If you shake the bottle, the oil is dispersed, but in a little while it all congregates again. This is hydrophobic interactions at work. The same process is functioning at the molecular level. Hydrophobic amino acids try to hide themselves away from the water on the outside of the protein by all congregating on the inside of the protein. This grouping together helps define the structure of a protein.
Ionic interactions are the attraction of opposite charges for one another.
Negatively charged amino acid side groups, such as glutamate and aspartate are attracted to positively charged amino acid side groups such as lysine, arginine, and histidine. Finally there are sulfhydryl linkages . These are covalent bonds between cysteine groups. Cysteine is a unique amino acid in that it has a sulfur group available for binding to other groups. Often in proteins, adjacent sulfhydryl groups on cysteines will form a covalent link to help stabilize a protein - Figure 5.