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The 20 Amino Acids Cheat Sheet by

The 20 Amino Acids and Their Role in Protein Structures
structure     chemistry     protein     role     amino     acids

Introd­uction

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

The hydrop­hobic amino acids include alanine, valine, leucine, isoleu­cine, proline, phenyl­ala­nine, trypto­phane, cysteine and methio­nine. You probably noticed that this classi­fic­ation is based on the type of the amino acid side chain. However, glycine, being one of the common amino acids, does not have a side chain and for this reason it is not straig­htf­orward to assign it to one of the above classes.

Generally, glycine is often found at the surface of proteins, within loop- or coil (without secondary structure) regions, providing high flexib­ility to the polype­ptide chain at these locations. This suggests that it is rather hydrop­hilic. Proline, on the other hand, is generally non-polar and is mostly found buried inside the protein, although similarly to glycine, it is often found in loop regions. In contrast to glycine, proline provides rigidity to the polype­ptide chain by imposing certain torsion angles on the segment of the structure. The reason for this is discussed in the section on torsion angles. Glycine and proline are often highly conserved within a protein family since they are essential for the conser­vation of a particular protein fold.

Charged

Arginine
Arg
R
Lysine
Lys
K
Aspartic acid
Asp
D
Glutamic acid
Glu
E
Side chains often make Salt bridges

Polar

Glutamine
Gln
Q
Asparagine
Asn
N
Histidine
His
H
Serine
Ser
S
Threonine
Thr
T
Tyrosine
Tyr
Y
Cysteine
Cys
C
Tryptophan
Trp
W
Usually partic­ipate in hydrogen bonds as proton donors or acceptors)
 

Periodic Chart of Amino Acids

Hydrop­hobic

Alanine
Ala
A
Isoleucine
Ile
I
Leucine
Leu
L
Methionine
Met
M
Phenyl­alanine
Phe
F
Valine
Val
V
Proline
Pro
P
Glycine
Gly
G
Normally buried inside the protein core.

Most protein molecules have a hydrop­hobic core

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

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