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

Bending of the helical axis

Title		`COMPLEX OF THE DNA BINDING CORE DOMAIN OF THE TRANSCRIPTION FACTOR MEF2A WITH A 20MER OLIGONUCLEOTIDE`
PDB code		`1C7U (PDB summary)`
NDB code		`1C7U (NDB atlas)`
Duplex length		`20 base pairs`
Protein		`MEF2A, Transcription factor, DNA binding domain: MADS box`

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	2.430
Straight line (x-axis)	5.503
Arc	3.026	Radius of curvature: r = 137 Å
Kinked line	3.409	Kink angle: alpha = 16° Lengths of straight segments: l₁ = 9 bp, l₂ = 11 bp
Double kinked line	0.524	Kink angles: alpha₁ = 27°, alpha₂ = 27° Twist angle: omega = 118° Lengths of straight segments: l₁ = 5 bp, l₂ = 10 bp, l₃ = 5 bp