The binding interface between cytochrome c and functionalized gold nanoparticles depends on the nanoparticle functionality, as shown by amide H/D exchange (amide HDX). Nanoparticles functionalized with simple carboxylates, or with the amino acid aspartate, bind to cytochrome c over a large surface. Nanoparticles functionalized with the amino acid phenylalanine binds a much smaller surface of cytochrome c, spanning from Tyr(67)-Phe(82), suggesting that adding the hydrophobic benzyl group increases the selectivity of nanoparticles for this specific cytochrome c surface. This suggests that a balance between electrostatics and hydrophobicity is necessary to recognize the different faces of cytochrome c.