ID code: '2O83' 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' G A 1 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 72 C1' IC A 3 alpha beta 77 87 84 73 109 C1' G A 4 alpha beta 104 127 110 107 143 C1' A A 5 alpha beta 138 160 144 141 170 C1' IG A 6 alpha beta 175 188 183 171 210 C1' C A 7 alpha beta 205 225 211 208 241 C1' C A 8 alpha beta 236 256 242 239 272 C1' A A 9 alpha beta 267 290 273 270 304 C1' G B 1 alpha beta 299 322 305 302 339 C1' G B 2 alpha beta 334 357 340 337 367 C1' IC B 3 alpha beta 372 382 379 368 404 C1' G B 4 alpha beta 399 422 405 402 438 C1' A B 5 alpha beta 433 455 439 436 465 C1' IG B 6 alpha beta 470 483 478 466 505 C1' C B 7 alpha beta 500 520 506 503 536 C1' C B 8 alpha beta 531 551 537 534 567 C1' A B 9 alpha beta 562 585 568 565 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 73 C2' IC A 3 OK OK 72 74 88 78 107 C2' G A 4 OK OK 109 105 125 108 141 C2' A A 5 OK OK 143 139 158 142 171 C2' IG A 6 OK OK 170 172 189 176 208 C2' C A 7 OK OK 210 206 223 209 239 C2' C A 8 OK OK 241 237 254 240 270 C2' A A 9 OK OK 272 268 288 271 302 C2' G B 1 OK OK 304 300 320 303 337 C2' G B 2 OK OK 339 335 355 338 368 C2' IC B 3 OK OK 367 369 383 373 402 C2' G B 4 OK OK 404 400 420 403 436 C2' A B 5 OK OK 438 434 453 437 466 C2' IG B 6 OK OK 465 467 484 471 503 C2' C B 7 OK OK 505 501 518 504 534 C2' C B 8 OK OK 536 532 549 535 565 C2' A B 9 OK OK 567 563 583 566 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' IC A 3 OK OK 75 89 71 73 105 C3' G A 4 OK OK 103 124 106 107 139 C3' A A 5 OK OK 137 157 140 141 172 C3' IG A 6 OK OK 173 190 169 171 206 C3' C A 7 OK OK 204 222 207 208 237 C3' C A 8 OK OK 235 253 238 239 268 C3' A A 9 OK OK 266 286 269 270 300 C3' G B 1 OK OK 298 319 301 302 335 C3' G B 2 OK OK 333 354 336 337 369 C3' IC B 3 OK OK 370 384 366 368 400 C3' G B 4 OK OK 398 419 401 402 434 C3' A B 5 OK OK 432 452 435 436 467 C3' IG B 6 OK OK 468 485 464 466 501 C3' C B 7 OK OK 499 517 502 503 532 C3' C B 8 OK OK 530 548 533 534 563 C3' A B 9 OK OK 561 581 564 565 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 75 C4' IC A 3 OK OK 74 90 76 77 103 C4' G A 4 OK OK 105 123 102 104 137 C4' A A 5 OK OK 139 156 136 138 173 C4' IG A 6 OK OK 172 191 174 175 204 C4' C A 7 OK OK 206 221 203 205 235 C4' C A 8 OK OK 237 252 234 236 266 C4' A A 9 OK OK 268 285 265 267 298 C4' G B 1 OK OK 300 318 297 299 333 C4' G B 2 OK OK 335 353 332 334 370 C4' IC B 3 OK OK 369 385 371 372 398 C4' G B 4 OK OK 400 418 397 399 432 C4' A B 5 OK OK 434 451 431 433 468 C4' IG B 6 OK OK 467 486 469 470 499 C4' C B 7 OK OK 501 516 498 500 530 C4' C B 8 OK OK 532 547 529 531 561 C4' A B 9 OK OK 563 580 560 562 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 76 C5' IC A 3 OK OK 70 91 92 75 102 C5' G A 4 OK OK 101 121 122 103 136 C5' A A 5 OK OK 135 154 155 137 174 C5' IG A 6 OK OK 168 192 193 173 203 C5' C A 7 OK OK 202 219 220 204 234 C5' C A 8 OK OK 233 250 251 235 265 C5' A A 9 OK OK 264 283 284 266 297 C5' G B 1 OK OK 296 316 317 298 332 C5' G B 2 OK OK 331 351 352 333 371 C5' IC B 3 OK OK 365 386 387 370 397 C5' G B 4 OK OK 396 416 417 398 431 C5' A B 5 OK OK 430 449 450 432 469 C5' IG B 6 OK OK 463 487 488 468 498 C5' C B 7 OK OK 497 514 515 499 529 C5' C B 8 OK OK 528 545 546 530 560 C5' A B 9 OK OK 559 578 579 561 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P IC A 3 distorted distorted 41 68 69 70 98 P G A 4 distorted distorted 71 99 100 101 132 P A A 5 distorted distorted 106 133 134 135 165 P IG A 6 distorted distorted 140 166 167 168 199 P C A 7 distorted distorted 169 200 201 202 230 P C A 8 distorted distorted 207 231 232 233 261 P A A 9 distorted distorted 238 262 263 264 328 P G B 2 distorted distorted 301 329 330 331 362 P IC B 3 distorted distorted 336 363 364 365 393 P G B 4 distorted distorted 366 394 395 396 427 P A B 5 distorted distorted 401 428 429 430 460 P IG B 6 distorted distorted 435 461 462 463 494 P C B 7 distorted distorted 464 495 496 497 525 P C B 8 distorted distorted 502 526 527 528 556 P A B 9 distorted distorted 533 557 558 559 ---------------------------------------------------------------------------------