Significance The hydration of molecules affects their physical and chemical properties. In particular, the functions and interactions of various proteins are determined by the conformation of water molecules around polar and nonpolar protein surface domains. Therefore, understanding the local interactions between water molecules and the polar and nonpolar protein surface domains such as water molecule conformations in protein hydration layers benefits targeted protein engineering, and recognition of molecules including proteins, DNA/RNA, cell membranes, and drugs. By using atomistic simulations, we show distinct correlations between the hydration water molecules and the different types of protein surface domains.