The field of molecular metal clusters protected by organothiolates is experiencing a very rapid growth. So far, however, a clear understanding of the fine interactions between the cluster core and the capping monolayer has remained elusive, despite the importance of the latter in interfacing the former to the surrounding medium. Here, we describe a very sensitive methodology that enables comprehensive assessment of these interactions. Pulse electron nuclear double resonance (ENDOR) was employed to study the interaction of the unpaired electron with the protons of the alkanethiolate ligands in four structurally related paramagnetic Au25(SR)018 clusters (R = ethyl, propyl, butyl, 2-methylpropyl). Whereas some of these structures were known, we present the first structural description of the highly symmetric Au25(SPr)018 cluster. Through knowledge of the structural data, the ENDOR signals could be successfully related to the types of ligand and the distance of the relevant protons from the central gold core. We found that orbital distribution affects atoms that can be as far as 6 Å from the icosahedral core. Simulations of the spectra provided the values of the hyperfine coupling constants. The resulting information was compared with that provided by 1H NMR spectroscopy, and molecular dynamics calculations provided useful hints to understanding differences between the ENDOR and NMR results. It is shown that the unpaired electron can be used as a very precise probe of the main structural features of the interface between the metal core and the capping ligands.