Here is a nonapeptide (green) sitting in an MHC class I groove
(rendered invisible by RasMol's "restrict" command).
The nonapeptide is shown as a green stick model, including all amino
acid side chains. RasMol's "within" command was used to find all atoms
within 2.5 Angstroms of atoms on the other chain. This is based on
a theoretical model which includes hydrogens (not resolvable by X-ray
diffraction). This allows us to see that most of the interactions
between the chains are hydrogen bonds. The only peptide carbon atom
this close to the MHC was that of the carboxy terminus. Notice the
absence of bonding to the center of the peptide.
This image was constructed from images in a
RasMol "movie" script.
The atomic coordinate file employed is
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