The reverse-sequence peptides CysAlaAla and AlaAlaCys may attach to gold nanoparticles through the thiol group, and they differ primarily by whether the charged amino or the carboxylate group is proximal to the sulfur. Alanine residues in these peptides are not expected to interact significantly with the gold surface and serve to place a large separation between the amino and carboxylate groups. Solid-state NMR experiments and DFT calculations were performed to explore the structural differences between CysAlaAla on gold nanoparticles and AlaAlaCys on gold nanoparticles. It is found that the relative positions between the thiol, amino, and carboxylate groups strongly influences the structures of the peptide gold systems. CysAlaAla orients parallel to the gold surface in a monolayer fashion, whereas AlaAlaCys forms an interdigitating bilayer-like structure that is oriented upright relative to the gold surface.