The degree of MHCI-peptide backbone “bulging” is proportional to peptide length. Supposition of pMHCI structures with increasing epitope length. The peptides have been superimposed on HLA A*0201, which is shown in cartoon representation. MHCIs were aligned using the MHC α1 and β2 domains. Peptide backbones are shown with ribbon representation and include the 8mer B*3501-VPLRPMTY (orange), 9mer A*0201-ILAKFLHRL (red), 10mer1 A*0201-ELAGIGILTV (green), 10mer A*0201-ALWGPDPAAA (dark green), 11mer B*3508-HPVGEADYFEY (blue), 12mer B*3508-CPSQEPMSIYVY (grey), 13mer B*3508-LPEPLPQGQLTAY (yellow), and 14mer B*3501-LPAVVGLSPGEQEY (purple). (A) Side view demonstrating the different peptide bulges out the MHCI groove depending on the length of the peptide. The scale on the left was calculated using the conserved position of peptide residue 2 from the Cα atom as 0 Å. The MHC α2 helix has been removed for clarity. (B) “Bird's eye view” demonstrating the different sideways displacement of peptides toward MHCI α1 or α2 helices depending on the length of the peptide. The scale on the left was calculated using the average central position of all of the peptides as 0 Å. The MHC α1 (above) and α2 helix (below) are shown. PDB codes are 1A1N, 10GA, 2GT9, 2FZ3, 3BW9, 1ZHL, 1XH3, and 414W.