The configuration of the molecule–electrode contact region plays an important role in determining the conductance of a single-molecule junction, and the variety of possible contact configurations have yielded multiple conductance values for a number of molecular families. In this report, we perform simultaneous conductance and electromechanical coupling parameter measurements on a series of oligophenylene–dithiol single-molecule junctions. These molecules show two distinct conductance values, and by examining the conductance changes, the electromechanical coupling, and the changes in the I–V characteristics coupled with a combination of analytical mechanical models and density functional theory (DFT) structure calculations, we are able to determine the most-probable binding configuration in each of the conductance states. We find that the lower-conductance state is likely due to the thiols binding to each electrode at a gold top site, and in the higher-conductance state, the phenylene π orbitals interact with electrodes, drastically modifying the transport behavior. This approach provides an expanded methodology for exploring the relationship between the molecule–electrode contact configuration and molecular conductance.