Proteins are made from 20 different amino acids. Some proteins do contain amino acids outside the standard set of 20, but these are produced by chemical modification after the protein is synthesized, or by incorporation of selenocysteine during translation in certain proteins.

All amino acids have an α-carbon that is connected to an amino group, carbonyl group, hydrogen atom and R-group (or side-chain). Amino acids differ based on the R-group subsituent. R-groups vary in size, hydrogen-bonding potential, and charge. Thus amino acids can be classified in many different ways. The classifications in this section will help you to understand how interactions of the side chains and main chain, with one another and with the solvent, determine protein structure. You also need to understand how serious a change in protein structure might be when one amino acid replaces another as proteins evolve or as molecular diseases appear.

You should be able to predict the properties from your knowledge of the side chain structures and basic principles of organic chemistry.

A JSmol flash card learning drill is provided to help you become familiar with the 3D structures.