Fig. 3: Contacts between residues in the central helices during S2 opening.
From: Simulation-driven design of stabilized SARS-CoV-2 spike S2 immunogens
a–c HexaPro-SS-Δstalk CHs in the closed conformation from a top-down view (a), side view in the context of the S2 trimer (gray cartoons) (b), and side view (c). CHs are highlighted with purple cartoons. The sidechains of the residue pointing toward the interior of the CHs are shown as sticks with the C atoms colored by the corresponding residue contact score as in the closed conformation of the HexaPro-SS-Δstalk. d, e Contact score heatmaps for the HexaPro-SS-Δstalk base construct (d) and HexaPro-SS-Δstalk tryptophan substitutions (e) in the closed, partially open, and open states. The scale ranges from 0 (weak or transient contacts) to 1 (persistent or extensive contacts, corresponding to the 95th percentile value of the HexaPro-SS-Δstalk contact scores). The star indicates the substituted residue.
