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

Bending of the helical axis

Title HUMAN TBX3, A TRANSCRIPTION FACTOR RESPONSIBLE FOR ULNAR-MAM SYNDROME, BOUND TO A PALINDROMIC DNA SITE
PDB code 1H6F   (PDB summary)
NDB code PD0311 (NDB atlas)
Duplex length 22 base pairs
Protein TBX3, Transcription Factor, DNA binding domain: Alpha-helix|beta-barrel, DNA binding domain: T-box


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  0.310  
 Straight line (x-axis) 0.922  
 Arc  1.037 Radius of curvature:  r = 797000000 Å
 Kinked line  1.106 Kink angle:  alpha = ill defined
 Lengths of straight segments:  l1 = 22 bp,  l2 = 0 bp  
 Double kinked line  0.366 Kink angles:  alpha1 = 13°,  alpha2 = 14°  
 Twist angle:  omega = -103°  
 Lengths of straight segments:  l1 = 4 bp,  l2 = 14 bp,  l3 = 4 bp