We discuss the stability of an entire protein and the influence of main chains and side chains of individual amino acids to investigate the protein-folding mechanism. For this purpose, we calculated the solvation free-energy contribution of individual atoms using the three-dimensional reference interaction site model with the atomic decomposition method. We generated structures of chignolin miniprotein by a molecular dynamics simulation and classified them into six types: native 1, native 2, misfolded 1, misfolded 2, intermediate, and unfolded states. The total energies of the native (-171.1 kcal/mol) and misfolded (-171.2 kcal/mol) states were almost the same and lower than those of the intermediate (-158.5 kcal/mol) and unfolded (-148.1 kcal/mol) states; however, their components were different. In the native state, the side-chain interaction between Thr6 and Thr8 is important for the formation of π-turn. On the other hand, the hydrogen bonds between the atoms of the main chains in the misfolded state become stronger than those in the intermediate state.