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?

  • $\begingroup$ 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. $\endgroup$ – marcin Jul 8 '18 at 10:07
  • $\begingroup$ The question seems to be a follow-up of bioinformatics.stackexchange.com/questions/860/… $\endgroup$ – marcin Jul 8 '18 at 10:08
  • $\begingroup$ @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 $\endgroup$ – Sara Jul 8 '18 at 13:09

If you were to treat the nucleotide like a ligand you could follow these steps 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 to measure against.

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