JenaLib Home    
[JenaLib Home]     [Helix Analysis Home]     [Image Library Entry]     [Sequence, Chains, Units]     [Bending Analysis Entry]     [Bending Classification]   

Analysis of nucleic acid double helix geometry

Title 3D SOLUTION NMR STRUCTURE OF THE M9I MUTANT OF THE HMG-BOX DOMAIN OF THE HUMAN MALE SEX DETERMINING FACTOR SRY COMPLEXED TO DNA
PDB code 1J47   (PDB summary)
NDB code 1J47 (NDB atlas)
Duplex length 14 base pairs
Protein Human male sex-determining factor SRY, hSRY(HMG), Transcription Factor, DNA binding domain: High mobility group

Only the nucleic acid double helix part of the structure is analysed here. Small ligands, proteins, and overhanging ends are not taken into account. Information on the complete structure is available at the Image Library Entry page and at the Sequence, Chains, Units page.

Strand 1    5' C101 C102 T103 G104 C105 A106 C107 A108 A109 A110 C111 A112 C113 C114 3'
Strand 2    3' G128 G127 A126 C125 G124 T123 G122 T121 T120 T119 G118 T117 G116 G115 5'

Side view 1 Top view
Side view 1 Top view
Side view 2 3-dimensional interactive models
(Help)
  

RASMOL, CHIME, VRML 2.0, PDB

Side view 2  

Figure 1   Three orthogonal views of the double helix (Help). Residues are colored according to the nucleotide type (Help: Color codes). The curvilinear helical axis (green) was calculated with CURVES. The double helix is oriented with respect to the principle axis of inertia of the curvilinear helical axis (see Help for further explanations). This drawing reveals immediately if there is any bending of the helical axis.


Analysis of helical axis bending


Inter base pair parameters

The six inter base pair parameters (rise, shift, slide, twist, roll, tilt) describe the translational and rotational displacement between neighbouring base pairs. See Help for further explanations.

Plot of inter base pair parameters with respect to global and local helical axes:  PDF,   GIF
(Global parameters from CURVES,  local parameters from CURVES and FREEHELIX)

Table 1.  Inter base pair parameters with respect to the global helical axis, calculated with CURVES.


  Strand 1      Strand 2        riseg          shiftg          slideg          twistg         rollg         tiltg    
    / Å / Å / Å      

C101 G128            
    3.6 -0.1 0.0 34°
C102 G127            
    3.6 -0.1 -0.0 34° -0° -1°
T103 A126            
    3.2 0.1 0.1 37° -7°
G104 C125            
    3.7 -0.1 0.1 34° -3° -1°
C105 G124            
    3.9 -0.0 0.2 36° -2°
A106 T123            
    3.6 0.2 -0.4 30° -4°
C107 G122            
    3.8 -0.3 0.1 40° -4°
A108 T121            
    3.2 0.0 0.3 25° -5°
A109 T120            
    3.9 0.1 -0.1 30° -2°
A110 T119            
    4.6 -0.1 -0.8 28° 12°
C111 G118            
    3.4 -0.3 0.8 38° -3°
A112 T117            
    3.4 0.1 -0.5 35° -1°
C113 G116            
    3.6 0.1 -0.1 36° -0°
C114 G115            


Backbone parameters

Table 2.  Selected torsional angles and sugar pucker phase angles describing the conformation of the sugar phosphate backbone. (See Help for further explanations.)


 gamma     epsilon-zeta       pucker        chi      Strand 1     Strand 2      chi        pucker       epsilon-zeta     gamma 

    C2'-endo -110° C101 G128 -98° C2'-endo    
 51°   -83° (BI)             -76° (BI)   49° 
    C2'-endo -107° C102 G127 -102° C2'-endo    
 49°   -80° (BI)             -79° (BI)   49° 
    C2'-endo -107° T103 A126 -103° C2'-endo    
 50°   -77° (BI)             -75° (BI)   53° 
    C1'-exo -100° G104 C125 -108° C2'-endo    
 54°   -74° (BI)             -73° (BI)   50° 
    C2'-endo -110° C105 G124 -106° C2'-endo    
 54°   -78° (BI)             -77° (BI)   49° 
    C2'-endo -101° A106 T123 -105° C1'-exo    
 45°   -81° (BI)             -78° (BI)   53° 
    C1'-exo -104° C107 G122 -107° C2'-endo    
 54°   -53° (BI)             -80° (BI)   60° 
    C3'-endo -145° A108 T121 -105° C2'-endo    
 54°   -74° (BI)             -75° (BI)   56° 
    C2'-endo -104° A109 T120 -148° C3'-endo    
 48°   -68° (BI)             -77° (BI)   57° 
    C2'-endo -106° A110 T119 -149° C4'-exo    
 50°   -72° (BI)             -72° (BI)   44° 
    C1'-exo -109° C111 G118 -95° C2'-endo    
 56°   -56° (BI)             -74° (BI)   52° 
    C2'-endo -100° A112 T117 -107° C2'-endo    
 49°   -84° (BI)             -83° (BI)   52° 
    C1'-exo -108° C113 G116 -106° C2'-endo    
 48°   -73° (BI)             -82° (BI)   56° 
    C1'-exo -108° C114 G115 -106° C3'-exo    


Groove width

Plot of minor groove width:   PDF,   GIF
Plot of major groove width:   PDF,   GIF
(See Help for further explanations.)

Further information

Full output from CURVES  (helical parameters with respect to global and local axes)

Full output from FREEHELIX  (helical parameters with respect to local axis, angles between normal vectors)

Chirality of ribose and phosphate atoms
Check the naming of phosphate and ribose substituents. Recommended for phosphate oxygens and for ribose hydrogens in NMR structures.


Go to    [JenaLib Home]    [Helix Analysis Home]    [Image Library Entry]    [Sequence, Chains, Units]    [Bending Analysis Entry]    [Bending Classification]   

Perl script:    helixparameter.pl  (15 Sep 2016)
Author:    Peter Slickers  (slickers@leibniz-fli.de),  IMB Jena,  Germany