Uploaded September 2023 | Updated September 2026, 1 day ago

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In this lesson, we’ll learn a PyMOL preset to display protein interfaces. Then, we’ll introduce the measurement wizard, and explore different types of molecular interactions.

00:00 Introduction and typical interaction distances
00:22 Interface preset
01:08 Peptide bond formation & the N- and C-terminus
02:10 Grayed out amino acids in the sequence display
02:30 Find polar contacts at the protein interface
03:09 The measurement wizard & van der Waals interactions
04:58 Polar vs. nonpolar amino acid side chains
05:26 Find polar contacts – a word of caution

REFERENCES:
• PDB ID: 1a0o
• Welch, M., Chinardet, N., Mourey, L. et al. Structure of the CheY-binding domain of histidine kinase CheA in complex with CheY. Nat Struct Mol Biol 5, 25–29 (1998). doi.org/10.1038/nsb0198-25
• proteopedia.org/wiki/index.php/Non-covalent_interactions