The thermodynamic stability and binding characteristics of Azurin-Cytochrome c551 (AZ/C551) complex in water solvent were investigated by an all-atom molecular dynamics (MD) simulation. Model complexes of AZ/C551 were prepared by protein-protein docking and MD simulations. The total free energy and binding free energy of model AZ/C551 complexes were evaluated using the conformational and solvation energies and entropy terms. The conformational and solvation free energies were found to largely depend on the hydrophilicity/hydrophobicity of the AZ/C551 complex, showing the importance of these characteristics in the thermodynamic stability and in the formation of the AZ/C551 complex. (C) 2012 Elsevier B. V. All rights reserved.