ID code: '2AB4' 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' C B 3 beta 4 10 7 29 C1' C B 4 beta 24 30 27 49 C1' A B 5 beta 44 50 47 71 C1' C B 6 beta 66 72 69 91 C1' G B 7 beta 86 92 89 114 C1' G B 8 beta 109 115 112 137 C1' U B 9 beta 132 138 135 154 C1' FHU B 10 beta 160 150 155 179 C1' C B 11 beta 174 180 177 199 C1' G B 12 beta 194 200 197 222 C1' A B 13 beta 217 223 220 244 C1' A B 14 beta 239 245 242 266 C1' U B 15 beta 261 267 264 286 C1' C B 16 beta 281 287 284 306 C1' C B 17 beta 301 307 304 326 C1' G B 18 beta 321 327 324 349 C1' U B 19 beta 344 350 347 369 C1' G B 20 beta 364 370 367 392 C1' G B 21 beta 387 393 390 415 C1' C B 22 beta 410 416 413 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C B 3 OK 9 5 8 27 C2' C B 4 OK 29 25 28 47 C2' A B 5 OK 49 45 48 69 C2' C B 6 OK 71 67 70 89 C2' G B 7 OK 91 87 90 112 C2' G B 8 OK 114 110 113 135 C2' U B 9 OK 137 133 136 155 C2' FHU B 10 OK 154 157 156 177 C2' C B 11 OK 179 175 178 197 C2' G B 12 OK 199 195 198 220 C2' A B 13 OK 222 218 221 242 C2' A B 14 OK 244 240 243 264 C2' U B 15 OK 266 262 265 284 C2' C B 16 OK 286 282 285 304 C2' C B 17 OK 306 302 305 324 C2' G B 18 OK 326 322 325 347 C2' U B 19 OK 349 345 348 367 C2' G B 20 OK 369 365 368 390 C2' G B 21 OK 392 388 391 413 C2' C B 22 OK 415 411 414 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C B 3 OK 3 6 7 25 C3' C B 4 OK 23 26 27 45 C3' A B 5 OK 43 46 47 67 C3' C B 6 OK 65 68 69 87 C3' G B 7 OK 85 88 89 110 C3' G B 8 OK 108 111 112 133 C3' U B 9 OK 131 134 135 157 C3' FHU B 10 OK 158 159 155 175 C3' C B 11 OK 173 176 177 195 C3' G B 12 OK 193 196 197 218 C3' A B 13 OK 216 219 220 240 C3' A B 14 OK 238 241 242 262 C3' U B 15 OK 260 263 264 282 C3' C B 16 OK 280 283 284 302 C3' C B 17 OK 300 303 304 322 C3' G B 18 OK 320 323 324 345 C3' U B 19 OK 343 346 347 365 C3' G B 20 OK 363 366 367 388 C3' G B 21 OK 386 389 390 411 C3' C B 22 OK 409 412 413 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C B 3 OK 5 2 4 23 C4' C B 4 OK 25 22 24 43 C4' A B 5 OK 45 42 44 65 C4' C B 6 OK 67 64 66 85 C4' G B 7 OK 87 84 86 108 C4' G B 8 OK 110 107 109 131 C4' U B 9 OK 133 130 132 158 C4' FHU B 10 OK 157 161 160 173 C4' C B 11 OK 175 172 174 193 C4' G B 12 OK 195 192 194 216 C4' A B 13 OK 218 215 217 238 C4' A B 14 OK 240 237 239 260 C4' U B 15 OK 262 259 261 280 C4' C B 16 OK 282 279 281 300 C4' C B 17 OK 302 299 301 320 C4' G B 18 OK 322 319 321 343 C4' U B 19 OK 345 342 344 363 C4' G B 20 OK 365 362 364 386 C4' G B 21 OK 388 385 387 409 C4' C B 22 OK 411 408 410 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C B 3 1 3 22 C5' C B 4 21 23 42 C5' A B 5 41 43 64 C5' C B 6 63 65 84 C5' G B 7 83 85 107 C5' G B 8 106 108 130 C5' U B 9 129 131 161 C5' FHU B 10 162 158 172 C5' C B 11 171 173 192 C5' G B 12 191 193 215 C5' A B 13 214 216 237 C5' A B 14 236 238 259 C5' U B 15 258 260 279 C5' C B 16 278 280 299 C5' C B 17 298 300 319 C5' G B 18 318 320 342 C5' U B 19 341 343 362 C5' G B 20 361 363 385 C5' G B 21 384 386 408 C5' C B 22 407 409 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P C B 4 distorted distorted 6 19 20 21 38 P A B 5 distorted distorted 26 39 40 41 60 P C B 6 distorted distorted 46 61 62 63 80 P G B 7 distorted distorted 68 81 82 83 103 P G B 8 distorted distorted 88 104 105 106 126 P U B 9 distorted distorted 111 127 128 129 163 P FHU B 10 distorted distorted 134 164 165 162 168 P C B 11 distorted distorted 159 169 170 171 188 P G B 12 distorted distorted 176 189 190 191 211 P A B 13 distorted distorted 196 212 213 214 233 P A B 14 distorted distorted 219 234 235 236 255 P U B 15 distorted distorted 241 256 257 258 275 P C B 16 distorted distorted 263 276 277 278 295 P C B 17 distorted distorted 283 296 297 298 315 P G B 18 distorted distorted 303 316 317 318 338 P U B 19 distorted distorted 323 339 340 341 358 P G B 20 distorted distorted 346 359 360 361 381 P G B 21 distorted distorted 366 382 383 384 404 P C B 22 distorted distorted 389 405 406 407 ---------------------------------------------------------------------------------