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. 2023 Jun 12;14:1142573. doi: 10.3389/fimmu.2023.1142573

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Copyright © 2023 Fonseca and Antunes

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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A3A-TCR contact maps construction. (A) A flowchart representing the contacts/interactions analysis. TCRpMHC interactions are depicted as black lines. The A3A crystal was submitted to two analyses (2), static, and (3) dynamic (molecular dynamics). (B) Each analysis produces a contact map summarized by peptide positions. The interaction types and frequency were retrieved using getcontacts. In total, nine interaction types can be detected, including hydrogen bond-related (hbbb, hbsb, hbss); salt bridge (sb); pi-cation (pc); pi-stacking (ps); t-stacking (ts); hydrophobic (hp); van der Waals (vdw). The dynamic contact map was summarized into four distinct time points: 0-20, 0-40, 0-60, and 0-80 nanoseconds. The overall profile showed similar hotspots compared to the static map. (C) Normalized contacts are displayed on the heatmap. Image created with BioRender.com.