ID code: '1KFO' 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' A A 2 beta 27 33 30 54 C1' A A 3 beta 49 55 52 76 C1' U A 4 beta 71 77 74 96 C1' G A 5 beta 91 97 94 119 C1' C A 6 beta 114 120 117 139 C1' C A 7 beta 134 140 137 159 C1' U A 8 beta 154 160 157 179 C1' G A 9 beta 174 180 177 202 C1' C A 10 beta 197 203 200 222 C1' G A 11 beta 217 223 220 245 C1' A A 12 beta 240 246 243 267 C1' G A 13 beta 262 268 265 290 C1' C A 14 beta 285 291 288 310 C1' A A 15 beta 305 311 308 332 C1' +U A 16 beta 327 333 330 352 C1' C A 17 beta 347 353 350 372 C1' C A 18 beta 367 373 370 390 C1' G B 1 beta 385 391 388 413 C1' A B 2 beta 408 414 411 435 C1' A B 3 beta 430 436 433 457 C1' U B 4 beta 452 458 455 477 C1' G B 5 beta 472 478 475 500 C1' C B 6 beta 495 501 498 520 C1' C B 7 beta 515 521 518 540 C1' U B 8 beta 535 541 538 560 C1' G B 9 beta 555 561 558 583 C1' C B 10 beta 578 584 581 603 C1' G B 11 beta 598 604 601 626 C1' A B 12 beta 621 627 624 648 C1' G B 13 beta 643 649 646 671 C1' C B 14 beta 666 672 669 691 C1' A B 15 beta 686 692 689 713 C1' +U B 16 beta 708 714 711 733 C1' C B 17 beta 728 734 731 753 C1' C B 18 beta 748 754 751 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 2 OK 32 28 31 52 C2' A A 3 OK 54 50 53 74 C2' U A 4 OK 76 72 75 94 C2' G A 5 OK 96 92 95 117 C2' C A 6 OK 119 115 118 137 C2' C A 7 OK 139 135 138 157 C2' U A 8 OK 159 155 158 177 C2' G A 9 OK 179 175 178 200 C2' C A 10 OK 202 198 201 220 C2' G A 11 OK 222 218 221 243 C2' A A 12 OK 245 241 244 265 C2' G A 13 OK 267 263 266 288 C2' C A 14 OK 290 286 289 308 C2' A A 15 OK 310 306 309 330 C2' +U A 16 OK 332 328 331 350 C2' C A 17 OK 352 348 351 370 C2' C A 18 OK 372 368 371 388 C2' G B 1 OK 390 386 389 411 C2' A B 2 OK 413 409 412 433 C2' A B 3 OK 435 431 434 455 C2' U B 4 OK 457 453 456 475 C2' G B 5 OK 477 473 476 498 C2' C B 6 OK 500 496 499 518 C2' C B 7 OK 520 516 519 538 C2' U B 8 OK 540 536 539 558 C2' G B 9 OK 560 556 559 581 C2' C B 10 OK 583 579 582 601 C2' G B 11 OK 603 599 602 624 C2' A B 12 OK 626 622 625 646 C2' G B 13 OK 648 644 647 669 C2' C B 14 OK 671 667 670 689 C2' A B 15 OK 691 687 690 711 C2' +U B 16 OK 713 709 712 731 C2' C B 17 OK 733 729 732 751 C2' C B 18 OK 753 749 752 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 28 C3' A A 2 OK 26 29 30 50 C3' A A 3 OK 48 51 52 72 C3' U A 4 OK 70 73 74 92 C3' G A 5 OK 90 93 94 115 C3' C A 6 OK 113 116 117 135 C3' C A 7 OK 133 136 137 155 C3' U A 8 OK 153 156 157 175 C3' G A 9 OK 173 176 177 198 C3' C A 10 OK 196 199 200 218 C3' G A 11 OK 216 219 220 241 C3' A A 12 OK 239 242 243 263 C3' G A 13 OK 261 264 265 286 C3' C A 14 OK 284 287 288 306 C3' A A 15 OK 304 307 308 328 C3' +U A 16 OK 326 329 330 348 C3' C A 17 OK 346 349 350 368 C3' C A 18 OK 366 369 370 386 C3' G B 1 OK 384 387 388 409 C3' A B 2 OK 407 410 411 431 C3' A B 3 OK 429 432 433 453 C3' U B 4 OK 451 454 455 473 C3' G B 5 OK 471 474 475 496 C3' C B 6 OK 494 497 498 516 C3' C B 7 OK 514 517 518 536 C3' U B 8 OK 534 537 538 556 C3' G B 9 OK 554 557 558 579 C3' C B 10 OK 577 580 581 599 C3' G B 11 OK 597 600 601 622 C3' A B 12 OK 620 623 624 644 C3' G B 13 OK 642 645 646 667 C3' C B 14 OK 665 668 669 687 C3' A B 15 OK 685 688 689 709 C3' +U B 16 OK 707 710 711 729 C3' C B 17 OK 727 730 731 749 C3' C B 18 OK 747 750 751 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 26 C4' A A 2 OK 28 25 27 48 C4' A A 3 OK 50 47 49 70 C4' U A 4 OK 72 69 71 90 C4' G A 5 OK 92 89 91 113 C4' C A 6 OK 115 112 114 133 C4' C A 7 OK 135 132 134 153 C4' U A 8 OK 155 152 154 173 C4' G A 9 OK 175 172 174 196 C4' C A 10 OK 198 195 197 216 C4' G A 11 OK 218 215 217 239 C4' A A 12 OK 241 238 240 261 C4' G A 13 OK 263 260 262 284 C4' C A 14 OK 286 283 285 304 C4' A A 15 OK 306 303 305 326 C4' +U A 16 OK 328 325 327 346 C4' C A 17 OK 348 345 347 366 C4' C A 18 OK 368 365 367 384 C4' G B 1 OK 386 383 385 407 C4' A B 2 OK 409 406 408 429 C4' A B 3 OK 431 428 430 451 C4' U B 4 OK 453 450 452 471 C4' G B 5 OK 473 470 472 494 C4' C B 6 OK 496 493 495 514 C4' C B 7 OK 516 513 515 534 C4' U B 8 OK 536 533 535 554 C4' G B 9 OK 556 553 555 577 C4' C B 10 OK 579 576 578 597 C4' G B 11 OK 599 596 598 620 C4' A B 12 OK 622 619 621 642 C4' G B 13 OK 644 641 643 665 C4' C B 14 OK 667 664 666 685 C4' A B 15 OK 687 684 686 707 C4' +U B 16 OK 709 706 708 727 C4' C B 17 OK 729 726 728 747 C4' C B 18 OK 749 746 748 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 25 C5' A A 2 24 26 47 C5' A A 3 46 48 69 C5' U A 4 68 70 89 C5' G A 5 88 90 112 C5' C A 6 111 113 132 C5' C A 7 131 133 152 C5' U A 8 151 153 172 C5' G A 9 171 173 195 C5' C A 10 194 196 215 C5' G A 11 214 216 238 C5' A A 12 237 239 260 C5' G A 13 259 261 283 C5' C A 14 282 284 303 C5' A A 15 302 304 325 C5' +U A 16 324 326 345 C5' C A 17 344 346 365 C5' C A 18 364 366 383 C5' G B 1 382 384 406 C5' A B 2 405 407 428 C5' A B 3 427 429 450 C5' U B 4 449 451 470 C5' G B 5 469 471 493 C5' C B 6 492 494 513 C5' C B 7 512 514 533 C5' U B 8 532 534 553 C5' G B 9 552 554 576 C5' C B 10 575 577 596 C5' G B 11 595 597 619 C5' A B 12 618 620 641 C5' G B 13 640 642 664 C5' C B 14 663 665 684 C5' A B 15 683 685 706 C5' +U B 16 705 707 726 C5' C B 17 725 727 746 C5' C B 18 745 747 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P A A 2 distorted distorted 6 22 23 24 43 P A A 3 distorted distorted 29 44 45 46 65 P U A 4 distorted distorted 51 66 67 68 85 P G A 5 distorted distorted 73 86 87 88 108 P C A 6 distorted distorted 93 109 110 111 128 P C A 7 distorted distorted 116 129 130 131 148 P U A 8 distorted distorted 136 149 150 151 168 P G A 9 distorted distorted 156 169 170 171 191 P C A 10 distorted distorted 176 192 193 194 211 P G A 11 distorted distorted 199 212 213 214 234 P A A 12 distorted distorted 219 235 236 237 256 P G A 13 distorted distorted 242 257 258 259 279 P C A 14 distorted distorted 264 280 281 282 299 P A A 15 distorted distorted 287 300 301 302 321 P +U A 16 OK OK 307 322 323 324 341 P C A 17 distorted distorted 329 342 343 344 361 P C A 18 distorted distorted 349 362 363 364 402 P A B 2 distorted distorted 387 403 404 405 424 P A B 3 distorted distorted 410 425 426 427 446 P U B 4 distorted distorted 432 447 448 449 466 P G B 5 distorted distorted 454 467 468 469 489 P C B 6 distorted distorted 474 490 491 492 509 P C B 7 distorted distorted 497 510 511 512 529 P U B 8 distorted distorted 517 530 531 532 549 P G B 9 distorted distorted 537 550 551 552 572 P C B 10 distorted distorted 557 573 574 575 592 P G B 11 distorted distorted 580 593 594 595 615 P A B 12 distorted distorted 600 616 617 618 637 P G B 13 distorted distorted 623 638 639 640 660 P C B 14 distorted distorted 645 661 662 663 680 P A B 15 distorted distorted 668 681 682 683 702 P +U B 16 OK OK 688 703 704 705 722 P C B 17 distorted distorted 710 723 724 725 742 P C B 18 distorted distorted 730 743 744 745 ---------------------------------------------------------------------------------