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All relevant data are within the paper and its Supporting Information files. Introduction {#sec001} ============ A major part of the development of a specific immune response to a pathogen belongs to MHC class II molecules \[[@pone.0205557.ref001], [@pone.0205557.ref002]\]. MHC class II molecules are constitutively expressed by professional antigen-presenting cells (APCs), such as dendritic cells, B cells and cells of the monocyte/macrophage lineage. In addition, non-professional APCs (e.g., fibroblasts, astrocytes, epithelial cells) acquire MHC class II expression when exposed to a variety of stimuli, most potent IFN-γ, during infection, inflammation or trauma. In humans, T cells can also be induced to express class II molecules after activation \[[@pone.0205557.ref003], [@pone.0205557.ref004]\]. MHC class II molecules classically present extracellular antigens such as bacteria, parasites, and toxins that enter the host cell by endocytosis or phagocytosis, to antigen-specific CD4+ T cells. However, mechanisms of an endogenous presentation by antigen-presenting cells have been described while sufficient TCD4+ engagement is an important predictor of outcome with several viral infectious diseases (including hepatitis A and B and influenza) \[[@pone.0205557.ref005]\]. The MHC class II region in humans (otherwise HLA, Human Leukocyte Antigen) contains three distinct gene loci, HLA-DP, -DQ, and--DR \[[@pone.0205557.ref006]\]. MHC class II molecules consist of two chains, α and β. DPA, DQA and DRA genes code for chain α, while DPB, DQB and DRB genes code for chain β. Except for DRA, which is dimorphic with just one substitution at the intra-cytoplasmic position 227, the MHC class II locus is highly polymorphic. Up to date 45 DPA1 alleles, 78 DQA1 alleles, 828 DPB1 alleles, 1,079 DQB alleles and 2,058 DRB1 alleles have been identified \[[@pone.0205557.ref007], [@pone.0205557.ref008], [@pone.0205557.ref009]\]. The high polymorphism observed is mainly located in exon 2 of these molecules that codes for the peptide-binding region (PBR). The PBR resides in a peptide antigen-binding groove, formed by both α and β chains. In the cleft, MHC molecules feature binding pockets into which anchoring peptides of the antigen can fit. The fitting is stabilized by hydrogen bonds and ion bridges between the side chains of α and β chains of the groove and along the backbone of the peptide ([Fig 1](#pone.0205557.g001){ref-type="fig"}). The groove of class II molecules is open, allowing the binding of a wide range of peptides; typically 12--26 amino acids long. The peptide segments that bind to groove are nonamers while their N and C termini may extend beyond the ends of the groove \[[@pone.0205557.ref010]\]. The flanking residues can increase the binding affinity to class II MHC molecules or can also be used directly by T cell receptor as contact residues \[[@pone.0205557.ref011]\]. ![MHC class II molecules are heterodimers consisting of α (green) and β (orange) chains.\ The antigen binding groove is formed by two alpha-helices above a beta-sheet floor. Antigens (red) fit in the cleft and stabilized by electrostatic interactions and/or hydrogen bonds to anchor peptides of the groove (regions with light shades). The structure being illustrated is based on the structure with PDB ID: 2NNA \[[@pone.0205557.ref012]\].](pone.0205557.g001){#pone.0205557.g001} The four major binding pockets are P1, P4, P6 and