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

Bending of the helical axis

Title 5'-R(*GP*AP*UP*CP*AP*CP*UP*UP*CP*GP*GP*U)-3'
PDB code 422D   (PDB summary)
NDB code AR0007 (NDB atlas)
Duplex length 8 base pairs

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  0.039  
 Straight line (x-axis) 6.111  
 Arc  2.287 Radius of curvature:  r = 14 Å
 Kinked line  1.338 Kink angle:  alpha = 53°
 Lengths of straight segments:  l1 = 4 bp,  l2 = 4 bp