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Rather than allow flexibility in the surface side-chains and/or backbones of the two proteins, ZDOCK uses searches that permit the proteins to interact only as rigid-bodies [99].
As we can see from the figure, the backbones of the two structures are almost the same as expected because the sequences of the two proteins are highly homologous.
These changes are mapped onto the backbones of the two zinc finger structures in Figure 8C.
The ribose-phosphate backbones of the two proposed duplicated segments map onto each other extremely closely.
The backbones of the two EcO145 chromosomes exhibit overall genomic synteny, with the exception of three major inversions.
The backbones of the two plasmids encoding the tra region and replication functions are nearly identical in gene compliment and with a GC content (64.1 66.1%) characteristic of pseudomonads.
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There are five molecules in each asymmetric unit; overall alignment of the backbones of the five molecules is shown in Supplementary Figure S1(A) at http://www.biochemj.org/bj/450/bj4500085add.htm.htm
The backbones of the seven CP subunits in the asymmetric unit, including their C-terminal extensions, are nearly identical, with an RMSD of 0.4 0.66 Å when superimposed.
The fit function of Molmol was used to align the backbones of the eight SH3 domains using 6 residues in the β1 sheet, 4 residues in the 3-10 helix and 6 residues in the β4 sheet [ 33].
The distance between the backbones of these two loops was the same for NTD and CTD though the composing residues are not conserved in their primary sequences.
The bending of DNA over the protein surface brings the phosphate backbone of the two strands closer together on the inside of the spiral, narrowing the major and minor grooves of DNA, while widening the grooves on the outside.
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