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Bending of the helical axis

Title		`THE COMPLEX BETWEEN PHAGE 434 REPRESSION DNA-BINDING DOMAIN AND OPERATOR SITE OR3: STRUCTURAL DIFFERENCES BETWEEN CONSENSUS AND NON-CONSENSUS HALF-SITES`
PDB code		`1PER (PDB summary)`
NDB code		`PDR015 (NDB atlas)`
Duplex length		`19 base pairs`
Protein		`Phage 434 repressor, Transcription factor, DNA binding domain: Prokaryotic 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	0.401
Straight line (x-axis)	5.050
Arc	0.612	Radius of curvature: r = 77 Å
Kinked line	0.981	Kink angle: alpha = 24° Lengths of straight segments: l₁ = 8 bp, l₂ = 11 bp
Double kinked line	0.188	Kink angles: alpha₁ = 22°, alpha₂ = 19° Twist angle: omega = -58° Lengths of straight segments: l₁ = 6 bp, l₂ = 8 bp, l₃ = 5 bp