ID code: '2U2A' 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' --------------------------------------------------------------------------------- 13 C1' G A 1 alpha beta 8 31 14 11 48 C1' G A 2 alpha beta 43 66 49 46 82 C1' U A 3 alpha beta 77 97 83 80 112 C1' C A 4 alpha beta 107 127 113 110 143 C1' A A 5 alpha beta 138 160 144 141 176 C1' G A 6 alpha beta 171 194 177 174 210 C1' U A 7 alpha beta 205 225 211 208 240 C1' G A 8 alpha beta 235 258 241 238 274 C1' U A 9 alpha beta 269 289 275 272 304 C1' A A 10 alpha beta 299 321 305 302 337 C1' A A 11 alpha beta 332 354 338 335 370 C1' C A 12 alpha beta 365 385 371 368 401 C1' A A 13 alpha beta 396 418 402 399 434 C1' A A 14 alpha beta 429 451 435 432 467 C1' C A 15 alpha beta 462 482 468 465 498 C1' U A 16 alpha beta 493 513 499 496 528 C1' G A 17 alpha beta 523 546 529 526 562 C1' A A 18 alpha beta 557 579 563 560 595 C1' C A 19 alpha beta 590 610 596 593 626 C1' C A 20 alpha beta 621 642 627 624 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G A 1 OK OK 13 9 29 12 46 C2' G A 2 OK OK 48 44 64 47 80 C2' U A 3 OK OK 82 78 95 81 110 C2' C A 4 OK OK 112 108 125 111 141 C2' A A 5 OK OK 143 139 158 142 174 C2' G A 6 OK OK 176 172 192 175 208 C2' U A 7 OK OK 210 206 223 209 238 C2' G A 8 OK OK 240 236 256 239 272 C2' U A 9 OK OK 274 270 287 273 302 C2' A A 10 OK OK 304 300 319 303 335 C2' A A 11 OK OK 337 333 352 336 368 C2' C A 12 OK OK 370 366 383 369 399 C2' A A 13 OK OK 401 397 416 400 432 C2' A A 14 OK OK 434 430 449 433 465 C2' C A 15 OK OK 467 463 480 466 496 C2' U A 16 OK OK 498 494 511 497 526 C2' G A 17 OK OK 528 524 544 527 560 C2' A A 18 OK OK 562 558 577 561 593 C2' C A 19 OK OK 595 591 608 594 624 C2' C A 20 OK OK 626 622 640 625 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G A 1 OK OK 7 28 10 11 44 C3' G A 2 OK OK 42 63 45 46 78 C3' U A 3 OK OK 76 94 79 80 108 C3' C A 4 OK OK 106 124 109 110 139 C3' A A 5 OK OK 137 157 140 141 172 C3' G A 6 OK OK 170 191 173 174 206 C3' U A 7 OK OK 204 222 207 208 236 C3' G A 8 OK OK 234 255 237 238 270 C3' U A 9 OK OK 268 286 271 272 300 C3' A A 10 OK OK 298 318 301 302 333 C3' A A 11 OK OK 331 351 334 335 366 C3' C A 12 OK OK 364 382 367 368 397 C3' A A 13 OK OK 395 415 398 399 430 C3' A A 14 OK OK 428 448 431 432 463 C3' C A 15 OK OK 461 479 464 465 494 C3' U A 16 OK OK 492 510 495 496 524 C3' G A 17 OK OK 522 543 525 526 558 C3' A A 18 OK OK 556 576 559 560 591 C3' C A 19 OK OK 589 607 592 593 622 C3' C A 20 OK OK 620 638 623 624 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G A 1 OK OK 9 27 6 8 42 C4' G A 2 OK OK 44 62 41 43 76 C4' U A 3 OK OK 78 93 75 77 106 C4' C A 4 OK OK 108 123 105 107 137 C4' A A 5 OK OK 139 156 136 138 170 C4' G A 6 OK OK 172 190 169 171 204 C4' U A 7 OK OK 206 221 203 205 234 C4' G A 8 OK OK 236 254 233 235 268 C4' U A 9 OK OK 270 285 267 269 298 C4' A A 10 OK OK 300 317 297 299 331 C4' A A 11 OK OK 333 350 330 332 364 C4' C A 12 OK OK 366 381 363 365 395 C4' A A 13 OK OK 397 414 394 396 428 C4' A A 14 OK OK 430 447 427 429 461 C4' C A 15 OK OK 463 478 460 462 492 C4' U A 16 OK OK 494 509 491 493 522 C4' G A 17 OK OK 524 542 521 523 556 C4' A A 18 OK OK 558 575 555 557 589 C4' C A 19 OK OK 591 606 588 590 620 C4' C A 20 OK OK 622 637 619 621 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G A 1 OK OK 5 25 26 7 41 C5' G A 2 OK OK 40 60 61 42 75 C5' U A 3 OK OK 74 91 92 76 105 C5' C A 4 OK OK 104 121 122 106 136 C5' A A 5 OK OK 135 154 155 137 169 C5' G A 6 OK OK 168 188 189 170 203 C5' U A 7 OK OK 202 219 220 204 233 C5' G A 8 OK OK 232 252 253 234 267 C5' U A 9 OK OK 266 283 284 268 297 C5' A A 10 OK OK 296 315 316 298 330 C5' A A 11 OK OK 329 348 349 331 363 C5' C A 12 OK OK 362 379 380 364 394 C5' A A 13 OK OK 393 412 413 395 427 C5' A A 14 OK OK 426 445 446 428 460 C5' C A 15 OK OK 459 476 477 461 491 C5' U A 16 OK OK 490 507 508 492 521 C5' G A 17 OK OK 520 540 541 522 555 C5' A A 18 OK OK 554 573 574 556 588 C5' C A 19 OK OK 587 604 605 589 619 C5' C A 20 OK OK 618 635 636 620 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G A 1 distorted distorted 3 4 5 37 P G A 2 distorted distorted 10 38 39 40 71 P U A 3 distorted distorted 45 72 73 74 101 P C A 4 distorted distorted 79 102 103 104 132 P A A 5 distorted distorted 109 133 134 135 165 P G A 6 distorted distorted 140 166 167 168 199 P U A 7 distorted distorted 173 200 201 202 229 P G A 8 distorted distorted 207 230 231 232 263 P U A 9 distorted distorted 237 264 265 266 293 P A A 10 distorted distorted 271 294 295 296 326 P A A 11 distorted distorted 301 327 328 329 359 P C A 12 distorted distorted 334 360 361 362 390 P A A 13 distorted distorted 367 391 392 393 423 P A A 14 distorted distorted 398 424 425 426 456 P C A 15 distorted distorted 431 457 458 459 487 P U A 16 distorted distorted 464 488 489 490 517 P G A 17 distorted distorted 495 518 519 520 551 P A A 18 distorted distorted 525 552 553 554 584 P C A 19 distorted distorted 559 585 586 587 615 P C A 20 distorted distorted 592 616 617 618 ---------------------------------------------------------------------------------