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Front Mol Biosci. 2015 Oct 13;2:56. doi: 10.3389/fmolb.2015.00056. eCollection 2015.

A script to highlight hydrophobicity and charge on protein surfaces.

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Cellular Protein Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University Utrecht, Netherlands.


The composition of protein surfaces determines both affinity and specificity of protein-protein interactions. Matching of hydrophobic contacts and charged groups on both sites of the interface are crucial to ensure specificity. Here, we propose a highlighting scheme, YRB, which highlights both hydrophobicity and charge in protein structures. YRB highlighting visualizes hydrophobicity by highlighting all carbon atoms that are not bound to nitrogen and oxygen atoms. The charged oxygens of glutamate and aspartate are highlighted red and the charged nitrogens of arginine and lysine are highlighted blue. For a set of representative examples, we demonstrate that YRB highlighting intuitively visualizes segments on protein surfaces that contribute to specificity in protein-protein interfaces, including Hsp90/co-chaperone complexes, the SNARE complex and a transmembrane domain. We provide YRB highlighting in form of a script that runs using the software PyMOL.


PyMOL; amino acid properties; charge pairs; protein-protein interaction; surface hydrophobicity

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