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Analysis of nucleic acid double helix geometry

Title LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSO
PDB code 1M1A   (PDB summary)
NDB code PD0330 (NDB atlas)
Duplex length 146 base pairs
Protein Histone H2A.1, H2B.1, H3.2, H4, 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' A1 T2 C3 A4 A5 T6 A7 T8 C9 C10 A11 C12 C13 T14 G15 C16 A17 G18 A19 T20 T21 C22 T23 A24 C25 C26 A27 A28 A29 A30 G31 T32 G33 T34 A35 T36 T37 T38 G39 G40 A41 A42 A43 C44 T45 G46 C47 T48 C49 C50 A51 T52 C53 A54 A55 A56 A57 G58 G59 C60 A61 T62 G63 T64 T65 C66 A67 G68 C69 G70 G71 A72 A73 T74 T75 C76 C77 G78 C79 T80 G81 A82 A83 C84 A85 T86 G87 C88 C89 T90 T91 T92 T93 G94 A95 T96 G97 G98 A99 G100 C101 A102 G103 T104 T105 T106 C107 C108 A109 A110 A111 T112 A113 C114 A115 C116 T117 T118 T119 T120 G121 G122 T123 A124 G125 A126 A127 T128 C129 T130 G131 C132 A133 G134 G135 T136 G137 G138 A139 T140 A141 T142 T143 G144 A145 T146 3'
Strand 2    3' T292 A291 G290 T289 T288 A287 T286 A285 G284 G283 T282 G281 G280 A279 C278 G277 T276 C275 T274 A273 A272 G271 A270 T269 G268 G267 T266 T265 T264 T263 C262 A261 C260 A259 T258 A257 A256 A255 C254 C253 T252 T251 T250 G249 A248 C247 G246 A245 G244 G243 T242 A241 G240 T239 T238 T237 T236 C235 C234 G233 T232 A231 C230 A229 A228 G227 T226 C225 G224 C223 C222 T221 T220 A219 A218 G217 G216 C215 G214 A213 C212 T211 T210 G209 T208 A207 C206 G205 G204 A203 A202 A201 A200 C199 T198 A197 C196 C195 T194 C193 G192 T191 C190 A189 A188 A187 G186 G185 T184 T183 T182 A181 T180 G179 T178 G177 A176 A175 A174 A173 C172 C171 A170 T169 C168 T167 T166 A165 G164 A163 C162 G161 T160 C159 C158 A157 C156 C155 T154 A153 T152 A151 A150 C149 T148 A147 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