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Analysis of nucleic acid double helix geometry

PDB code 4FRN   (PDB summary)
Duplex length 102 base pairs

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' G1 G2 G3 C4 U5 A6 A7 A8 A9 G10 C11 A12 U13 G14 G15 U16 G17 G18 G19 A20 A21 A22 G23 U24 G25 A26 C27 G28 U29 G30 U31 A32 A33 U34 U35 C36 G37 U38 C39 C40 A41 C42 A43 U44 U45 A46 C47 U48 U49 G50 A51 U52 A53 C54 G55 G56 U57 U58 A59 U60 A61 C62 U63 C64 C65 G66 A67 A68 U69 G70 C71 C72 A73 C74 C75 U76 A77 G78 C79 C80 C81 A82 A83 A84 G85 U86 A87 G88 A89 G90 C91 A92 A93 G94 G95 A96 G97 A98 C99 U100 C101 A102 3'
Strand 2    3' A102 C101 U100 C99 A98 G97 A96 G95 G94 A93 A92 C91 G90 A89 G88 A87 U86 G85 A84 A83 A82 C81 C80 C79 G78 A77 U76 C75 C74 A73 C72 C71 G70 U69 A68 A67 G66 C65 C64 U63 C62 A61 U60 A59 U58 U57 G56 G55 C54 A53 U52 A51 G50 U49 U48 C47 A46 U45 U44 A43 C42 A41 C40 C39 U38 G37 C36 U35 U34 A33 A32 U31 G30 U29 G28 C27 A26 G25 U24 G23 A22 A21 A20 G19 G18 G17 U16 G15 G14 U13 A12 C11 G10 A9 A8 A7 A6 U5 C4 G3 G2 G1 5'

CURVES analysis failed.
  No curvilinear helical axis determined.
  No helix parameters determined.

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.

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