Contact matrices

Keyboard is a contact matrix of dimension 3x4. In order to handle it, the principle of scanning buttons at running zero on input lines is used in SC EDC. 

Fig. 1.6 Residue-residue contact matrix for predicted 3 D structure of 3c2c (blue and green lines). The constant part Ac is shown in red, the noncontact matrix An is shown in green, and predicted variable contacts Ax are shown in blue. Numbers correspond to the predicted loops.

Due to a combination of the modified technique for sensor analysis of composite gas mixture with unique properties of the gas-sensitive point-contact matrix, a complex dynamic of interaction between sensitive matter and volatile compounds of exhaled air has been observed. This interaction is characterized by longer adsorption times. This behavior was not observed in our previous work on breath analysis where fihn samples were used [11]. 

The contact matrix mimics side chain interactions covalently linked amino acids are not considered to be in contact. Despite the clear similarity to the spin-glass representation, several important difference exist. In spin glasses, the contacts between residues are taken as either... 

The system of intraglobular residue-residue contacts of a protein of N residues may be represented as an N x N matrix of the carbon-alphas, whose elements are ones (contact) or zeros (lack of contact). Any reasonable definition of contact provides ones in the positions (i, i + l)that correspond to a peptide bond between two adjacent residues in the sequence. The same is true for the residues corresponding to the pair of cysteines forming a disulfide bond (these data may not be available as input and may be used as a test of correct prediction). This set of contacts describes the sequential covalent topology and is a constant part of the contact matrix which does not depend on the spatial structure of the polypeptide chain however, any additional information on existing intraglobular contacts (e.g., from NMR data or disulfide linkage) can easily be introduced in the constant part of the contact matrix A ... 

This is simple, but we have to explain the notations. First, i and j label monomers along the chain, from 1 to N. Second, sequence is described in terms of A i) (or A j)) chemical name of aminoacid for each position along the chain. Third, and final, Cij is the so-called contact matrix, it is simply 1 if i is in contact with j and it is zero otherwise. Thus, formula (10.1)... 

It appears that protein conformations are also like that, they can be viewed as nodes of a scale-free network. What plays the role of bonds in this network, or handshakes between conformations The answer would appear natural if the reader remembers the protein conformation contact matrix — we discussed it around formula (10.1) in Section 10.5. Indeed, the distance between two conformations can be characterized by the number of permutations by which the contact matrix of one conformation is transformed into the other. Then, two conformations are declared neighbors , and are connected by a bond ( handshake ), if the distance between them is smaller than a certain threshold (and the results appear rather insensitive to the specific value of this threshold, within reasonable limits). With such definition, the network of protein conformations turns out to be scale-free. Obviously, this fact must be somehow the result of evolution. But how did it happen in evolution And what does it lead to Those are all topics of active current research. 

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