The folding of the polypeptide chain allows the van der Waals surfaces of atoms to fit together snugly, filling up most of the space in the interior. The entire volume of a molecule is divided by planes which delimit the polyhedra, each of which effectively correpsonds to one atom. Note that the volume of amino acids in crystals has been found to be the same as the mean volume of the amino acid in protein interiors. Thermal fluctuations of surrounding atoms vary the cavities' sizes. This allows dynamic behaviour such as side-chain rotation.
Solvent molecules do occur internally where a cavity is large enough to accommodate it.
Protein-solvent interactions will be examined in a later section of the course. The packing surfaces of protein atoms Nonpolar, uncharged polar and charged atomic surface areas are all involved in packing. As well as van der Waals interactions between nonpolar atoms, polar and charged atoms take part in hydrogen bonds and salt bridges within the protein. Refer to the section on Non-bonded Interactions in Section 7. Therefore a large amount of polar surface is necessarily buried, considering that backbone hydrogen bonds are the basis of secondary structures.