Self-assembled supramolecular structures of peptide derivatives often reflect a kinetically trapped state rather than the thermodynamically most favoured structure, which presents a challenge when trying to elucidate the molecular design rules for these systems. In this article we use thermodynamically controlled self-assembly, driven by enzymatic condensation of amino acid derivatives, to elucidate chemical composition/nanostructure relationships for four closely related Fmoc-dipeptide-methyl esters which form hydrogels; SF, SL, TF and TL. We demonstrate that each of the four systems self-assemble to form extended arrays of β-sheets which interlock via π-stacking of Fmoc-moieties, yet with subtle differences in molecular organisation as supported by rheology, fluorescence emission spectroscopy, infrared spectroscopy, X-ray diffraction analysis and molecular mechanics minimisation.