ID code: '2F8K' CHIRALITY (03 Nov 1998) Checks the chirality and the naming of substituents of chiral and prochiral centers in nucleic acid structures. The molecular structure is read from a PDB file. Only the first model is evaluated. ---------------------------------------------------------- Center Reference for correct naming ---------------------------------------------------------- C1' alpha/beta nomenclature of anomeric sugars, base in beta position in natural nucleosids. C2' IUPAC. 1983. Eur J Biochem, 131: 9-15. C3' IUPAC. 1983. Eur J Biochem, 131: 9-15. C4' IUPAC. 1983. Eur J Biochem, 131: 9-15. C5' IUPAC. 1983. Eur J Biochem, 131: 9-15. P Brookhaven PDB entry '1BNA', O1P -> major groove, O2P -> minor groove. ---------------------------------------------------------- Author: Peter Slickers (slickers@imb-jena.de) Biocomputing, IMB Jena, Germany --------------------------------------------------------------------------------- Seq No Atom Residue H1' base O4' H1' base C2' --------------------------------------------------------------------------------- 9 C1' U B 0 beta 4 10 7 29 C1' A B 1 beta 24 30 27 51 C1' A B 2 beta 46 52 49 73 C1' U B 3 beta 68 74 71 93 C1' C B 4 beta 88 94 91 113 C1' U B 5 beta 108 114 111 133 C1' U B 6 beta 128 134 131 153 C1' U B 7 beta 148 154 151 173 C1' G B 8 beta 168 174 171 196 C1' A B 9 beta 191 197 194 222 C1' A B 11 beta 217 223 220 244 C1' G B 12 beta 239 245 242 267 C1' A B 13 beta 262 268 265 289 C1' U B 14 beta 284 290 287 309 C1' U B 15 beta 304 310 307 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U B 0 OK 9 5 8 27 C2' A B 1 OK 29 25 28 49 C2' A B 2 OK 51 47 50 71 C2' U B 3 OK 73 69 72 91 C2' C B 4 OK 93 89 92 111 C2' U B 5 OK 113 109 112 131 C2' U B 6 OK 133 129 132 151 C2' U B 7 OK 153 149 152 171 C2' G B 8 OK 173 169 172 194 C2' A B 9 OK 196 192 195 220 C2' A B 11 OK 222 218 221 242 C2' G B 12 OK 244 240 243 265 C2' A B 13 OK 267 263 266 287 C2' U B 14 OK 289 285 288 307 C2' U B 15 OK 309 305 308 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U B 0 OK 3 6 7 25 C3' A B 1 OK 23 26 27 47 C3' A B 2 OK 45 48 49 69 C3' U B 3 OK 67 70 71 89 C3' C B 4 OK 87 90 91 109 C3' U B 5 OK 107 110 111 129 C3' U B 6 OK 127 130 131 149 C3' U B 7 OK 147 150 151 169 C3' G B 8 OK 167 170 171 192 C3' A B 9 OK 190 193 194 218 C3' A B 11 OK 216 219 220 240 C3' G B 12 OK 238 241 242 263 C3' A B 13 OK 261 264 265 285 C3' U B 14 OK 283 286 287 305 C3' U B 15 OK 303 306 307 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U B 0 OK 5 2 4 23 C4' A B 1 OK 25 22 24 45 C4' A B 2 OK 47 44 46 67 C4' U B 3 OK 69 66 68 87 C4' C B 4 OK 89 86 88 107 C4' U B 5 OK 109 106 108 127 C4' U B 6 OK 129 126 128 147 C4' U B 7 OK 149 146 148 167 C4' G B 8 OK 169 166 168 190 C4' A B 9 OK 192 189 191 216 C4' A B 11 OK 218 215 217 238 C4' G B 12 OK 240 237 239 261 C4' A B 13 OK 263 260 262 283 C4' U B 14 OK 285 282 284 303 C4' U B 15 OK 305 302 304 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U B 0 1 3 22 C5' A B 1 21 23 44 C5' A B 2 43 45 66 C5' U B 3 65 67 86 C5' C B 4 85 87 106 C5' U B 5 105 107 126 C5' U B 6 125 127 146 C5' U B 7 145 147 166 C5' G B 8 165 167 189 C5' A B 9 188 190 215 C5' A B 11 214 216 237 C5' G B 12 236 238 260 C5' A B 13 259 261 282 C5' U B 14 281 283 302 C5' U B 15 301 303 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P A B 1 distorted distorted 6 19 20 21 40 P A B 2 distorted distorted 26 41 42 43 62 P U B 3 distorted distorted 48 63 64 65 82 P C B 4 distorted distorted 70 83 84 85 102 P U B 5 distorted distorted 90 103 104 105 122 P U B 6 distorted distorted 110 123 124 125 142 P U B 7 distorted distorted 130 143 144 145 162 P G B 8 distorted distorted 150 163 164 165 185 P A B 9 distorted distorted 170 186 187 188 207 P C B 10 distorted distorted 193 208 209 210 211 P A B 11 distorted distorted 212 213 214 233 P G B 12 distorted distorted 219 234 235 236 256 P A B 13 distorted distorted 241 257 258 259 278 P U B 14 distorted distorted 264 279 280 281 298 P U B 15 distorted distorted 286 299 300 301 ---------------------------------------------------------------------------------