Understanding the process which regulates electron transport in molecular nanostructures is one of the major issues for future technological applications. The conceptual idea of a nano-device based on a single atom/molecule contact is realized for different functions, but the practical realization of such circuits is still facing several challenges. Molecular structure, adsorption geometry, and molecule-electrode interaction are a few of the parameters that influence the electron transport. Scanning tunneling microscope allows to access these parameters and to measure the conductance through single atoms and molecules at different tip-sample distances ranging from tunneling to point contact regime. A comprehensive view of these experiments allows determining the influence of the local atomic arrangement at the junction as well as of the molecular orientation on the transport properties at the nanoscale-contact.