Answers.Body: <p>Use a distance cutoff of 12Å between Cᵦ atoms.</p>
  
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Answers.Text: If this is part of your previous answer, consider editing it, otherwise it would be nice to provide bit more explanation.
Answers.UserDisplayName: Kamil S Jaron
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Answers.CreationDate: 2017-10-11T16:23:48.183Z
Answers.Text: 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?
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Answers.CreationDate: 2017-06-21T13:48:17.480Z
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Answers.UserDisplayName: Dan
Answers.Body: <p>A popular (and I would say, respected and trusted) website is PDBsum <a href="https://www.ebi.ac.uk/pdbsum" rel="noreferrer">https://www.ebi.ac.uk/pdbsum</a> (which also has a Wikipedia article about it: <a href="https://en.wikipedia.org/wiki/PDBsum" rel="noreferrer">https://en.wikipedia.org/wiki/PDBsum</a>)</p>
  
  <p>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.</p>
  
  <p>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".</p>
  
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Answers.Body: <p>You should read my <a href="https://bmcstructbiol.biomedcentral.com/articles/10.1186/1472-6807-8-53" rel="nofollow noreferrer">paper</a>, where I did a comprehensive parameter sweep across different thresholds and definitions and benchmarked the resulting empirical potentials on a decoy ranking challenge:</p>
  
  <p>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".</p>
  
  <p>Cite me if you use my paper for your research. </p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-06-21T15:59:28.343Z
Answers.Text: Most papers give 5 or 6 angstrom distance for physical interactions. I don't know this distance is between which atoms exactly
Answers.UserDisplayName: Sara
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Answers.CreationDate: 2017-06-25T21:52:14.633Z
Answers.Text: 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.
Answers.UserDisplayName: Dan
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Body: <p>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?</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-21T13:08:24.507Z
Comments.Text: Which kind of physical interaction are you looking for: an hydrogen bound, a covalent bond, a ionic bond...?
Comments.UserDisplayName: llrs
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Comments.CreationDate: 2017-06-21T15:55:27.797Z
Comments.Text: There is no different for me which kind of physical interaction. The least distance and the farthest no different just physical
Comments.UserDisplayName: Sara
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-09-10T21:33:06.837Z
Comments.Text: The CASP experiment uses an 8 Angstrom distance between C-beta atoms (C-alpha for glycine) to determine residue-residue contacts.
Comments.UserDisplayName: jgreener
Tags: <protein-structure><pdb>
Title: Best distance parameter for estimating physical interaction between residues in a PDB file
ThreadText: # Best distance parameter for estimating physical interaction between residues in a PDB file
  
  (Asked by: username_0 on 2017-06-21)
  
  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?
  
  **Tags:** protein-structure, pdb
  
  > **Comments:**
  > **username_1**: Which kind of physical interaction are you looking for: an hydrogen bound, a covalent bond, a ionic bond...?  
  > **username_0**: There is no different for me which kind of physical interaction. The least distance and the farthest no different just physical  
  > **username_2**: The CASP experiment uses an 8 Angstrom distance between C-beta atoms (C-alpha for glycine) to determine residue-residue contacts.  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_3 on 2017-06-21. Score: 2 | Accepted answer
  
  Use a distance cutoff of 12Å between Cᵦ atoms.
  
  > **Comments:**
  > **username_4**: If this is part of your previous answer, consider editing it, otherwise it would be nice to provide bit more explanation.  
  > **username_5**: 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?  
  
  ---
  
  ### Answer by username_5 on 2017-10-11. Score: 6
  
  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".
  
  
  ---
  
  ### Answer by username_3 on 2017-06-21. Score: 1
  
  You should read my [paper](https://bmcstructbiol.biomedcentral.com/articles/10.1186/1472-6807-8-53), 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.
  
  > **Comments:**
  > **username_0**: Most papers give 5 or 6 angstrom distance for physical interactions. I don't know this distance is between which atoms exactly  
  > **username_3**: 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.  
  
  ---
  
  