Empirical knowledge suggests that the process of protein folding does exhibit a generally stochastic behavior similar to that of turbulence. The statistical theory of turbulence is one of the most extensively studies stochastic processes. On the basis of existing evidence, it seems that the eddy viscosity transfer theory due to Heisenberg is to be preferred. Theoretical analysis in this paper shows that structure factor and radial distribution function are Fourier transform pair function. Based on this relationship, the potential energy of protein system can be expressed as a function of structure factor. With the help of a thin rod model, the potential energy can be distinguished as two parts: the communication energy between different wave number structure and the “dissipated” part converted into hydrogen bonding energy. The form of this tow parts are to be determined by detailed study of the formation of hydrogen bonds.