Many key features of the protein adsorption On the silica Surfaces still remain unraveled. One of the open questions the interaction of nonpolar side chains with siloxane cavities. Her we use nonequilibrium molecular dynamics simulations for the detailed investigation of the binding of Several hydrophobic and amphiphilic protein side chains with silica surface. These interactions were found to be a posiible driving force for protein adsorption. The free energy gain was larger for the disordered surface of amorphous silica gel as compared to alpha-quartz; but the impact depended on the type of amino acid. The dependence was analyzed from the structural point of view. For every amino acid an enthalpy-entropy Compensation behavior was observed. These results confirm a hypothesis of an essential role of hydrophobic interactions in protein unfolding and irreversible adsorption on the silica surface.