ID code: '2G92' 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 A 1 beta 4 10 7 29 C1' G A 2 beta 24 30 27 52 C1' C A 3 beta 47 53 50 70 C1' NF2 A 4 71 72 93 C1' A A 5 beta 88 94 91 115 C1' A A 6 beta 110 116 113 137 C1' U A 7 beta 132 138 135 157 C1' U A 8 beta 152 158 155 177 C1' A A 9 beta 172 178 175 199 C1' G A 10 beta 194 200 197 222 C1' C A 11 beta 217 223 220 242 C1' G A 12 beta 237 243 240 263 C1' C B 13 beta 258 264 261 283 C1' G B 14 beta 278 284 281 306 C1' C B 15 beta 301 307 304 324 C1' NF2 B 16 325 326 347 C1' A B 17 beta 342 348 345 369 C1' A B 18 beta 364 370 367 391 C1' U B 19 beta 386 392 389 411 C1' U B 20 beta 406 412 409 431 C1' A B 21 beta 426 432 429 453 C1' G B 22 beta 448 454 451 476 C1' C B 23 beta 471 477 474 496 C1' G B 24 beta 491 497 494 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 1 OK 9 5 8 27 C2' G A 2 OK 29 25 28 50 C2' C A 3 OK 52 48 51 72 C2' NF2 A 4 OK 70 74 73 91 C2' A A 5 OK 93 89 92 113 C2' A A 6 OK 115 111 114 135 C2' U A 7 OK 137 133 136 155 C2' U A 8 OK 157 153 156 175 C2' A A 9 OK 177 173 176 197 C2' G A 10 OK 199 195 198 220 C2' C A 11 OK 222 218 221 240 C2' G A 12 OK 242 238 241 261 C2' C B 13 OK 263 259 262 281 C2' G B 14 OK 283 279 282 304 C2' C B 15 OK 306 302 305 326 C2' NF2 B 16 OK 324 328 327 345 C2' A B 17 OK 347 343 346 367 C2' A B 18 OK 369 365 368 389 C2' U B 19 OK 391 387 390 409 C2' U B 20 OK 411 407 410 429 C2' A B 21 OK 431 427 430 451 C2' G B 22 OK 453 449 452 474 C2' C B 23 OK 476 472 475 494 C2' G B 24 OK 496 492 495 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK 3 6 7 25 C3' G A 2 OK 23 26 27 48 C3' C A 3 OK 46 49 50 74 C3' NF2 A 4 OK 76 75 72 89 C3' A A 5 OK 87 90 91 111 C3' A A 6 OK 109 112 113 133 C3' U A 7 OK 131 134 135 153 C3' U A 8 OK 151 154 155 173 C3' A A 9 OK 171 174 175 195 C3' G A 10 OK 193 196 197 218 C3' C A 11 OK 216 219 220 238 C3' G A 12 OK 236 239 240 259 C3' C B 13 OK 257 260 261 279 C3' G B 14 OK 277 280 281 302 C3' C B 15 OK 300 303 304 328 C3' NF2 B 16 OK 330 329 326 343 C3' A B 17 OK 341 344 345 365 C3' A B 18 OK 363 366 367 387 C3' U B 19 OK 385 388 389 407 C3' U B 20 OK 405 408 409 427 C3' A B 21 OK 425 428 429 449 C3' G B 22 OK 447 450 451 472 C3' C B 23 OK 470 473 474 492 C3' G B 24 OK 490 493 494 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK 5 2 4 23 C4' G A 2 OK 25 22 24 46 C4' C A 3 OK 48 45 47 76 C4' NF2 A 4 OK 74 77 71 87 C4' A A 5 OK 89 86 88 109 C4' A A 6 OK 111 108 110 131 C4' U A 7 OK 133 130 132 151 C4' U A 8 OK 153 150 152 171 C4' A A 9 OK 173 170 172 193 C4' G A 10 OK 195 192 194 216 C4' C A 11 OK 218 215 217 236 C4' G A 12 OK 238 235 237 257 C4' C B 13 OK 259 256 258 277 C4' G B 14 OK 279 276 278 300 C4' C B 15 OK 302 299 301 330 C4' NF2 B 16 OK 328 331 325 341 C4' A B 17 OK 343 340 342 363 C4' A B 18 OK 365 362 364 385 C4' U B 19 OK 387 384 386 405 C4' U B 20 OK 407 404 406 425 C4' A B 21 OK 427 424 426 447 C4' G B 22 OK 449 446 448 470 C4' C B 23 OK 472 469 471 490 C4' G B 24 OK 492 489 491 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 1 3 22 C5' G A 2 21 23 45 C5' C A 3 44 46 77 C5' NF2 A 4 78 76 86 C5' A A 5 85 87 108 C5' A A 6 107 109 130 C5' U A 7 129 131 150 C5' U A 8 149 151 170 C5' A A 9 169 171 192 C5' G A 10 191 193 215 C5' C A 11 214 216 235 C5' G A 12 234 236 256 C5' C B 13 255 257 276 C5' G B 14 275 277 299 C5' C B 15 298 300 331 C5' NF2 B 16 332 330 340 C5' A B 17 339 341 362 C5' A B 18 361 363 384 C5' U B 19 383 385 404 C5' U B 20 403 405 424 C5' A B 21 423 425 446 C5' G B 22 445 447 469 C5' C B 23 468 470 489 C5' G B 24 488 490 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P G A 2 distorted distorted 6 19 20 21 41 P C A 3 distorted distorted 26 42 43 44 79 P NF2 A 4 distorted distorted 49 80 81 78 82 P A A 5 distorted distorted 75 83 84 85 104 P A A 6 distorted distorted 90 105 106 107 126 P U A 7 distorted distorted 112 127 128 129 146 P U A 8 distorted distorted 134 147 148 149 166 P A A 9 distorted distorted 154 167 168 169 188 P G A 10 distorted distorted 174 189 190 191 211 P C A 11 distorted distorted 196 212 213 214 231 P G A 12 distorted distorted 219 232 233 234 272 P G B 14 distorted distorted 260 273 274 275 295 P C B 15 distorted distorted 280 296 297 298 333 P NF2 B 16 distorted distorted 303 334 335 332 336 P A B 17 distorted distorted 329 337 338 339 358 P A B 18 distorted distorted 344 359 360 361 380 P U B 19 distorted distorted 366 381 382 383 400 P U B 20 distorted distorted 388 401 402 403 420 P A B 21 distorted distorted 408 421 422 423 442 P G B 22 distorted distorted 428 443 444 445 465 P C B 23 distorted distorted 450 466 467 468 485 P G B 24 distorted distorted 473 486 487 488 ---------------------------------------------------------------------------------