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

Bending of the helical axis

Title CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO GROOVE BINDING BY ALPHA HELICES
PDB code 2PUA   (PDB summary)
NDB code PDR040 (NDB atlas)
Duplex length 16 base pairs
Protein Purine 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  0.350  
 Straight line (x-axis) 10.679  
 Arc  1.425 Radius of curvature:  r = 41 Å
 Kinked line  0.561 Kink angle:  alpha = 42°
 Lengths of straight segments:  l1 = 8 bp,  l2 = 8 bp  
 Double kinked line  0.586 Kink angles:  alpha1 = 109°,  alpha2 = 73°  
 Twist angle:  omega = -159°  
 Lengths of straight segments:  l1 = 8 bp,  l2 = 1 bp,  l3 = 7 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.