[JenaLib Home] [Helix analysis Home] [JenaLib Entry] [Sequence, Chains, Units] [Helix analysis Entry] [Bending Classification]

Bending of the helical axis

Title		`TESTING THE WATER-MEDIATED HIN RECOMBINASE DNA RECOGNITION BY SYSTEMATIC MUTATIONS.`
PDB code		`1IJW (PDB summary)`
NDB code		`PD0213 (NDB atlas)`
Duplex length		`11 base pairs`
Protein		`Hin Recombinase, Recombinase, DNA binding domain: Alpha-helix, DNA binding domain: Helix-turn-helix`

Table 1. Bending parameters determined with the program ARC_FIT.
The curvilinear helical axis is calculated with CURVES, and bending of this axis is analysed with ARC_FIT. This program allows to fit a straight line, a plane, an arc, a kinked line, and a double kinked line to the helical axis. Good fits are indicated by low values of sigma². An arc is fitted if there are at least 7 bp. A kinked line requires at least 8 bp, and the double kinked line requires at least 13 bp. The geometrical parameters are given for all models fitted, but they characterize the shape of the helical axis only if the fit is good. See Help for further explanations.

Model	sigma² / Å²	Geometrical parameters
Plane	0.067
Straight line (x-axis)	0.534
Arc	0.225	Radius of curvature: r = 97 Å
Kinked line	0.208	Kink angle: alpha = 13° Lengths of straight segments: l₁ = 4 bp, l₂ = 7 bp

The length of the central segments of the double kinked line is 1 bp. Segments 1 and 3 should be interpreted as two warped lines. See Help for further explanations.