The electronic transport properties of molecular junctions are very sensitive to the contact configuration which is usually not very well known. One type of setup which allows more control over the contact geometry uses an STM (scanning tunneling microscope) tip as one of the electrodes enabling the investigation of both the electronic and geometric structure of the junction. Using the nonequilibrium Green function formalism in combination with DFT, we can systematically investigate the effect of the contact geometry on the transport properties of STM-based molecular junctions. This allows us to shed new light on the transport mechanisms in of STM junction experiments and in turn to improve our modeling tools.