Nanoscale gold contacts were investigated both experimentally and theoretically. Simulations of in situ processes in a new combined TEM-AFM microscope were performed by molecular dynamics and theoretical mechanics methods. Atomistic transformations of gold nanometer-sized wires (nanowires) between Au-probe and Au-surface were studied in processes both of loading-unloading and in the normal, lateral, diagonal and zigzag directions of the probe motion. Molecular dynamics was used for studies of "adhesion avalanche", shear and strain deformations. Theoretical mechanics was used for studies of jump-to-contact and jump-off-contact phenomena. Reorientations from (100) to (111) planes with formation of extended zigzag, vacancy cavities, a double-neck creation and a slip along the (110) plane with formation of twins and steps were observed. Deformation mechanisms were shown to depend on schemes of motions and on the ratio between the relative velocity of the probe and surface motion and the velocity of the defect relaxation.