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. 2009 Jan 23;5(1):e1000267. doi: 10.1371/journal.pcbi.1000267

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Engelen et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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Structure of the catalytic subunit of cAMP-dependent protein kinase (PDB file 1apm). The experimental interaction site is colored blue in (C). Clustering based on surface residues detects one conserved cluster that gives rise to two non-contiguous surface patches. One of them (A) corresponds to the actual interface and the other (B), which is positioned opposite to (A), does not. Clustering based on surface atoms distinguishes the two patches and considers only one of them (A) as a cluster seed.