The degree of protein folding is characterized either by the solvent-accessible surface area (S ASA ) or the actual number of native contacts (N cont). Evidently, these values should correlate with each other, as a decrease in S ASA caused by the change in protein conformation during its folding must be accompanied by the corresponding increase in the number of native contacts. It is shown that this correlation does exist and is very strong (the correlation coefficient exceeds 99%), which can be used for an accurate and rapid estimation of the protein surface area from the number of native contacts. Among the methods commonly used for calculating the native contacts, the atom-atom approach gives the best fit if hydrogen atoms are taken into account and the cutoff value for the distance between the centers of atoms is taken to be 8 Å. The latter means that two layers of surface atoms are required to shield the protein core from the solvent.
- Native contacts
- Protein compactness
- Solvent-accessible surface area