Interresidue contacts

Fig. 2. Examples of protein conformations for maximally compact, two-dimensional (top), and three-dimensional (bottom) lattices. The balls and solid lines represent residues and covalent bonds, respectively. The dotted lines are the interresidue contacts captured by the matrix AtJ.

Interresidue Contact Energies From Protein Crystal Structures Quasi-Chemical Approximation. 

S. Miyazawa, R. Jernigan (1985) Estimation of effective interresidue contact energies from protein crystal-structures - quasi-chemical approximation. Macromolecules 18, p. 534... 

Normality indices for structures, on the other hand, already have proven their power in structure verification. Many characteristics of protein structures lend themselves to normality analysis. Most of them are directly or indirectly based on the analysis of contacts, either interresidue contacts or contacts with water. Some published examples are ... 

Most lattice methods rely on an extremely simple potential function, either a two state interresidue contact energy corresponding to native/nonnative contacts, or a three state model, corresponding to hydrophobic-hydrophobic, hydrophilic-hydrophilic, and hydrophobic-hydrophilic interactions. The interaction of the twenty naturally-occurring amino acids in real proteins are obviously more complex. 

S. Miyazawa and R. L. Jernigan, Macromolecules, 18, 534 (1985), Estimation of Effective Interresidue Contact Energies from Protein Crystal Structures Quasi-Chemical Approximation. 

One simplification of the problem of predicting interresidue contacts focuses on predicting the contacts between residues in adjacent strands (Figure 1). Such an attempt is motivated by the hope that such interactions are more specific than are sequence-distant (long-range) contacts in general, and hence are easier to predict. 

The overall approach to determining the structure of a protein is to use computational power to take into account concurrently (1) the known sequence of the amino acids in the protein (2) the known molecular structure of each of those amino acid residues, including bond distances and angles (3) the known planar structure of the peptide group (4) internuclear distances and interresidue bond angles, as determined from NMR data (5) correlations of chemical shifts and structural features and (6) minimization of energy and avoidance of unreasonable atomic contacts. There are a number of ways to handle the computations and to derive the molecular structure, but all of them depend critically on the data supplied by NMR. 

In the spectra at low mixing time (80 ms) as well as in the frame of the signal-to-noise ratio, which was attainable with the existing equipment and the available sample concentrations, only those cross peaks were found that are particularly strong for A-RNA helices, as 2 -ribose-aromatic interresidue cross peaks, beyond the contacts which always give rise to intense cross peaks independent of helix type (T-2 -ribose NOEs, 5-6 pyrimidine contacts). From these results, a regular hehcal structure was deduced. 

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