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Analysis of nucleic acid double helix geometry

PDB code 3PDR   (PDB summary)
Duplex length 161 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' G15 G16 G17 C18 U19 U20 C21 G22 U23 U24 A25 G26 G27 U28 G29 A30 G31 G32 C33 U34 C35 C36 U37 G38 U39 A40 U41 G42 G43 A44 G45 A46 U47 A48 C49 G50 C51 U52 G53 C54 U55 G56 C57 C58 C59 A60 A61 A62 A63 A64 U65 G66 U67 C68 C69 A70 A71 A72 G73 A74 C75 G76 C77 C78 A79 A80 U81 G82 G83 G84 U85 C86 A87 A88 C89 A90 G91 A92 A93 A94 U95 C96 A97 U98 C99 G100 A101 C102 A103 U104 A105 A106 G107 G108 U109 G110 A111 U112 U113 U114 U115 U116 A117 A118 U119 G120 C121 A122 G123 C124 U125 G126 G127 A128 U129 G130 C131 U132 U133 G134 U135 C136 C137 U138 A139 U140 G141 C142 C143 A144 U145 A146 C147 A148 G149 U150 G151 C152 U153 A154 A155 A156 G157 C158 U159 C160 U161 A162 C163 G164 A165 U166 U167 G168 A169 A170 G171 C172 C173 C174 A175 3'
Strand 2    3' A175 C174 C173 C172 G171 A170 A169 G168 U167 U166 A165 G164 C163 A162 U161 C160 U159 C158 G157 A156 A155 A154 U153 C152 G151 U150 G149 A148 C147 A146 U145 A144 C143 C142 G141 U140 A139 U138 C137 C136 U135 G134 U133 U132 C131 G130 U129 A128 G127 G126 U125 C124 G123 A122 C121 G120 U119 A118 A117 U116 U115 U114 U113 U112 A111 G110 U109 G108 G107 A106 A105 U104 A103 C102 A101 G100 C99 U98 A97 C96 U95 A94 A93 A92 G91 A90 C89 A88 A87 C86 U85 G84 G83 G82 U81 A80 A79 C78 C77 G76 C75 A74 G73 A72 A71 A70 C69 C68 U67 G66 U65 A64 A63 A62 A61 A60 C59 C58 C57 G56 U55 C54 G53 U52 C51 G50 C49 A48 U47 A46 G45 A44 G43 G42 U41 A40 U39 G38 U37 C36 C35 U34 C33 G32 G31 A30 G29 U28 G27 G26 A25 U24 U23 G22 C21 U20 U19 C18 G17 G16 G15 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