Contact area and possible applicaitons of proligy-lig in designing new proteins

I wish to use the prodigy-lig tool. In the results below, please let me know if the last digits (from left to right) represent the contact area between the atoms of binding amino acid and the ligand in the below results?

Is the unit for this contact Å2? In other words, is this contact a distance with Å unit, or it is a contact area with Å2 unit?

If it is a measure of distance between atoms, why they are greater than the length of any possible interaction bonds between the ligand and residues of the binding pocket?

Also, as per your recommendation, how can one use the prodigy-lig tool to find the amino acids with the most and the least contribution to the affinity? Is it possible to classify the pocket amino acids according to their contribution to the affinity?

Moreover, in the results, I see many residues with the same information except for the last digits (from left to right) are repeated many times, which I could not understand the reason. For example, “ASN H 35 C STR H 229 C” line is repeated 56 times. Would you please help me to understand the reason for these reparations?

Lastly, I wish to thank you in advance for your invaluable recommendations and your precious time reading my lengthy letter.

Thank you,


As already answered directly from email you sent to the haddock support email:

reported values are distances in Angstrom

And make sure you have unique atom names per residue in your input PDB… most likely this is not the case if you see those repeated lines…