Fig. 3

Comparison of contact residues in the binding pockets based on SLA-specific contacts (Ssc) and HLA contacts (Hc). Top: Schematic representation of the crystal structure of SLA-1*0401 (PDB:3QQ4; residues 1 to 181 rendered with PyMOL (Schrodinger, LLC)) showing the residues involved in the binding pockets. SLA contact residues and the ligand (ATAAATEAY, yellow) are represented as sticks. Residues common for both Hc and Ssc approaches are show in light blue; residues unique to Ssc in green and unique to Hc in orange. Bottom: Positions in the SLA binding pockets are shown. The first column (SLA position) is the residue and position number in the SLA-1*0401 protein sequence (Genbank:2352988). Residue positions shown in bold and underlined are identical (i.e. amino acid involved in the same pocket(s)) for both approaches. Positions in light blue are common for both approaches; positions in orange are unique to Hc. The next columns show, shaded in gray, the positions involved in pockets A through F that interact with relative ligand positions (peptide position). The last column (Count) is the number of pockets in which an amino acid participates. The last row (Total) is the total number of residues in each pocket