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Figure 4.
Figure 4. Chemical Interactions Involved in Peptide
Binding(A) Stereo view of the peptide-binding site demonstrating
protein–peptide interactions via hydrogen bonds (dashed white
lines) and the location of the Val 0 side chain in the
hydrophobic pocket. Oxygen atoms are shown in red and nitrogen
atoms in blue. The green sphere shows a well-ordered water
molecule linking the carboxylate group to Arg-318. The picture
was drawn with MOLSCRIPT and Raster3D.(B) Schematic view of the
contacts identified in the crystal structure of the complex.
Dashed lines represent hydrogen bonds, and the two closest
atom-to-atom distances between the Val 0 side chain and all
atoms in the hydrophobic pocket of the PDZ domain are drawn as
solid black lines. The Val 0 side chain makes numerous other Van
der Waals contacts within the range of 3.9 to 4.3 Å;
however, for clarity they are not indicated in this diagram. The
fixed orientation of the arginine guanidinium head group via
hydrogen bonds with backbone carbonyl groups is also shown.
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