Conformational Entropy - production of a single folded molecule from a multitude
of random-coil conformations involves a decrease in randomness
and thus a decrease in entropy. From 
G = H - TS, a negative S makes a
positive contribution to G. This must
be offset by either a negative H or some
other increase in entropy as a result of folding.
Internal Interactions
- energetically favorable interactions between groups within
the folded molecule. These interactions, which include charge-charge,
internal hydrogen bonding, and van der Waals interactions, are
the major source of the negative H of folding.
Charge-Charge Interactions - occur between positively and negatively charged side chain groups. Interactions between oppositely charged groups (attraction) are also called salt bridges. Repulsive forces between like charges can also contribute to the overall structure.
Internal Hydrogen Bonds - interactions between amino acid side chains that are either good hydrogen bond donors (such as the hydroxyls of serine or threonine) or good acceptors (such as the carbonyl oxygens of asparagine or glutamine) (Figure 6.21). Though hydrogen bonds are relatively weak, the large number of them can make a considerable contribution to stability.
van der Waals Interactions - weak interactions between uncharged molecular groups in the tightly packed environment of a folded protein. The contributions of these interactions to the negative enthalpy of folding is diminished by giving up favorable interactions with water via folding.
The Hydrophobic Effect - interactions between hydrophobic regions of a protein,
which actually increase entropy by destroying the ordered clathrate
structures of water around these residues in the unfolded state.
The hydrophobic effect is sometimes incorrectly called hydrophobic
bonding. Table 6.4 shows numerical
values assigned to the relative hydrophobicities of the amino
acids. In Table 6.3, the hydrophobic
effect can be seen by the more positive S values for
cytochrome c and myoglobin.