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Bending of the helical axis

Title CRYSTAL STRUCTURE OF MAD-MAX RECOGNIZING DNA
PDB code 1NLW   (PDB summary)
NDB code PD0387 (NDB atlas)
Duplex length 18 base pairs
Protein MAD-MAX, Transcription Factor, DNA binding domain: Alpha-helix, DNA binding domain: Basic helix-loop-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  0.061  
 Straight line (x-axis) 0.755  
 Arc  0.170 Radius of curvature:  r = 183 Å
 Kinked line  0.185 Kink angle:  alpha = 10°
 Lengths of straight segments:  l1 = 7 bp,  l2 = 11 bp  
 Double kinked line  0.153 Kink angles:  alpha1 = 9°,  alpha2 = 6°  
 Twist angle:  omega = -1°  
 Lengths of straight segments:  l1 = 4 bp,  l2 = 6 bp,  l3 = 8 bp