2.2.   Analysis of the action vectors in the area of bond  N_iH….O_i-4=C

 

Recall that in the framework of model of topological encoding of proteins the side chains of amino acids are considered as physical operators (http://genetic-code.narod.ru/operators.htm): connectivity operators (amino acids capable of forming H-bonds), contributing to the formation of bonds N_iH….O_i-4=C and anti-connectivity operators (mostly do not form H-bonds), preventing the formation of this bond. Let's consider possible directions, in which physical operators influence on this bond, (Fig. 5, а-в), naming these directions as vectors of action or simply as vectors, and designating by arrows.

 

 

 Within the plane I (Fig. 5, a) two variants of the vectors of action on the bond N_iH….O_i-4=C  are possible - along this bond, and perpendicular to it. Under the action in the direction along the bond N_iH….O_i-4=C  may be two vectors:

- vector directed towards group N_iH (yellow arrow upwards), will contribute to preserve the hydrogen bond;

- symmetrical vector directed towards group  O_i-4=C (yellow arrow downwards) aims to break the hydrogen bond.

In the case of action of vector perpendicular to the bond N_iH….O_i-4=C  both vectors (green arrows) are oriented in opposite directions (symmetric) and aim to break the hydrogen bond.

 

The entered planes I - III can serve as planes of symmetry in relation to which action of physical operators can be considered. For example, if the vector of action is directed along the planes I and II, then, due to symmetry, appears a series of 8 vectors directed along these planes (Fig. 5, b, red arrows).

    

Similarly, if the vectors are directed along the planes II and III, then appears another series of 8 vectors directed along the planes II and III (Fig. 5, c, blue arrows).

 

 Thus, totally in Figures 5, а-c 20 directions of action of physical operators (20 vectors) that corresponds to total number of amino acid side chains in the canonical set (http://amino-acids-20.narod.ru ) are allocated. However, as side chains of amino acids have the real physical sizes, the direction of their action cannot be any. Presumably, they should fit in whatever geometric figure. Section 2.3 is devoted to this question.

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