Contact map

The isolated 5 helices were free of any objectionable contacts. Since there is no special relationship between two chains in the 5-fold double helix, the relative orientation parameters, Ay and AW, were obtained from the contacts map for each conformation. For both 5, and 5, double helices, conformations without fatal short contacts could be constructed. These double helices were subjected to a packing analysis in the... 

Milik et al. (1995) developed a neural network system to evaluate side-chain packing in protein structures. Instead of using protein sequence as input to the neural network as in most other studies, protein structure represented by a side-chain-side-chain contact map was used. Contact maps of globular protein structures in the Protein Data Bank were scanned using 7x7 windows, and converted to 49 binary numbers for the neural network input. One output unit was used to determine whether the contact pattern is popular in... 

L. Mirny, E. Domany. Protein fold recognition and dynamics in the space of contact maps. Proteins. 1996, 26, 391-410. 

Computational proteomics refers to the large-scale generation and analysis of 3D protein structural information. Accurate prediction of protein contact maps is the beginning and essential step for computational proteomics. The major resource for computational proteomics is the currently available information on protein and nucleic acid structures. The 3D-GENOM1CS (www.sbg.bio.ic.au.uk/3dgenomics/) and PDB (http // www.rcsb.org/pdb/), and other databases provide a broad range of structural and functional annotations for proteins from sequenced genomes and protein 3D structures, which make a solid foundation for computational proteomics. 

FIGURE 1 4 (See color insert following page 172.) Native contact maps for kinesin dimer (left) and the interface between the kinesin and tubulin binding site (right). The neck-linker zipper contacts that play several important roles for the kinesin function are enclosed in the circles (the green circles for the MT-bound head, and the yellow circles for the tethered head). 

The information contained in the matrix d can be displayed in contact maps. Several alternatives have been proposed with applications in structural analysis and pattern recognition. For instance, the maps can be displayed as contour levels of distance d,y, where the indices i and / (1 i,j n) are the axes of a 2D diagram. 

Usually, the contact maps are displayed in its simplest form, where a point is indicated whenever i and j have a contact. This information can be stored in a family of integer contact matrices (8), defined in terms of a scalar 8. The parameter 8 is the distance cutoff so = 1, if 8 (a contact ) and %i = 0, if dij > 8 (no contact). 

Anisometry. Characterized by properties depending on inertia axes, symmetry axes, and distance distributions. Descriptors include the moments of inertia X,, the molecular eccentricity e, the asphericity fl, and the length of the principal axes of minimal ellipsoidal cavities, as well as distance matrices, contact maps, and some graph-theoretical indices. 

Fig. 3 Left Top view of an LHCII trimer (colors according to chain or molecule type blue chain A, red chain B, green chain C, cyan Chlh, pink Chla). Middle and right Contact maps between Chi pigments and protein residues of LHCn trimer drawn as distance maps between the Ca atrans of the proteins (y-axis) and the Mg atcnns of all Chi pigments (x-axis) within a 2.5 nm cut-off fw atomistic (AA) simulations of 70 ns (middle) and coarse-grained (CG) simulations of 100 ns (right). The maps show that the pigments are stably located in their binding sites for both levels of resolution...

In the first stage, the two protein structures to be compared are divided into overlapping hexapeptides. A contact map, which contains all internal distances, is generated for each hexapeptide. Although residues in the proteins... 

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