The amino acids are put together into a polypeptide chain on the ribosome during protein synthesis. In this process the peptide bond, the covalent bond between two amino acid residues, is formed. There are 20 different amino acids most commonly occurring in nature. Each of them has its specific characteristics defined by the side chain, which provides it with its unique role in a protein structure. Based on the propensity of the side chain to be in contact with polar solvent like water, it may be classified as hydrophobic (low propensity to be in contact with water), polar or charged (energetically favorable contact with water). The charged amino acid residues include lysine (+), arginine (+), aspartate (-) and glutamate (-). Polar amino acids include serine, threonine, asparagine, glutamine, histidine and tyrosine. The hydrophobic amino acids include alanine, valine, leucine, isoleucine, proline, phenylalanine, tryptophane, cysteine and methionine. The amino acid glycine does not have a side chain and is hard to assign to one of the above classes. However, glycine is often found at the surface of proteins, often within loops, providing high flexibility to these regions. Proline has the opposite effect, providing rigidity to the protein structure by imposing certain torsion angles on the segment of the polypeptide chain. The reason for these effects is discussed in the section on torsion angles. Glycine and proline are often highly conserved within a protein family since they are essential for conservation of a particular protein three-dimensional fold.
Below the 20 most common amino acids in proteins are listed with their three-letter and one-letter codes:
Charged (side chains often make salt bridges):
• Arginine - Arg - R
• Lysine - Lys - K
• Aspartic acid - Asp - D
• Glutamic acid - Glu - E
Polar (usually participate in hydrogen bonds as proton donors or acceptors):
• Glutamine - Gln - Q
• Asparagine - Asn - N
• Histidine - His - H
• Serine - Ser - S
• Threonine - Thr - T
• Tyrosine - Tyr - Y
• Cysteine - Cys - C
• Methionine - Met - M
• Tryptophan - Trp - W
Hydrophobic (normally buried inside the protein core):
• Alanine - Ala - A
• Isoleucine - Ile - I
• Leucine - Leu - L
• Phenylalanine - Phe - F
• Valine - Val - V
• Proline - Pro - P
• Glycine - Gly - G
Most protein molecules have a hydrophobic core, which is not accessible to solvent and a polar surface in contact with the environment (although membrane proteins follow a different pattern). While hydrophobic amino acid residues build up the core, polar and charged amino acids preferentially cover the surface of the molecule and are in contact with solvent due to their ability to form hydrogen bonds. For a hydrogen bond to be formed, two electronegative atoms (for example in the case of an alpha-helix the amide N, and the carbonyl O) have to interact with the same hydrogen. The hydrogen is covalently attached to one of the atoms (called the hydrogen-bond donor), but interacts electrostatically with the other atom (the hydrogen bond acceptor, O). 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. Due to their electronic structure, water molecules may accept 2 hydrogen bonds, and donate 2, thus being simultaneously engaged in a total of 4 hydrogen bonds. Water molecules may also be involved in the stabilization of protein structure by making hydrogen bonds with the main chain and side chain groups in proteins and even linking different protein groups to each other. In addition, water is often found to be involved in ligand binding to proteins, mediating ligand interactions with polar or charged side chain- or main chain atoms. 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. A detailed atlas of hydrogen bonding for all 20 amino acids in protein structures was compiled by Ian McDonald and Janet Thornton.
Positively and negatively charged amino acids often form so called salt bridges. These interactions may be important for the stabilization of the protein three-dimensional structure - for example proteins from thermophilic organisms (organisms that live at elevated temperatures, up 80-90 deg 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.
The preferred location of different amino acids in protein molecules can be characterized by calculating the extent by which an amino acid is buried in the structure or exposed to solvent. Below you can see a figure showing the distribution of the different amino acids within protein molecules:
While hydrophobic amino acids are mostly buried within the core of the structure, a smaller fraction of polar groups are found to be buried. Charged residues are exposed to solvent to a much higher degree.
The vertical axis shows the fraction of highly buried residues, while the horizontal axis shows the amino acid names in one-letter code.
Taken from the tutorial by J.E. Wampler,