I have predicted the binding affinity of two proteins with Prodigy, with the input being the relevant protein-protein complex that I generated through docking with HADDOCK. I am now using PyMOL to visualise the polar contacts between the Prodigy-defined contacts at the interace (ICs) in my protein-protein complex. The Prodigy output tells me that Phe191 on protein B (pink) and Ser136 on protein A (blue) are involved in a polar-apolar IC but this contact doesn’t appear on PyMol. Other polar-apolar ICs do show up on PyMOL so I am not sure why this one isn’t.

Prodigy output with relevant IC highlighted

Screenshot of PyMOL session with Ser136 and Phe191 selected

I have tried selecting each of these atoms individually and then clicking Action > Find > Polar contacts >to any atoms. But this has not worked for me. Also, selecting either residue and then clicking Action > Find > Any Contacts >between chains within 4.0A also doesn’t show the interaction. I have also used the Show_Contacts plugin [https://pymolwiki.org/index.php/Show_contacts]  with the command:

contacts Clust1_NR1_BestStructure, iface2, result=contacts, cutoff=3.6, bigcutoff=4.0

But this also did not show the interaction.

For Prodigy, the distance threshold for two atoms to be classified as being in contact is 5.5 A https://wenmr.science.uu.nl/prodigy/method. But even when I change the “Show Contacts” plugin parameters to cutoff=7.0 and bigcutoff=7.5this contact still does not show up (although other interactions between other residues that are further away do appear). I have also tried increasing the h_bond cutoff: set h_bond_cutoff_center 6 and set h_bond_cutoff_edge 5.6 but I haven’t had any luck with this either.