I am currently learning about PyMol to utilize in my project. I used PyMol to visualize potential H-bond interactions in specific amino acid residues. However, I have discovered that Arg465 and Ser461 show a distinct interaction, as shown.
Please help identify this interaction.
The broken yellow line with the distance indicator (6.2) looks like a simple distance monitor which you generate with a "measure" command, although I do not know how you generated the blue tubes around it. At 6.2Å, the Ca-Ca distance indicated by the broken line is far larger than the sum of the carbon Van der Waals radii (3.4Å). It is just about short enough that you might classify the contact as a solvent excluding contact (hydrophobic interaction)
Thank you for your response.
I found this blue tubes between Ca of Arg and Ser while looking for H-bond. However, I wonder what could be the possible interaction/bond it is. To measure the distance of this blue tubes, I generated the yellow line with measure command.
Can you please suggest what this might be? Annemarie Honegger
As I said before, the distance between the two carbons is about equal to the sum of the carbon VdW radii plus the diameter of a water molecule. Given that the Calpha hydrogens also fit in, the distance is at the upper level of a solvent excluding contact.
However, these types of contact are not usually enumerated even when looking at complexes, but accounted for by the reduction of solvent accessible surface upon complex formation.
Basically, the two C-alphas are too far apart from each other to directly contribute to the interaction energy (VdW), but too close for a water molecule to squeeze in between, thereby contribute to the solvatation energy.
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