<p>If you were to treat the nucleotide like a ligand you could follow <a href="http://vlab.amrita.edu/?sub=3&amp;brch=275&amp;sim=1446&amp;cnt=2" rel="nofollow noreferrer">these steps</a> on pymol, and find the measurements you desire. </p>

<p>Calculating distances to centroids is a little bit more complex, as you have to make a <a href="https://pymolwiki.org/index.php/Center_of_mass" rel="nofollow noreferrer">pseudo atom</a> to measure against. </p>

CC BY-SA 4.0
2018-07-17T09:58:27.397Z
2018-08-21T10:44:53.283Z
2018-08-21T10:44:53.283Z
pazchem
<p>We all know that for physical protein-protein interaction, we need to find the distance between residues from PDB file of that interaction (finding distance between carbon alpha, carbon beta or centroid of two residues in PDB data of two proteins). I need to investigate the physical interaction between a protein and an RNA and I have PDB ID for this interaction but I don't exactly know to find the distance between which parts of residues (calpha, cbeta, centroid and etc.) with which parts of nucleotides (bases, phosphate group, or ribose backbone) from a PDB ID. Is there anyone who knows what can I do for this purpose?</p>

CC BY-SA 4.0
2018-07-08T10:07:01.263Z
I have reservations about the "We all know..." part. I'd use distance between the interacting atoms rather than between arbitrary points of the residue.
marcin
CC BY-SA 4.0
2018-07-08T10:08:29.050Z
The question seems to be a follow-up of https://bioinformatics.stackexchange.com/questions/860/best-distance-parameter-for-estimating-physical-interaction-between-residues-in
marcin
CC BY-SA 4.0
2018-07-08T13:09:30.253Z
@marcin, that question was about residue-residue interactions but this question is about nucleotide-residue interactions. For my special purposes I didn't need to find the distance between all atoms but I just needed to find the distance between arbitarary points of the residues and here in this question between residue and nucleotides
Sara
<pdb><interactions>
finding RNA-protein physical interaction
# finding RNA-protein physical interaction

(Asked by: username_0 on 2018-07-07)

We all know that for physical protein-protein interaction, we need to find the distance between residues from PDB file of that interaction (finding distance between carbon alpha, carbon beta or centroid of two residues in PDB data of two proteins). I need to investigate the physical interaction between a protein and an RNA and I have PDB ID for this interaction but I don't exactly know to find the distance between which parts of residues (calpha, cbeta, centroid and etc.) with which parts of nucleotides (bases, phosphate group, or ribose backbone) from a PDB ID. Is there anyone who knows what can I do for this purpose?

**Tags:** pdb, interactions
> **Comments:**
> **username_1**: I have reservations about the "We all know..." part. I'd use distance between the interacting atoms rather than between arbitrary points of the residue.  
> **username_1**: The question seems to be a follow-up of https://bioinformatics.stackexchange.com/questions/860/best-distance-parameter-for-estimating-physical-interaction-between-residues-in  
> **username_0**: @marcin, that question was about residue-residue interactions but this question is about nucleotide-residue interactions. For my special purposes I didn't need to find the distance between all atoms but I just needed to find the distance between arbitarary points of the residues and here in this question between residue and nucleotides  

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## 1 answers

### Answer by username_2 on 2018-07-17. Score: 1

If you were to treat the nucleotide like a ligand you could follow [these steps](http://vlab.amrita.edu/?sub=3&brch=275&sim=1446&cnt=2) on pymol, and find the measurements you desire.

Calculating distances to centroids is a little bit more complex, as you have to make a [pseudo atom](https://pymolwiki.org/index.php/Center_of_mass) to measure against.


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