These characteristics make these side chains hydrophilic. Five of them can also form strong hydrogen-bonding interactions with water molecules (containing either an alcohol group or an amide group). These side chains contain highly polar bonds whose dipoles do not cancel most can also have strong hydrogen bonding attractions.Īll of these amino acids have a side chain that contains a functional group with significant dipole moment. Figure: Amino acids with polar neutral side chains. The six amino acids shown in below have side chains that are polar, but neither acidic nor basic. Tryptophan side chain, as a whole, is still classified as hydrophobic. However, the N-H bond can have hydrogen-bonding interactions with water molecules, although it is insufficient to overcome the hydrophobic nature of the rest of the side chain. The double ring structure is aromatic, meaning that the nitrogen-containing part of the side chain is more similar to an amide than an amine, and it is not basic. Tryptophan has a large side chain, composed mostly of carbon and hydrogen. Hence, methionine’s side chain is also classified as hydrophobic. Methionine’s side side contains a thioether group (similar to an ether, but with an S instead of an O), which is somewhat polar but cannot form hydrogen-bonding interactions with water molecules. These weak intermolecular interactions with water molecules make them hydrophobic. Seven of these amino acids have an entirely alkyl side chain (glycine’s side chain is simply an H atom, proline’s side chain forms a ring with its amine group), which can only interact with water molecules via London dispersion forces. The side chains of these amino acids are mainly composed of carbon and hydrogen. The nine amino acids that have hydrophobic side chains are shown below: Figure: Amino acids with hydrophobic side chains. Knowing the nature of these side chains is important for understanding protein structure. Therefore, in a strand of protein, the side chains of each amino acid branch off the protein backbone and can influence protein 3D structure. Moreover, the amine and carboxylic acid groups undergo condensation reactions to form amide linkages when amino acids polymerize to form proteins. The amine and carboxylic acid groups are present in all amino acids, hence they are not used to classify different amino acids.