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Bending of the helical axis

Title CATABOLITE GENE ACTIVATOR PROTEIN/DNA COMPLEX, ADENOSINE-3', 5'-CYCLIC-MONOPHOSPHATE
PDB code 2CGP   (PDB summary)
NDB code PDT049 (NDB atlas)
Duplex length 26 base pairs
Protein Catabolite gene activator protein (CAP), Transcription factor, DNA binding domain: CAP


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  1.417  
 Straight line (x-axis) 31.752  
 Arc  2.099 Radius of curvature:  r = 54 Å
 Kinked line  5.579 Kink angle:  alpha = 47°
 Lengths of straight segments:  l1 = 13 bp,  l2 = 13 bp  
 Double kinked line  0.153 Kink angles:  alpha1 = 37°,  alpha2 = 37°  
 Twist angle:  omega = -44°  
 Lengths of straight segments:  l1 = 8 bp,  l2 = 10 bp,  l3 = 8 bp