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 1ROG.PDB.

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