Rarely is a single amino acid responsible for the entirety of an interaction, be it a ligand, a surface, another protein, etc. It's as much of a secondary/tertiary effect as it is anything else. There are going to be other atoms within the short-range nonbonded cutoff in the simulation, so the forces between your protein and your nanoparticle are going to be affected by other residues.

Thank you for your response Justin. I know there are other atoms such as water molecules, salts and other protein residues that will affect the interaction. However, when I am looking at the interaction and consider a particular residue and it's effect for eg from the VDW energy, would I be seeing the same effect if this residue now is linked to an entirely different combination of other residues?

Are you using a classical additive force field? They are named for just that reason - their terms are additive. If you simply decompose the van der Waals energy of Thr-nanoparticle in a pairwise fashion, yes, that interaction energy will be totally agnostic of the flanking residues (assuming similar conformational sampling). The underlying dynamics that give rise to that interaction and/or local conformational sampling, however, can depend on the other residues.