Similar HLA-DRB1*0101 peptide-contacting residue conformations observed in X-ray structures.

<p>All HLA-DRB1*0101 peptide-MHC complexes were superimposed by aligning the backbones of the MHC peptide binding domains (chain A residues 1–82 and chain B residues 1–92). MHC chains A and B are shown in red and blue ribbon representation, respectively. The MHC residues contacting the bound peptides, shown in stick representation, generally adopt similar conformations despite contacting different peptides. Much of the small side chain deviations are due to imperfect alignment of the MHC backbone atoms. This observation motivates the use of a rigid potential map representation of the MHC binding cleft in the docking procedure for efficiency rather than computationally expensive sampling of the contacting portion of the MHC.