Amino acids containing an amino group bonded directly to the alpha carbon are referred to as alpha amino acids. In proteins essentially all groups capable of forming H-bonds (both main chain and side chain, independently of whether the residues are within a secondary structure or some other type of structure) are usually H-bonded to each other or to water molecules. These residues are often found close to the surface of proteins. In addition, the side chains of histidine, tyrosine, phenylalanine and tryptophan are also able to form weak hydrogen bonds of the types, OH−π, and CH−O, by other words using electron clouds within their ring structures.

Other amino acids − the aromatic tyrosine (Tyr) and tryptophan (Trp) and the non-aromatic methionine (Met) are often called amphipathic due to their ability to have both polar and non-polar character.
It is useful to remember that the energy of a hydrogen bond, depending on the distance between the donor and the acceptor and the angle between them, is in the range of 2-10 kcal/mol. Amino acids that are usually negative (i.e. Please cite: Russell.

Dr. Helmenstine holds a Ph.D. in biomedical sciences and is a science writer, educator, and consultant. Amino acid, any of a group of organic molecules that consist of a basic amino group (―NH 2), an acidic carboxyl group (―COOH), and an organic R group (or side chain) that is unique to each amino acid.


Glycine (Gly), being one of the common amino acids, does not have a side chain. Definition and Examples, Ph.D., Biomedical Sciences, University of Tennessee at Knoxville, B.A., Physics and Mathematics, Hastings College. The side chain has a pKa of approximately 6.5, which The general formula for an amino acid is given below. Their side chains are fully protonated at pH 7.4.

Glycine and proline are often highly conserved within a protein family since they are essential for the conservation of a particular protein fold. Salt bridges formed by positively and negatively charged amino acids have also been found to be important for the stabilization of protein three-dimensional structure - for example proteins from thermophilic organisms (organisms that live at elevated temperatures, up to 80-90 C, or even higher) often have an extensive network of salt bridges on their surface, which contributes to the thermostability of these proteins, preventing their denaturation at high temperatures.Being able to recognize the properties of the different amino acids is a valuable skill when making sequence alignments - in this case functional and even structural information can be extracted from the analysis of the conservation pattern within an alignment. Except for glycine, the polar and uncharged (hydrophilic) amino acids can hydrogen bond to water and are usually more soluble than the nonpolar amino acids.


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