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Analysis of nucleic acid double helix geometry

Title INTEGRATION HOST FACTOR/DNA COMPLEX
PDB code 1IHF   (PDB summary)
NDB code PDT040 (NDB atlas)
Duplex length 34 base pairs
Protein Integration host factor, DNA packing/chromatin

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' G-49 G-48 T-47 G-46 C-45 A-44 A-43 C-42 A-41 A-40 A-39 T-38 T-37 G-36 A-35 T-34 A-33 A-32 G-31 C-30 A-29 A-28 T-27 G-26 C-25 T-24 T-23 T-22 T-21 T-20 T-19 G-18 G-17 C-16 3'
Strand 2    3' C49 C48 A47 C46 G45 T44 T43 G42 T41 T40 T39 A38 A37 C36 T35 A34 T33 T32 C31 G30 T29 T28 A27 C26 G25 A24 A23 A22 A21 A20 A19 C18 C17 G16 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      
G-49 C49            
    3.7 -0.6 -0.3 38° 2° 2°
G-48 C48            
    3.3 0.4 -0.9 30° 1° 5°
T-47 A47            
    3.3 0.4 0.8 40° -12° 4°
G-46 C46            
    3.0 -0.5 -0.5 28° 4° -1°
C-45 G45            
    3.6 -0.0 1.5 48° -18° -0°
A-44 T44            
    3.1 0.0 -0.4 33° -3° -10°
A-43 T43            
    3.7 -0.2 -0.9 35° -1° -9°
C-42 G42            
    3.5 0.0 -0.1 36° 15° 3°
A-41 T41            
    3.2 -0.3 -0.2 30° 5° -3°
A-40 T40            
    3.0 0.1 -0.2 29° 4° -1°
A-39 T39            
    2.9 -0.4 -0.5 28° 9° 2°
T-38 A38            
    7.1 0.3 -0.4 26° 57° 6°
T-37 A37            
    3.4 0.5 0.5 31° 0° 9°
G-36 C36            
    2.7 -0.9 0.9 35° -8° -7°
A-35 T35            
    3.5 0.4 -0.6 32° -5° 3°
T-34 A34            
    3.2 -0.1 -0.3 39° -6° 5°
A-33 T33            
    3.5 0.2 -0.2 33° -3° 8°
A-32 T32            
    3.6 0.4 -0.3 35° 3° 10°
G-31 C31            
    3.1 0.9 -0.6 31° -6° 11°
C-30 G30            
    4.3 -1.5 -1.1 -36° -35° 75°
A-29 T29            
    6.5 0.3 3.0 32° -16° -27°
A-28 T28            
    3.1 -1.0 -0.4 15° 75° 22°
T-27 A27            
    3.7 -0.3 -0.2 36° 176° 11°
G-26 C26            
    3.4 0.2 0.4 33° -5° -369°
C-25 G25            
    3.6 -0.3 -0.1 38° -7° 535°
T-24 A24            
    3.3 -0.2 0.2 33° -6° -183°
T-23 A23            
    3.2 0.0 0.2 36° -2° -2°
T-22 A22            
    3.3 -0.0 0.0 36° -6° -6°
T-21 A21            
    3.2 -0.0 0.2 36° -4° -3°
T-20 A20            
    3.1 -0.1 0.1 35° -3° -3°
T-19 A19            
    3.2 0.7 -0.1 35° -1° 8°
G-18 C18            
    3.2 -0.1 -0.2 35° 5° -3°
G-17 C17            
    3.0 0.1 0.3 34° -1° -0°
C-16 G16            

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 -102° G-49 C49 -146° C2'-endo    
 34°   -5° (BI)             -4° (BI)   18° 
    C2'-endo -113° G-48 C48 -106° C1'-exo    
 16°   -65° (BI)             -58° (BI)   41° 
    C2'-endo -97° T-47 A47 -96° C2'-endo    
 59°   24° (BII)             117° (BII)   28° 
    C2'-endo -101° G-46 C46 -79° C2'-endo    
 33°   21° (BII)             -79° (BI)   44° 
    C1'-exo -94° C-45 G45 -100° C2'-endo    
 62°   75° (BII)             89° (BII)   63° 
    C2'-endo -97° A-44 T44 -97° C2'-endo    
 40°   -74° (BI)             -88° (BI)   40° 
    C2'-endo -104° A-43 T43 -113° C2'-endo    
 98°   -88° (BI)             -82° (BI)   47° 
    C4'-exo -163° C-42 G42 -124° C1'-exo    
 45°   -95° (BI)             -3° (BI)   44° 
    C1'-exo -120° A-41 T41 -94° C2'-endo    
 33°   -66° (BI)             -60° (BI)   44° 
    O1'-endo -121° A-40 T40 -111° C2'-endo    
 14°   -40° (BI)             -90° (BI)   24° 
    C4'-exo -123° A-39 T39 -115° O1'-endo    
 -106°   -67° (BI)             -45° (BI)   25° 
    C1'-endo -126° T-38 A38 -112° C2'-endo    
 33°   -88° (BI)             16° (BI)   72° 
    C3'-exo -98° T-37 A37 -113° C3'-endo    
 69°   -98° (BI)             -97° (BI)   -161° 
    C2'-endo -94° G-36 C36 -93° C4'-exo    
 38°   29° (BII)             -18° (BI)   52° 
    C2'-endo -91° A-35 T35 -114° C2'-endo    
 47°   -87° (BI)             -81° (BI)   42° 
    C1'-exo -113° T-34 A34 -109° C2'-endo    
 52°   -78° (BI)             -74° (BI)   46° 
    C1'-exo -117° A-33 T33 -117° C1'-exo    
 55°   -92° (BI)             -68° (BI)   51° 
    C1'-exo -118° A-32 T32 -111° C2'-endo    
 44°   -71° (BI)             -81° (BI)   43° 
    C1'-exo -117° G-31 C31 -94° C2'-endo    
 24°   -56° (BI)             -87° (BI)   68° 
    C2'-endo -102° C-30 G30 -101° C3'-exo    
 -161°   79° (BII)             0° (BI)   57° 
    O1'-endo -120° A-29 T29 -166° C3'-endo    
 54°   -82° (BI)             -90° (BI)   39° 
    C3'-exo -108° A-28 T28 -158° C2'-endo    
 32°   -73° (BI)             -102° (BI)   42° 
    C2'-endo -79° T-27 A27 -123° C3'-endo    
 49°   89° (BII)             -69° (BI)   32° 
    C2'-endo -109° G-26 C26 -121° C1'-exo    
 49°   -20° (BI)             -65° (BI)   38° 
    C1'-exo -121° C-25 G25 -110° C2'-endo    
 49°   -69° (BI)             -52° (BI)   53° 
    C2'-endo -116° T-24 A24 -117° C2'-endo    
 44°   -42° (BI)             -120° (BI)   31° 
    C1'-exo -118° T-23 A23 -115° O1'-endo    
 66°   -78° (BI)             -45° (BI)   41° 
    C1'-exo -125° T-22 A22 -115° C1'-exo    
 30°   -44° (BI)             -18° (BI)   55° 
    C1'-exo -117° T-21 A21 -108° C2'-endo    
 43°   -86° (BI)             -66° (BI)   47° 
    C2'-endo -111° T-20 A20 -103° C2'-endo    
 40°   -74° (BI)             -105° (BI)   29° 
    C1'-exo -106° T-19 A19 -91° C3'-exo    
 36°   -17° (BI)             -38° (BI)   38° 
    C1'-exo -92° G-18 C18 -113° C2'-endo    
 62°   -72° (BI)             -89° (BI)   -8° 
    C1'-exo -126° G-17 C17 -110° C2'-endo    
 -73°   -108° (BI)             -50° (BI)   49° 
    C4'-endo -121° C-16 G16 -125° C2'-endo    

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.

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