Hi Mario, We recommend the chimerax-users@cgl.ucsf.edu address CC'd here for questions. The Help describes all the options in the Contacts tool: https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html

It sounds like the settings in the Contacts dialog you need to pay attention to are:

"Limit by selection" : if you selected the compound and you want interactions between the compound and the protein, then you want this option to be turned on and "with exactly one end selected" because that means it will find contacts where one atom is in the selection and the other atom is not.

Then if the compound and protein came from two different files they are different models, so you need to turn on "Include intermodel".

If the compound and protein are in the same PDB file they are in the same model as each other, so you need to turn on "Include intramodel".

For example if I open PDB entry 2gbp and select the glucose, I make sure "Limit by selection: with exactly one end selected" is turned on and "Include intramodel" is also turned on. Using the default contact parameters and also turning on "Write information to: Log", I get this reported in the Log:

contacts sel ignoreHiddenModels true reveal true log true Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True

46 contacts atom1 atom2 overlap distance /A BGC 310 C6 /A TYR 10 CE2 0.018 3.622 /A BGC 310 O3 /A ASP 236 OD1 0.014 2.466 /A BGC 310 O2 /A ASP 236 CG 0.005 3.335 /A BGC 310 C6 /A ASN 91 OD1 -0.022 3.322 /A BGC 310 O3 /A ASN 211 CB -0.030 3.370 /A BGC 310 C1 /A ASP 154 OD1 -0.038 3.338 /A BGC 310 O6 /A ASN 91 OD1 -0.040 2.520 /A BGC 310 O4 /A ASP 14 CG -0.083 3.423 /A BGC 310 O2 /A ARG 158 NH1 -0.088 2.788 /A BGC 310 O4 /A TRP 183 CB -0.102 3.442 /A BGC 310 O3 /A PHE 16 CB -0.109 3.449 /A BGC 310 O2 /A ASP 236 OD2 -0.111 2.591 /A BGC 310 O6 /A HIS 152 NE2 -0.134 2.834 /A BGC 310 O3 /A ASP 236 CG -0.140 3.480 /A BGC 310 O1 /A ASP 154 OD1 -0.169 2.649 /A BGC 310 O4 /A ASP 14 OD1 -0.170 2.650 /A BGC 310 C3 /A ASN 211 ND2 -0.178 3.698 /A BGC 310 O6 /A LYS 92 CE -0.199 3.539 /A BGC 310 O4 /A TRP 183 CG -0.202 3.272 /A BGC 310 C3 /A ASN 211 CB -0.224 3.984 /A BGC 310 C3 /A TRP 183 CE3 -0.253 3.893 /A BGC 310 C4 /A ASP 14 OD1 -0.254 3.554 /A BGC 310 C4 /A ASP 14 CG -0.257 4.017 /A BGC 310 C4 /A PHE 16 CB -0.267 4.027 /A BGC 310 O1 /A ASP 154 CG -0.272 3.612 /A BGC 310 C1 /A ARG 158 NH1 -0.276 3.796 /A BGC 310 C2 /A ASN 256 ND2 -0.283 3.803 /A BGC 310 C1 /A ARG 158 NH2 -0.285 3.805 /A BGC 310 C2 /A ASP 236 OD2 -0.287 3.587 /A BGC 310 O6 /A LYS 92 CG -0.290 3.630 /A BGC 310 C2 /A PHE 16 CD1 -0.323 3.963 /A BGC 310 O3 /A ASN 211 ND2 -0.328 3.028 /A BGC 310 O5 /A ASN 91 ND2 -0.335 3.035 /A BGC 310 C2 /A ASP 236 CG -0.335 4.095 /A BGC 310 C3 /A PHE 16 CB -0.347 4.107 /A BGC 310 O2 /A ARG 158 CZ -0.355 3.425 /A BGC 310 C4 /A ASP 14 OD2 -0.357 3.657 /A BGC 310 C5 /A HIS 152 NE2 -0.360 3.880 /A BGC 310 C6 /A ASP 14 OD1 -0.366 3.666 /A BGC 310 C6 /A HIS 152 NE2 -0.366 3.886 /A BGC 310 C2 /A PHE 16 CB -0.367 4.127 /A BGC 310 O6 /A ASN 91 CG -0.368 3.438 /A BGC 310 C2 /A ARG 158 NH1 -0.369 3.889 /A BGC 310 C1 /A ASN 91 ND2 -0.371 3.891 /A BGC 310 C3 /A ASP 236 OD1 -0.372 3.672 /A BGC 310 C1 /A ASP 154 CG -0.393 4.153

46 contacts

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

From: Mario Rodriguez Monteverde mrodriguez.81@alumni.unav.es Subject: protein-molecule contact log issue Date: February 26, 2024 at 2:52:17 PM PST

Good afternoon.

To whom it may concern.

I am attempting to identify the residues with which a compound (A) is interacting with a target protein (B). I opened both pdb files in ChimeraX, I selected the compound and did as follows: Tools > Structure Analysis > Contacts (selected output info to log). The results which I get are the contacts inside the same protein (prot(B) with prot(B)), instead of compound(A) with protein(B). I have tried selecting only the target protein, selecting both, creating a new pdb file with the comp and the compound together, but nothing works, I still can not get to know which residues from the compound are contacting my target prot.

How could I solve this?

Thank you

Best, Mario