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

Bending of the helical axis

PDB code 1GTW   (PDB summary)
Duplex length 15 base pairs
Protein C/EBPBETA BZIP, Transcription Factor, DNA binding domain: Alpha-helix, DNA binding domain: Leucine zipper

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  0.075  
 Straight line (x-axis) 0.683  
 Arc  0.341 Radius of curvature:  r = 158 Å
 Kinked line  0.199 Kink angle:  alpha = 12°
 Lengths of straight segments:  l1 = 10 bp,  l2 = 5 bp  
 Double kinked line  0.212 Kink angles:  alpha1 = 8°,  alpha2 = 16°  
 Twist angle:  omega = 164°  
 Lengths of straight segments:  l1 = 5 bp,  l2 = 4 bp,  l3 = 6 bp