ID code: '2OE6' 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 beta 4 10 7 32 C1' G A 2 beta 27 33 30 55 C1' G A 3 beta 50 56 53 78 C1' C A1404 beta 73 79 76 98 C1' G A1405 beta 93 99 96 121 C1' U A1406 beta 116 122 119 141 C1' C A1407 beta 136 142 139 161 C1' G A1408 beta 156 162 159 184 C1' C A1409 beta 179 185 182 204 C1' U A1410 beta 199 205 202 224 C1' A A1411 beta 219 225 222 246 C1' G A1412 beta 241 247 244 269 C1' U A1413 beta 264 270 267 289 C1' A A 14 beta 284 290 287 311 C1' C A 15 beta 306 312 309 331 C1' C A 16 beta 326 332 329 349 C1' C B 83 beta 344 350 347 369 C1' G B 84 beta 364 370 367 392 C1' G B 85 beta 387 393 390 415 C1' U B 86 beta 410 416 413 435 C1' A B1487 beta 430 436 433 457 C1' C B1488 beta 452 458 455 477 C1' U B1489 beta 472 478 475 497 C1' A B1490 beta 492 498 495 519 C1' A B1491 beta 514 520 517 541 C1' A B1492 beta 536 542 539 563 C1' A B1493 beta 558 564 561 585 C1' G B1494 beta 580 586 583 608 C1' U B1495 beta 603 609 606 628 C1' C B1496 beta 623 629 626 648 C1' G B1497 beta 643 649 646 671 C1' C B 98 beta 666 672 669 691 C1' C B 99 beta 686 692 689 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 9 5 8 30 C2' G A 2 OK 32 28 31 53 C2' G A 3 OK 55 51 54 76 C2' C A1404 OK 78 74 77 96 C2' G A1405 OK 98 94 97 119 C2' U A1406 OK 121 117 120 139 C2' C A1407 OK 141 137 140 159 C2' G A1408 OK 161 157 160 182 C2' C A1409 OK 184 180 183 202 C2' U A1410 OK 204 200 203 222 C2' A A1411 OK 224 220 223 244 C2' G A1412 OK 246 242 245 267 C2' U A1413 OK 269 265 268 287 C2' A A 14 OK 289 285 288 309 C2' C A 15 OK 311 307 310 329 C2' C A 16 OK 331 327 330 347 C2' C B 83 OK 349 345 348 367 C2' G B 84 OK 369 365 368 390 C2' G B 85 OK 392 388 391 413 C2' U B 86 OK 415 411 414 433 C2' A B1487 OK 435 431 434 455 C2' C B1488 OK 457 453 456 475 C2' U B1489 OK 477 473 476 495 C2' A B1490 OK 497 493 496 517 C2' A B1491 OK 519 515 518 539 C2' A B1492 OK 541 537 540 561 C2' A B1493 OK 563 559 562 583 C2' G B1494 OK 585 581 584 606 C2' U B1495 OK 608 604 607 626 C2' C B1496 OK 628 624 627 646 C2' G B1497 OK 648 644 647 669 C2' C B 98 OK 671 667 670 689 C2' C B 99 OK 691 687 690 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 28 C3' G A 2 OK 26 29 30 51 C3' G A 3 OK 49 52 53 74 C3' C A1404 OK 72 75 76 94 C3' G A1405 OK 92 95 96 117 C3' U A1406 OK 115 118 119 137 C3' C A1407 OK 135 138 139 157 C3' G A1408 OK 155 158 159 180 C3' C A1409 OK 178 181 182 200 C3' U A1410 OK 198 201 202 220 C3' A A1411 OK 218 221 222 242 C3' G A1412 OK 240 243 244 265 C3' U A1413 OK 263 266 267 285 C3' A A 14 OK 283 286 287 307 C3' C A 15 OK 305 308 309 327 C3' C A 16 OK 325 328 329 345 C3' C B 83 OK 343 346 347 365 C3' G B 84 OK 363 366 367 388 C3' G B 85 OK 386 389 390 411 C3' U B 86 OK 409 412 413 431 C3' A B1487 OK 429 432 433 453 C3' C B1488 OK 451 454 455 473 C3' U B1489 OK 471 474 475 493 C3' A B1490 OK 491 494 495 515 C3' A B1491 OK 513 516 517 537 C3' A B1492 OK 535 538 539 559 C3' A B1493 OK 557 560 561 581 C3' G B1494 OK 579 582 583 604 C3' U B1495 OK 602 605 606 624 C3' C B1496 OK 622 625 626 644 C3' G B1497 OK 642 645 646 667 C3' C B 98 OK 665 668 669 687 C3' C B 99 OK 685 688 689 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 26 C4' G A 2 OK 28 25 27 49 C4' G A 3 OK 51 48 50 72 C4' C A1404 OK 74 71 73 92 C4' G A1405 OK 94 91 93 115 C4' U A1406 OK 117 114 116 135 C4' C A1407 OK 137 134 136 155 C4' G A1408 OK 157 154 156 178 C4' C A1409 OK 180 177 179 198 C4' U A1410 OK 200 197 199 218 C4' A A1411 OK 220 217 219 240 C4' G A1412 OK 242 239 241 263 C4' U A1413 OK 265 262 264 283 C4' A A 14 OK 285 282 284 305 C4' C A 15 OK 307 304 306 325 C4' C A 16 OK 327 324 326 343 C4' C B 83 OK 345 342 344 363 C4' G B 84 OK 365 362 364 386 C4' G B 85 OK 388 385 387 409 C4' U B 86 OK 411 408 410 429 C4' A B1487 OK 431 428 430 451 C4' C B1488 OK 453 450 452 471 C4' U B1489 OK 473 470 472 491 C4' A B1490 OK 493 490 492 513 C4' A B1491 OK 515 512 514 535 C4' A B1492 OK 537 534 536 557 C4' A B1493 OK 559 556 558 579 C4' G B1494 OK 581 578 580 602 C4' U B1495 OK 604 601 603 622 C4' C B1496 OK 624 621 623 642 C4' G B1497 OK 644 641 643 665 C4' C B 98 OK 667 664 666 685 C4' C B 99 OK 687 684 686 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 25 C5' G A 2 24 26 48 C5' G A 3 47 49 71 C5' C A1404 70 72 91 C5' G A1405 90 92 114 C5' U A1406 113 115 134 C5' C A1407 133 135 154 C5' G A1408 153 155 177 C5' C A1409 176 178 197 C5' U A1410 196 198 217 C5' A A1411 216 218 239 C5' G A1412 238 240 262 C5' U A1413 261 263 282 C5' A A 14 281 283 304 C5' C A 15 303 305 324 C5' C A 16 323 325 342 C5' C B 83 341 343 362 C5' G B 84 361 363 385 C5' G B 85 384 386 408 C5' U B 86 407 409 428 C5' A B1487 427 429 450 C5' C B1488 449 451 470 C5' U B1489 469 471 490 C5' A B1490 489 491 512 C5' A B1491 511 513 534 C5' A B1492 533 535 556 C5' A B1493 555 557 578 C5' G B1494 577 579 601 C5' U B1495 600 602 621 C5' C B1496 620 622 641 C5' G B1497 640 642 664 C5' C B 98 663 665 684 C5' C B 99 683 685 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P G A 2 distorted distorted 6 22 23 24 44 P G A 3 distorted distorted 29 45 46 47 67 P C A1404 distorted distorted 52 68 69 70 87 P G A1405 distorted distorted 75 88 89 90 110 P U A1406 distorted distorted 95 111 112 113 130 P C A1407 distorted distorted 118 131 132 133 150 P G A1408 distorted distorted 138 151 152 153 173 P C A1409 distorted distorted 158 174 175 176 193 P U A1410 distorted distorted 181 194 195 196 213 P A A1411 distorted distorted 201 214 215 216 235 P G A1412 distorted distorted 221 236 237 238 258 P U A1413 distorted distorted 243 259 260 261 278 P A A 14 distorted distorted 266 279 280 281 300 P C A 15 distorted distorted 286 301 302 303 320 P C A 16 distorted distorted 308 321 322 323 358 P G B 84 distorted distorted 346 359 360 361 381 P G B 85 distorted distorted 366 382 383 384 404 P U B 86 distorted distorted 389 405 406 407 424 P A B1487 distorted distorted 412 425 426 427 446 P C B1488 distorted distorted 432 447 448 449 466 P U B1489 distorted distorted 454 467 468 469 486 P A B1490 distorted distorted 474 487 488 489 508 P A B1491 distorted distorted 494 509 510 511 530 P A B1492 distorted distorted 516 531 532 533 552 P A B1493 distorted distorted 538 553 554 555 574 P G B1494 distorted distorted 560 575 576 577 597 P U B1495 distorted distorted 582 598 599 600 617 P C B1496 distorted distorted 605 618 619 620 637 P G B1497 distorted distorted 625 638 639 640 660 P C B 98 distorted distorted 645 661 662 663 680 P C B 99 distorted distorted 668 681 682 683 ---------------------------------------------------------------------------------