Measure the relevant distances and angles to identify hydrogen bonds. Calculate inter-residual van der Waals interaction energies to quantify non-polar interactions.

If you are using gromacs you can use gmx hbond and gmx sasa tools respectively

Nikhil Maroli yes I am using gromacs. But will gmx sasa list the residues ? I already have contact maps where I can see some hydrophobic amino acid within 0.5nm with one another but I want to confirm if truly its the hydrophobic side chains interacting with one another i.e that they are truly forming hydrophobic interactions.

Hi Martin Klvana thanks for your response how do I calculate the inter residual van der waals interaction energies?

Using sasa tool you can calculate hydrophobic and hydrophilic area separatly, with gmx energy you will get van der Waals energy, gmx distance gives distances. Collective analysis of these can give some information about hydrophobic and hydrophilic interactions.

Nikhil Maroli Thank you