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The chemical properties of the R-groups dominate the primary physical and chemical differences between AAs. Likewise, R-group differences also dominate the physical and chemical contribution each AA residue makes to the inherent properties of a polypeptide or protein. Therefore, it is useful to review the fundamental physical or chemical properties of the R-groups themselves. Based on physical properties, the R-groups of the standard amino acids can be more-or-less be classified into three basic categories -- nonpolar,charged polar, and neutral polar, .

The standard AAs with nonpolar R-groups range in size from the smallest (Gly) to the largest (Trp). By clicking the mouse button a 3-letter or 1-letter abbreviation below, an image of the selected AA image will be generated in the lower left or right window, respectively. The nonpolar R-group of that AA can then be viewed in a different structural representation by clicking thebutton below an abbreviation.

Note that the larger R-groups in this class of AAs tend to be highly hydrophobic ("water fearing") in character. In other words, the R-groups of the larger AAs (i.e., those AAs excluding Ala, Gly and Pro) tend to be repelled by water and thus tend to be thermodynamically sequestered into "oily" clusters in aqueous solutions. These R-groups are typically abundant in the core of folded protein in aqueous solution, giving the protein an oil-droplet-like center shielded from contact with water molecules in the immediate environment. It is important to note, however, that these R-groups can also exist in contact with water and most folded proteins will have a certain percentage of its AA residues with nonpolar R-groups in direct contact with the aqueous environment. Typically, a relatively delicate thermodynamic balance exists between the numbers of nonpolar R-groups of a protein that are in contact the aqueous environment as opposed to those that exist in the hydrophobic core of a protein. The delicacy of this balance is revealed by the fact that relatively mild perturbations in the environment of a protein - e.g., changes in temperature, pH, ionic strength, electrolyte concentrations or composition, etc. -- often leads to sharp transitions in the structure of a protein and loss of biological activity, in other words, denaturation.

AAs with charged polar R-groups repesent the opposite extreme in terms of physical properties.