection of peptide-contacting domain positions in different PDZ-peptide structures.
For each PDZ domain of the alignment, we extracted from available structural data all domain residues that had at least one atom within a distance of 5 Å to bound peptide atoms. Blue letters indicate residues, which have been selected both, by Chen et al. and our approach. Red letters indicate residues, which have been selected by our approach but not by the model of Chen et al. Asterisks above the alignment indicate the PDZ residues chosen by Chen et al. to be close to peptide residues based on the structure -syntrophin (SNTA1, first line of alignment). Arrows and rectangles above the alignment indicate the positions of conserved
-sheets and
-helices, respectively. Note that the sequence of the Par6 PDZ domain occurs twice in the alignment, corresponding to two different structures of Par6, one bound to an internal peptide, the other one bound to a regular C-terminal peptide.