The 20 Amino Acids and Their Role in Protein Structures

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. These two residues are often highly conserved in protein families since they are essential for preserving 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:
• Arginine - Arg - R
• Lysine - Lys - K
• Aspartic acid - Asp - D
• Glutamic acid - Glu - E

Polar (may participate in hydrogen bonds):
• 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 (by donating or accepting a proton from an electronegative atom). Very often they also interact with each other: positively and negatively charged amino acids form so called salt bridges, while polar amino acid side chains may form side chain-side chain or side chains-main chain hydrogen bonds (with polar amide carbonyl groups). It has been observed that all polar groups capable of forming hydrogen bonds in proteins do form such bonds. And since these interactions are often crucial for the stabilization of the protein three-dimensional structure, they are normally conserved. A detailed atlas of hydrogen bonding for all 20 amino acids in protein structures was compiled by Ian McDonald and Janet Thornton and can be found here. Below you can see a figure showing the distribution of the different amino acids within protein molecules.

buried2

The figure demonstrates that while a high fraction of the hydrophobic amino acids are buried within the core of the structure, this number gradually decreases for amino acids with polar groups and reaches a minimum for charged residues (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,

In the next chapter I will go through the basics of protein structure hierarchy starting with the torsion angles.

Basics of Protein Structure