4.2. The side chains of amino acids as the physical operators

 

In this section in the presented tables all 20 amino acids of proteins will be considered as physical operators. Practically nobody was able to show so far work of amino acids in a role of operators of anti-connectivity experimentally. Therefore our pictures devoted to operators of anti-connectivity, generally, are assumptions. However they take into account both structural features of the given group of amino acids, and their sizes.

 

OPERATORS OF ANTI-CONNECTIVITY

 

 

 

 

 

 

Proline is the imino acid (nitrogen atom is in five-membered cycle) and in principle cannot form a hydrogen bond with the Oi-4=C.

 

Occupies the first line of block С.

 

 

 

 

 

 

 

 

 

Alanine has a very short side chain, which can shield the nitrogen atom, thereby preventing the formation of a hydrogen bond with the Oi-4=C.

 

Located on the second line of the block С.

 

 

 

 

 

Serine and threonine, as observed in the structures of the studied proteins, often forming a hydrogen bond with the Oi-3=C. In this case, a 4-link cycle does not occur.

They occupy the 3rd and 4th lines in the block С.

 

 

 

 

 

 

 

 

Leucine and valine - are close analogues. Methyl groups of side chains can block the bond NiH...Oi-4=C.

 

They are in 1st and 2nd lines of block U.

 

 

 

 

 

 

 

 

Phenylalanine and isoleucine are also analogues of leucine and valine. Their side chains may also block the bond NiH...Oi-4=C.

 

They are located in 3 and 4th lines of block U.

 

 

 

 

 

 

 

 

Methionine is a sulfur-containing amino acid and by its action is probably similar to isoleucine.

 

Located in the fourth line of the block U.

 

 

 

Thus, all amino acids located in blocks C and U, in principle are capable to recreate opened conformation of the protein pentafragments and are suitable for performance of functions of operators of anti-connectivity.

 

 

The group of the amino acids, capable to carry out function of operators of connectivity, is presented on the basis of the analysis of protein structures studied by X-ray analysis. Their existence is the real fact. Pay attention, how in process of increase in length of the side chain the slope of the hydrogen bonds changes.

 

OPERATORS OF CONNECTIVITY

 

 

 

 

 

 

 

 

 

 

 

Glycine has no side chain, and readily forms a 4-link cycle - Gly1.

 Because of easy mobility of HNi+1-C=O-group it often forms a hydrogen bond Ni+1H...Oi-4=C,  which works as an operator of connectivity (Gly2).

 

Located in block G.

 

 

 

 

 

 

 

 

 

The side chains of serine and threonine form hydrogen bonds with the Oi-4=C and may contribute to formation of a 4-link cycle.

 

Two serine belong to the triplets of block G,, and threonine is in block C on the border with the block G,.

 

 

 

 

 

 

 

 

 

 

Cysteine ​​is a sulfur-containing analog of serine. His side chain can participate in the formation of a 4- link cycle.

 

Located in the third line of block G.

 

 

The side chains of aspartic acid and asparagine are structurally similar. They form hydrogen bonds with the        Oi-4=C

 

Located in block A.

 

 

 

 

The side chains of histidine and tryptophan contain heterocycles. Despite the rare occurrence, both of them form hydrogen bonds with the Oi-4=C.

 

Located, respectively, in blocks A and G.

 

 

 

 

 

Glutamic acid and glutamine are structural analogs of aspartic acid and asparagine. They are also often involved in the formation of hydrogen bonds with the с Oi-4=C.

 

Located in block A.

 

 

 

The side chains of arginine and lysine are close  both by the structural and physical properties. Despite the large size, form hydrogen bonds with the Oi-4=C.

 

Located, respectively, in blocks of G and A.

 

 

 

 

 

 

 

 

 

Tyrosine has the longest side chain. Analysis of over 300 protein structures did not reveal  4-link cycles with the simultaneous formation of a hydrogen bond of its side chain to the main chain. It was usually found out, that in the formation of a hydrogen bond of the side chain with Oi-4=C hydrogen bond NiH...Oi-4=C was broken.

 

It is located in block A.

 

 

 

 

Thus, practically all the amino acids can apply for a role of operators of connectivity, are in blocks G and A.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

The result of our analysis of the side chains of amino acids as physical operators summarized in section 4.3. in section 4.3.

 

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