In this report we present a general formulation to calculate the van der Waals interaction between two protein molecules in an electrolyte solution using boundary element method of solving linearized Poisson–Boltzmann equation. Our formulation is based upon an inhomogeneous dielectric model of proteins at the residue level. Our results for bovine pancreatic trypsin inhibitor at various relative orientations indicate that the anisotropy of the interaction can be tens of kBT.