1.   Canonical set of amino acids


1.1. What are amino acids


Living beings are composed of various types of structures, including proteins. Amino acids are part of the proteins in the form of separate units containing side chains. Amino acids links in proteins can be allocated in different ways. On our website link is allocated as follows (Fig. 1):









Fig. 1.
Amino acids link in a protein chain





1.    The link is in the brackets, marked in with red color;

2.    In the middle of the link is Ca - carbon atom, which bonds are in the shape of a tetrahedron;

3.    On the left is an amino-group of the  link (green), on the right - the carbonyl group (containing an oxygen atom in red);

4.    Amino acids side chain is attached to the top of Ca-carbon atom (indicated by the letters Ri The letter ‘i’ can take different numerical values. If the side chains are numbered from 1 to 20, the letter ‘i’ will be from 1 to 20.

5.    The atom of hydrogen (blue color) is also attached to the tetrahedral Ca-carbon atom.


1.1.   How do the side chains of amino acids look?


There are different classifications of the side chains of amino acids. We will present a classification of the side chains, which are often found in textbooks. This systematization divides the side chains of amino acids into three groups:

1. Nonpolar

2. Weakly polar and polar

3. Cyclic

Nonpolar side chains

Nonpolar side chains do not contain polar groups and do not form hydrogen bonds

This group includes:

Glycine  (Gly),

Alanine  (Ala),

Valine  (Val),

Isoleucine (Ile),

Leucine  (Leu).

Glycine has no side chain. Alanine has the shortest side chain, leucine has the longest one.








Weakly polar and polar side chains

Typically, the side chains of this group form hydrogen bonds. These bonds arise between two atoms through atom of hydrogen, and are written as: XH ... Y.


Hydrogen bonds are proton donor when a hydrogen atom attached to atom X and the proton acceptor, when an atom, which forms a hydrogen bond (Y), has no hydrogen atom.


Proton donor hydrogen bonds form groups: COH of serine and threonine, O=COH - of aspartic acid and glutamic acids, O=CNH2- of asparagine and glutamine, CNH2 - lysine, HN= CNH2 - of arginine,  C–SH - of cysteine.


Proton acceptor hydrogen bonds are formed with atoms O of the amino acids serine, threonine, aspartic acid, glutamic acid, glutamine and aspragina, as well as the S atom of methionine.

Weakly polar side chains concern:
Serine (Ser) and
Threonine (Thr),
which contain the C-OH group, as well as
Cysteine ​​( Cys), which has a group 


Polar are the following:
side chain

Aspartic acid (Asp) and Glutamic acid (Glu), containing O=COH group, as well as
Arginine (Arg),
with the guanidine group (group N= C
NH) and
Lysine (Lys) with the amino group (C


Neutral, forming H-bonds are:
asparagine (Asn),

Glutamine (Gln), with group O=CNH2, and

methionine (Met), containing a sulfur atom (group CS)




Aspartic acid

Glutamic acid









Cyclic side chains

All cyclic amino acids, except proline, form hydrogen bonds. Phenylalanine forms a  weak hydrogen bonds at the expense of CH groups, which are highlighted in pink in a molecule.

Cyclic side chains:

Proline (Pro), its 5-membered ring is included in the main chain of the protein;

Histidine (His), Tryptophane (Trp),
they all have a 5-membered ring,

Phenylalanine (Phe), Tyrosine (Tyr), contain 6-membered ring








Knowing the structure of the side chains of amino acids will help you in understanding the principles of constructing a model of the spatial structure of the canonical set of amino acids. If you need to remember one or another amino acid, one can look at this section.

The next stage of our work was to build on the dodecahedron model of the structure of twenty formal elements. The model described in Section 2.


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