Contact comparison atlas

How to compare your structures and identify interaction patterns?

You can do this in three simple steps:

1. Generate structural alignment and map structurally equivalent positions
2. Compute interactions
3. Interactively visualize interaction patterns

The following example compares the two structures with PDB ids 2RH1 and 3UON:

1. Generate structural alignment and map structurally equivalent positions
• Prepare your structures by adding hydrogen. This can be done using e.g. pymol.
• Save the structures that have hydrogens added to them: 3UON_h_added.pdb and 2RH1_h_added.pdb.
• Generate a multiple sequence alignment using Gesamt (v1.09/v1.15) from CCP4 (www.ccp4.ac.uk) and save the output:
  $ gesamt 3UON_h_added.pdb 2RH1_h_added.pdb > output.txt
• Generate residue-label files using get_resilabels.py
$ get_resilabels.py --input_gesamt output.txt --output_path label_files/ --proteins 3UON 2RH1
2. Compute interactions using GetContacts:
• $ get_static_contacts.py --structure 3UON_h_added.pdb --output 3UON_contacts.tsv --itypes all
• $ get_static_contacts.py --structure 2RH1_h_added.pdb --output 2RH1_contacts.tsv --itypes all
3. Using this webpage, upload the the pdb files and the above-generated interaction files and label files.

How to compare to simulations?

When using a simulation in the comparison, the approach is similar to the one described above. The only difference is that the contact file now contains multiple frames so it has to be reduced to a single frame based on frequency of interactions.

• $ get_dynamic_contacts.py --topology top.pdb --trajectory trj.xtc --output sim_contacts.tsv --itypes all
• $ get_contact_singleframe.py --input sim_contacts.tsv --output sim_single.tsv --min_frequency 0.6

Using this webpage, upload the the pdb files and the above-generated interaction files and label files.