ID code: '3D0M' 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' --------------------------------------------------------------------------------- 8 C1' G X 1 beta 3 9 6 31 C1' U X 2 beta 26 32 29 51 C1' G X 3 beta 46 52 49 74 C1' G X 4 beta 69 75 72 97 C1' U X 5 beta 92 98 95 117 C1' C X 6 beta 112 118 115 137 C1' U X 7 beta 132 138 135 157 C1' G X 8 beta 152 158 155 180 C1' A X 9 beta 175 181 178 202 C1' U X 10 beta 197 203 200 222 C1' G X 11 beta 217 223 220 245 C1' A X 12 beta 240 246 243 267 C1' G X 13 beta 262 268 265 290 C1' G X 14 beta 285 291 288 313 C1' C X 15 beta 308 314 311 333 C1' C X 16 beta 328 334 331 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 6 C2' G X 1 OK 8 4 7 29 C2' U X 2 OK 31 27 30 49 C2' G X 3 OK 51 47 50 72 C2' G X 4 OK 74 70 73 95 C2' U X 5 OK 97 93 96 115 C2' C X 6 OK 117 113 116 135 C2' U X 7 OK 137 133 136 155 C2' G X 8 OK 157 153 156 178 C2' A X 9 OK 180 176 179 200 C2' U X 10 OK 202 198 201 220 C2' G X 11 OK 222 218 221 243 C2' A X 12 OK 245 241 244 265 C2' G X 13 OK 267 263 266 288 C2' G X 14 OK 290 286 289 311 C2' C X 15 OK 313 309 312 331 C2' C X 16 OK 333 329 332 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4 C3' G X 1 OK 2 5 6 27 C3' U X 2 OK 25 28 29 47 C3' G X 3 OK 45 48 49 70 C3' G X 4 OK 68 71 72 93 C3' U X 5 OK 91 94 95 113 C3' C X 6 OK 111 114 115 133 C3' U X 7 OK 131 134 135 153 C3' G X 8 OK 151 154 155 176 C3' A X 9 OK 174 177 178 198 C3' U X 10 OK 196 199 200 218 C3' G X 11 OK 216 219 220 241 C3' A X 12 OK 239 242 243 263 C3' G X 13 OK 261 264 265 286 C3' G X 14 OK 284 287 288 309 C3' C X 15 OK 307 310 311 329 C3' C X 16 OK 327 330 331 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2 C4' G X 1 OK 4 1 3 25 C4' U X 2 OK 27 24 26 45 C4' G X 3 OK 47 44 46 68 C4' G X 4 OK 70 67 69 91 C4' U X 5 OK 93 90 92 111 C4' C X 6 OK 113 110 112 131 C4' U X 7 OK 133 130 132 151 C4' G X 8 OK 153 150 152 174 C4' A X 9 OK 176 173 175 196 C4' U X 10 OK 198 195 197 216 C4' G X 11 OK 218 215 217 239 C4' A X 12 OK 241 238 240 261 C4' G X 13 OK 263 260 262 284 C4' G X 14 OK 286 283 285 307 C4' C X 15 OK 309 306 308 327 C4' C X 16 OK 329 326 328 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1 C5' G X 1 2 24 C5' U X 2 23 25 44 C5' G X 3 43 45 67 C5' G X 4 66 68 90 C5' U X 5 89 91 110 C5' C X 6 109 111 130 C5' U X 7 129 131 150 C5' G X 8 149 151 173 C5' A X 9 172 174 195 C5' U X 10 194 196 215 C5' G X 11 214 216 238 C5' A X 12 237 239 260 C5' G X 13 259 261 283 C5' G X 14 282 284 306 C5' C X 15 305 307 326 C5' C X 16 325 327 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P U X 2 distorted distorted 5 21 22 23 40 P G X 3 distorted distorted 28 41 42 43 63 P G X 4 distorted distorted 48 64 65 66 86 P U X 5 distorted distorted 71 87 88 89 106 P C X 6 distorted distorted 94 107 108 109 126 P U X 7 distorted distorted 114 127 128 129 146 P G X 8 distorted distorted 134 147 148 149 169 P A X 9 distorted distorted 154 170 171 172 191 P U X 10 distorted distorted 177 192 193 194 211 P G X 11 distorted distorted 199 212 213 214 234 P A X 12 distorted distorted 219 235 236 237 256 P G X 13 distorted distorted 242 257 258 259 279 P G X 14 distorted distorted 264 280 281 282 302 P C X 15 distorted distorted 287 303 304 305 322 P C X 16 distorted distorted 310 323 324 325 ---------------------------------------------------------------------------------