Based on the physicochemical properties of R groups, the amino acids of proteins may be classified as follows.
1. Acidic: including aspartic acid (aspartate) and glutamatic acid (glutamate). In a neutral solution, the R group of an acidic amino acid may lose a proton and become negatively charged.
2. Basic: including lysine, arginine and histidine. In a neutral solution, the R group of a basic amino acid may gain a proton and become positively charged. Interaction between positive and negative R groups may form a salt bridge, which is an important stabilizing force in proteins.
3. Aromatic: including tyrosine, tryptophan and phenylalanine. Their R groups contain an aromatic ring.
4. Sulfur: including cysteine and methionine. Their R groups contain a sulfur atom (S). The disulfide bond formed between two cysteine residues provides a strong force for stabilizing the globular structure. A unique feature about methionine is that the synthesis of all peptide chains starts from methionine (Chapter 5 Section C).
5. Uncharged hydrophilic: including serine, threonine, asparagine and glutamine. Their R groups are hydrophilic and capable of forming hydrogen bonds.
6. Inactive hydrophobic: including glycine, alanine, valine, leucine and isoleucine. These amino acids are more likely to be buried in the protein interior. Their R groups do not form hydrogen bonds and rarely participate in chemical reactions.
7. Special structure: including proline. In most amino acids, the R group and the amino group are not directly connected. Proline is the only exception among amino acids found in protein. Due to this special feature, proline is often located at the turn of a peptide chain in the three-dimensional structure of a protein.
Figure 2-A-2. Names, symbols, chemical structures and hydrophobicity indices of the amino acids found in proteins. They are arranged in the order as discussed above.
Note: The hydrophobicity index tells the relative hydrophobicity among amino acids. More positive value indicates stronger hydrophobicity. Hydrophilic amino acids have negative values. In a protein, hydrophobic amino acids are more likely to be located in the protein interior, whereas hydrophilic amino acids are more likely to face the aqueous environment.