The changes of molecular conformation, contact geometry, and metal-molecule bonding are revealed by inelastic-electron-tunneling spectroscopy measurements characterizing the molecular vibrational modes and the metal-phonon modes in alkanedithiol molecular junctions at low temperature. Combining inelastic-electron-tunneling spectroscopy with mechanical control and electrode material variation (Au or Pt) enables separating the influence of contact geometry and of molecular conformation. The mechanical strain of different electrode materials can be imposed onto the molecule, opening a new route for controlling the charge transport through individual molecules.