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

Bending of the helical axis

Title NMR STRUCTURE OF LAC REPRESSOR HP62-DNA COMPLEX
PDB code 1CJG   (PDB summary)
NDB code 1CJG (NDB atlas)
Duplex length 22 base pairs
Protein Lactose operon repressor, Transcription factor, DNA binding domain: Lac I family

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  0.908  
 Straight line (x-axis) 15.327  
 Arc  2.741 Radius of curvature:  r = 58 Å
 Kinked line  1.309 Kink angle:  alpha = 38°
 Lengths of straight segments:  l1 = 11 bp,  l2 = 11 bp  
 Double kinked line  0.294 Kink angles:  alpha1 = 88°,  alpha2 = 100°  
 Twist angle:  omega = -144°  
 Lengths of straight segments:  l1 = 10 bp,  l2 = 1 bp,  l3 = 11 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.