ID code: '1C0W' 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' --------------------------------------------------------------------------------- 11 C1' A E 401 beta 7 12 10 32 C1' T E 402 beta 28 33 31 52 C1' T E 403 beta 48 53 51 72 C1' A E 404 beta 68 73 71 93 C1' G E 405 beta 89 94 92 115 C1' G E 406 beta 111 116 114 137 C1' T E 407 beta 133 138 136 157 C1' T E 408 beta 153 158 156 177 C1' A E 409 beta 173 178 176 198 C1' G E 410 beta 194 199 197 220 C1' C E 411 beta 216 221 219 239 C1' C E 412 beta 235 240 238 258 C1' T E 413 beta 254 259 257 278 C1' A E 414 beta 274 279 277 299 C1' C E 415 beta 295 300 298 318 C1' C E 416 beta 314 319 317 337 C1' C E 417 beta 333 338 336 356 C1' T E 418 beta 352 357 355 376 C1' A E 419 beta 372 377 375 397 C1' A E 420 beta 393 398 396 418 C1' T E 421 beta 414 419 417 439 C1' A F 501 beta 435 440 438 460 C1' T F 502 beta 456 461 459 480 C1' T F 503 beta 476 481 479 500 C1' A F 504 beta 496 501 499 521 C1' G F 505 beta 517 522 520 543 C1' G F 506 beta 539 544 542 565 C1' T F 507 beta 561 566 564 585 C1' T F 508 beta 581 586 584 605 C1' A F 509 beta 601 606 604 626 C1' G F 510 beta 622 627 625 648 C1' G F 511 beta 644 649 647 670 C1' C F 512 beta 666 671 669 689 C1' T F 513 beta 685 690 688 709 C1' A F 514 beta 705 710 708 730 C1' C F 515 beta 726 731 729 749 C1' C F 516 beta 745 750 748 768 C1' C F 517 beta 764 769 767 787 C1' T F 518 beta 783 788 786 807 C1' A F 519 beta 803 808 806 828 C1' A F 520 beta 824 829 827 849 C1' T F 521 beta 845 850 848 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' A E 401 11 8 31 C2' T E 402 32 29 51 C2' T E 403 52 49 71 C2' A E 404 72 69 92 C2' G E 405 93 90 114 C2' G E 406 115 112 136 C2' T E 407 137 134 156 C2' T E 408 157 154 176 C2' A E 409 177 174 197 C2' G E 410 198 195 219 C2' C E 411 220 217 238 C2' C E 412 239 236 257 C2' T E 413 258 255 277 C2' A E 414 278 275 298 C2' C E 415 299 296 317 C2' C E 416 318 315 336 C2' C E 417 337 334 355 C2' T E 418 356 353 375 C2' A E 419 376 373 396 C2' A E 420 397 394 417 C2' T E 421 418 415 438 C2' A F 501 439 436 459 C2' T F 502 460 457 479 C2' T F 503 480 477 499 C2' A F 504 500 497 520 C2' G F 505 521 518 542 C2' G F 506 543 540 564 C2' T F 507 565 562 584 C2' T F 508 585 582 604 C2' A F 509 605 602 625 C2' G F 510 626 623 647 C2' G F 511 648 645 669 C2' C F 512 670 667 688 C2' T F 513 689 686 708 C2' A F 514 709 706 729 C2' C F 515 730 727 748 C2' C F 516 749 746 767 C2' C F 517 768 765 786 C2' T F 518 787 784 806 C2' A F 519 807 804 827 C2' A F 520 828 825 848 C2' T F 521 849 846 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A E 401 OK 6 9 10 29 C3' T E 402 OK 27 30 31 49 C3' T E 403 OK 47 50 51 69 C3' A E 404 OK 67 70 71 90 C3' G E 405 OK 88 91 92 112 C3' G E 406 OK 110 113 114 134 C3' T E 407 OK 132 135 136 154 C3' T E 408 OK 152 155 156 174 C3' A E 409 OK 172 175 176 195 C3' G E 410 OK 193 196 197 217 C3' C E 411 OK 215 218 219 236 C3' C E 412 OK 234 237 238 255 C3' T E 413 OK 253 256 257 275 C3' A E 414 OK 273 276 277 296 C3' C E 415 OK 294 297 298 315 C3' C E 416 OK 313 316 317 334 C3' C E 417 OK 332 335 336 353 C3' T E 418 OK 351 354 355 373 C3' A E 419 OK 371 374 375 394 C3' A E 420 OK 392 395 396 415 C3' T E 421 OK 413 416 417 436 C3' A F 501 OK 434 437 438 457 C3' T F 502 OK 455 458 459 477 C3' T F 503 OK 475 478 479 497 C3' A F 504 OK 495 498 499 518 C3' G F 505 OK 516 519 520 540 C3' G F 506 OK 538 541 542 562 C3' T F 507 OK 560 563 564 582 C3' T F 508 OK 580 583 584 602 C3' A F 509 OK 600 603 604 623 C3' G F 510 OK 621 624 625 645 C3' G F 511 OK 643 646 647 667 C3' C F 512 OK 665 668 669 686 C3' T F 513 OK 684 687 688 706 C3' A F 514 OK 704 707 708 727 C3' C F 515 OK 725 728 729 746 C3' C F 516 OK 744 747 748 765 C3' C F 517 OK 763 766 767 784 C3' T F 518 OK 782 785 786 804 C3' A F 519 OK 802 805 806 825 C3' A F 520 OK 823 826 827 846 C3' T F 521 OK 844 847 848 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A E 401 OK 8 5 7 27 C4' T E 402 OK 29 26 28 47 C4' T E 403 OK 49 46 48 67 C4' A E 404 OK 69 66 68 88 C4' G E 405 OK 90 87 89 110 C4' G E 406 OK 112 109 111 132 C4' T E 407 OK 134 131 133 152 C4' T E 408 OK 154 151 153 172 C4' A E 409 OK 174 171 173 193 C4' G E 410 OK 195 192 194 215 C4' C E 411 OK 217 214 216 234 C4' C E 412 OK 236 233 235 253 C4' T E 413 OK 255 252 254 273 C4' A E 414 OK 275 272 274 294 C4' C E 415 OK 296 293 295 313 C4' C E 416 OK 315 312 314 332 C4' C E 417 OK 334 331 333 351 C4' T E 418 OK 353 350 352 371 C4' A E 419 OK 373 370 372 392 C4' A E 420 OK 394 391 393 413 C4' T E 421 OK 415 412 414 434 C4' A F 501 OK 436 433 435 455 C4' T F 502 OK 457 454 456 475 C4' T F 503 OK 477 474 476 495 C4' A F 504 OK 497 494 496 516 C4' G F 505 OK 518 515 517 538 C4' G F 506 OK 540 537 539 560 C4' T F 507 OK 562 559 561 580 C4' T F 508 OK 582 579 581 600 C4' A F 509 OK 602 599 601 621 C4' G F 510 OK 623 620 622 643 C4' G F 511 OK 645 642 644 665 C4' C F 512 OK 667 664 666 684 C4' T F 513 OK 686 683 685 704 C4' A F 514 OK 706 703 705 725 C4' C F 515 OK 727 724 726 744 C4' C F 516 OK 746 743 745 763 C4' C F 517 OK 765 762 764 782 C4' T F 518 OK 784 781 783 802 C4' A F 519 OK 804 801 803 823 C4' A F 520 OK 825 822 824 844 C4' T F 521 OK 846 843 845 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A E 401 4 6 26 C5' T E 402 25 27 46 C5' T E 403 45 47 66 C5' A E 404 65 67 87 C5' G E 405 86 88 109 C5' G E 406 108 110 131 C5' T E 407 130 132 151 C5' T E 408 150 152 171 C5' A E 409 170 172 192 C5' G E 410 191 193 214 C5' C E 411 213 215 233 C5' C E 412 232 234 252 C5' T E 413 251 253 272 C5' A E 414 271 273 293 C5' C E 415 292 294 312 C5' C E 416 311 313 331 C5' C E 417 330 332 350 C5' T E 418 349 351 370 C5' A E 419 369 371 391 C5' A E 420 390 392 412 C5' T E 421 411 413 433 C5' A F 501 432 434 454 C5' T F 502 453 455 474 C5' T F 503 473 475 494 C5' A F 504 493 495 515 C5' G F 505 514 516 537 C5' G F 506 536 538 559 C5' T F 507 558 560 579 C5' T F 508 578 580 599 C5' A F 509 598 600 620 C5' G F 510 619 621 642 C5' G F 511 641 643 664 C5' C F 512 663 665 683 C5' T F 513 682 684 703 C5' A F 514 702 704 724 C5' C F 515 723 725 743 C5' C F 516 742 744 762 C5' C F 517 761 763 781 C5' T F 518 780 782 801 C5' A F 519 800 802 822 C5' A F 520 821 823 843 C5' T F 521 842 844 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A E 401 OK OK 2 3 4 22 P T E 402 distorted distorted 9 23 24 25 42 P T E 403 distorted distorted 30 43 44 45 62 P A E 404 distorted distorted 50 63 64 65 83 P G E 405 distorted distorted 70 84 85 86 105 P G E 406 distorted distorted 91 106 107 108 127 P T E 407 distorted distorted 113 128 129 130 147 P T E 408 distorted distorted 135 148 149 150 167 P A E 409 distorted distorted 155 168 169 170 188 P G E 410 distorted distorted 175 189 190 191 210 P C E 411 distorted distorted 196 211 212 213 229 P C E 412 distorted distorted 218 230 231 232 248 P T E 413 distorted distorted 237 249 250 251 268 P A E 414 distorted distorted 256 269 270 271 289 P C E 415 distorted distorted 276 290 291 292 308 P C E 416 distorted distorted 297 309 310 311 327 P C E 417 distorted distorted 316 328 329 330 346 P T E 418 distorted distorted 335 347 348 349 366 P A E 419 distorted distorted 354 367 368 369 387 P A E 420 distorted distorted 374 388 389 390 408 P T E 421 distorted distorted 395 409 410 411 429 P A F 501 OK OK 430 431 432 450 P T F 502 distorted distorted 437 451 452 453 470 P T F 503 distorted distorted 458 471 472 473 490 P A F 504 distorted distorted 478 491 492 493 511 P G F 505 distorted distorted 498 512 513 514 533 P G F 506 distorted distorted 519 534 535 536 555 P T F 507 distorted distorted 541 556 557 558 575 P T F 508 distorted distorted 563 576 577 578 595 P A F 509 distorted distorted 583 596 597 598 616 P G F 510 distorted distorted 603 617 618 619 638 P G F 511 distorted distorted 624 639 640 641 660 P C F 512 distorted distorted 646 661 662 663 679 P T F 513 distorted distorted 668 680 681 682 699 P A F 514 distorted distorted 687 700 701 702 720 P C F 515 distorted distorted 707 721 722 723 739 P C F 516 distorted distorted 728 740 741 742 758 P C F 517 distorted distorted 747 759 760 761 777 P T F 518 distorted distorted 766 778 779 780 797 P A F 519 distorted distorted 785 798 799 800 818 P A F 520 distorted distorted 805 819 820 821 839 P T F 521 distorted distorted 826 840 841 842 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