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Bending of the helical axis

Title STRUCTURE OF TRANSCRIPTION FACTOR GENESIS/DNA COMPLEX
PDB code 2HDC   (PDB summary)
NDB code 2HDC (NDB atlas)
Duplex length 17 base pairs
Protein Hepatocyte nuclear factor-3 forkhead homolog 2 (HFH-2), Transcription factor, DNA binding domain: Helix-turn-helix, winged 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  0.023  
 Straight line (x-axis) 0.083  
 Arc  0.075 Radius of curvature:  r = 1010 Å
 Kinked line  0.070 Kink angle:  alpha = 2°
 Lengths of straight segments:  l1 = 8 bp,  l2 = 8 bp  
 Double kinked line  0.041 Kink angles:  alpha1 = 91°,  alpha2 = 91°  
 Twist angle:  omega = -179°  
 Lengths of straight segments:  l1 = 11 bp,  l2 = 1 bp,  l3 = 5 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.