Fig. 6: Interactions of SARS-CoV-2-specific TCRs with the RLQ and YLQ peptides.

a Interactions between TCR RLQ3 and the RLQ peptide. The side chains of contacting residues are shown in stick representation with carbon atoms in green (TCR α chain), pink (TCR β chain), or orange (RLQ), nitrogen atoms in blue, oxygen atoms in red, and water molecules as yellow spheres. Peptide residues are identified by one-letter amino acid designation followed by position (p) number. Hydrogen bonds are indicated by red dashed lines. Water-mediated hydrogen bonds are drawn as yellow dashed lines. b Schematic representation of RLQ3–RLQ interactions. Hydrogen bonds are red dotted lines, water-mediated hydrogen bonds are yellow dotted lines, and van der Waals contacts are black dotted lines. For clarity, not all van der Waals contacts are shown. c Close-up of interactions of RLQ3 with P6 Gln of the RLQ peptide. d Interactions between TCR YLQ7 and the YLQ peptide (cyan). TCR α chain, blue; TCR β chain, magenta. e Schematic representation of YLQ7–YLQ interactions. f Close-up of interactions of YLQ7 with P5 Arg and P6 Thr of the YLQ peptide.