Distance between residues forming active site constriction

I want to compute time dependent variations in area between four residues (forming a bottle neck for ligand entry). I was looking at pairdist and dist tools of gromacs but i couldnot conclude which one can i use for my analysis.

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lets say i have to calculate changes in the area between theses four residue. should i make index for four single residues or in pairs, to calculate dist and area eventually?