Protein structure analysis

Molecular interactions

On the Protein Tools website, there are several tools for analysing intra-protein interactions including hydrophobic clusters, hydrogen bond networks, salt bridges and contact maps.
Extract chain A of protein PDB-ID 3A2M and save it in a separate pdb file; use this structure as input to run all four analyses and answer the following questions based on the results.

How many hydrophobic clusters were identified? How many contacts are there in the biggest and second biggest clusters?
How many hydrogen bond networks were identified? Which one has the most hydrogen bonds? Which hydrogen bond has the most ideal parameters (Donor - Acceptor distance closest to 2 Å and D-H-A angle between 150º and 180º)?
How many salt bridges were identified? Which one has the most residues involved?
Study the contact map (online or download it locally), identify 2–3 residues with a large number of contacts to other residues. View the identified residues in PyMOL and study their contacts.

use the ConSurf tool to predict the evolutionary conservation of individual positions of the target protein
- precalculated results: ConSurf
view the conservation mapped to the protein structure in PyMOL
- download and open the PyMOL session with mapped Conservation Scores
- OR download and open PDB file, remove waters and ligands, color by B-factors
which regions of the protein are most conserved? Is this a surprising finding?
try to guess if any of the highly conserved regions may represent a potential binding site for small molecules or a macromolecule
how conserved are the 2-3 residues you picked before based on the contact map analysis? Is this something you would expect?

use the CASTp tool to identify pockets and cavities in the structure of the target protein
- precalculated results: CASTp
study the results in JMol
try to guess which pocket or cavity represents the binding site
use the Cavity Plus server to identify pockets and cavities in the target protein structure
study the results in PyMOL and compare them to the CASTp prediction

analyze the target structure with ProFunc
- precomputed results: ProFunc
based on the results obtained by searching the databases of 3D functional templates for active and binding sites, determine (if possible) the residues of the active or binding site of the target protein
are there any predicted DNA binding sites on the target protein
do the results obtained by searching the 3D template databases correspond with the results of the evolutionary conservation analysis and the identified cavities/pockets?

use the meta-PPISP meta-server to predict potential protein binding sites on a target protein
- precalculated results: meta-PPISP
view the results mapped to the protein structure in PyMOL (color as spectrum according to B-factors) and determine the potentially most likely protein binding sites
compare the prediction results with reality - load the structure with PDB-ID 3A2M - was the interaction site predicted correctly?
if multiple interaction sites were predicted, must only one of them be correct?

study the structure of the target protein in PyMOL - do you expect tunnels or pores (channels) to be present?
open the CAVER Web server
select Upload PDB file and load the target protein structure
tick the box to agree with the academic license and non/commercial software use and click Next
click on the ligand tab and select the chloride ion in the cavity of the active site to be used as the starting point for the calculation
click the Submit job button
- precalculated results: CAVER Web
what is the width in the narrowest part of the tunnels and the length of the tunnels found? Are these really tunnels?
which residues form the first tunnel? (info icon → Residues & atoms tab)