Figure 3.
Fig. 3. Interactions between the -helical
peptide and the C219 binding site. (A) Two-dimensional LIGPLOT
(33) representation of the interactions between residues of the
minimal NBD-epitope peptide (P), C219 heavy (H) and light chain
(L) residues, and solvent molecules (S), as seen in molecule I.
The residues that form van der Waals contacts with the peptide
are depicted as labeled arcs with radial spokes pointing toward
the peptide atoms with which they interact. C219 residues that
form hydrogen bonds are shown in a ball-and-stick
representation, and the hydrogen bonds are presented as dashed
lines. Of all of the intrapeptide hydrogen bonds present in the
structure, only the bonds between Gln 3P and Asp 7P are shown.
(B) Stereoplot of the Fv-peptide interactions seen in molecule
II. (C) Comparison of the bound NBD-epitope peptide in molecule
I and II. In B and C, light (L) and heavy chain (H) residues and
backbone positions of the scFv C219 are shown in green and
magenta. Peptide backbone and side chains are shown in khaki for
molecule I and in gold for molecule II. Positions of water
molecules are indicated as red spheres. Different positions of
binding site residues and water molecules in molecule I are also
colored khaki. B and C were generated by using MOLSCRIPT (34)
and RASTER3D (35).
-helical
peptide and the C219 binding site. (A) Two-dimensional LIGPLOT
(33) representation of the interactions between residues of the
minimal NBD-epitope peptide (P), C219 heavy (H) and light chain
(L) residues, and solvent molecules (S), as seen in molecule I.
The residues that form van der Waals contacts with the peptide
are depicted as labeled arcs with radial spokes pointing toward
the peptide atoms with which they interact. C219 residues that
form hydrogen bonds are shown in a ball-and-stick
representation, and the hydrogen bonds are presented as dashed
lines. Of all of the intrapeptide hydrogen bonds present in the
structure, only the bonds between Gln 3P and Asp 7P are shown.
(B) Stereoplot of the Fv-peptide interactions seen in molecule
II. (C) Comparison of the bound NBD-epitope peptide in molecule
I and II. In B and C, light (L) and heavy chain (H) residues and
backbone positions of the scFv C219 are shown in green and
magenta. Peptide backbone and side chains are shown in khaki for
molecule I and in gold for molecule II. Positions of water
molecules are indicated as red spheres. Different positions of
binding site residues and water molecules in molecule I are also
colored khaki. B and C were generated by using MOLSCRIPT (34)
and RASTER3D (35).