We can calculate the distance between residues in a PDB file regarding different parameters like closest atoms, alpha carbon, beta carbon, centroid and etc. Which one of these parameters are better to show physical interaction between residues in a PDB file?
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2$\begingroup$ Which kind of physical interaction are you looking for: an hydrogen bound, a covalent bond, a ionic bond...? $\endgroup$– llrsJun 21, 2017 at 13:08
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$\begingroup$ There is no different for me which kind of physical interaction. The least distance and the farthest no different just physical $\endgroup$– SaraJun 21, 2017 at 15:55
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$\begingroup$ The CASP experiment uses an 8 Angstrom distance between C-beta atoms (C-alpha for glycine) to determine residue-residue contacts. $\endgroup$– jgreenerSep 10, 2019 at 21:33
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3 Answers
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Use a distance cutoff of 12Å between Cᵦ atoms.
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3$\begingroup$ If this is part of your previous answer, consider editing it, otherwise it would be nice to provide bit more explanation. $\endgroup$ Jun 22, 2017 at 9:12
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2$\begingroup$ Please could you clarify what types of interactions can happen at such distances, as I am currently unaware of interaction being possible at such a long distance? $\endgroup$– AalawlxOct 11, 2017 at 16:23
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A popular (and I would say, respected and trusted) website is PDBsum https://www.ebi.ac.uk/pdbsum (which also has a Wikipedia article about it: https://en.wikipedia.org/wiki/PDBsum)
They measure protein-protein (prot-prot) contacts as any Nitrogen, Carbon, or Oxygen element atoms (N, C, O) within 4.0 Angstroms (Å) when measuring the 3d euclidean distance.
If your atomic contacts are not close enough, the amino acids may not actually interact at all, even though they theoretically could. Since in PPIs you generally want to use reliable ground-truth information, it is better to use cautious parameters. Often, in PPIs, the answer to "does it interact?" is not "yes" or "no" but rather "yes" or "don't know / unknown".
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You should read my paper, where I did a comprehensive parameter sweep across different thresholds and definitions and benchmarked the resulting empirical potentials on a decoy ranking challenge:
The relevant phrase from the abstract is "compared using 90 different definitions of residue-residue contact". However, it boils down (as always) to the question, "what do you want to do".
Cite me if you use my paper for your research.
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$\begingroup$ Most papers give 5 or 6 angstrom distance for physical interactions. I don't know this distance is between which atoms exactly $\endgroup$– SaraJun 21, 2017 at 15:59
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$\begingroup$ People use what other people use, which is why I did a 'parameter sweep'. I've seen other work using a strict 'information maximization' criteria, which was nice. $\endgroup$– DanJun 25, 2017 at 21:52