We are looking at a sendai virus peptide sitting in the groove (magenta) of a class I MHC molecule (mouse H-2Kb). We are looking at the face to which the T cell antigen receptor would bind. Most of the nonapeptide's side chains interact with the lips and floor (yellow) of the groove, but two stick up (asparagine and phenylalanine) forming the T cell determinant for this peptide. Contrast this with the VSV peptide in the same MHC allele.

The apparent gap between the peptide and the top alpha helix, in which you see a patch of the yellow floor, is actually largely filled by bound water molecules resolved in the X-ray diffraction. The oxygens of these water molecules can be displayed with RasMol's "select hetero" command.

The peptide uses RasMol's Corey/Pauling/Koltun color scheme: carbon is gray, oxygen is red, and nitrogen is blue. Hydrogens would be white but are not resoved by X-ray crystallography.

This image was constructed from images in a RasMol "movie" script. The atomic coordinate file employed is 1VAB.PDB.

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