ID code: '1GXP' 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 G 2 beta 7 12 10 32 C1' G G 3 beta 28 33 31 54 C1' C G 4 beta 50 55 53 73 C1' T G 5 beta 69 74 72 93 C1' G G 6 beta 89 94 92 115 C1' T G 7 beta 111 116 114 135 C1' C G 8 beta 131 136 134 154 C1' A G 9 beta 150 155 153 175 C1' T G 10 beta 171 176 174 195 C1' A G 11 beta 191 196 194 216 C1' A G 12 beta 212 217 215 237 C1' A G 13 beta 233 238 236 258 C1' G G 14 beta 254 259 257 280 C1' T G 15 beta 276 281 279 300 C1' T G 16 beta 296 301 299 320 C1' G G 17 beta 316 321 319 342 C1' T G 18 beta 338 343 341 362 C1' C G 19 beta 358 363 361 381 C1' A G 20 beta 377 382 380 402 C1' C G 21 beta 398 403 401 421 C1' G G 22 beta 417 422 420 443 C1' G G 23 beta 439 444 442 466 C1' C H 2 beta 462 467 465 485 C1' C H 3 beta 481 486 484 504 C1' G H 4 beta 500 505 503 526 C1' T H 5 beta 522 527 525 546 C1' G H 6 beta 542 547 545 568 C1' A H 7 beta 564 569 567 589 C1' C H 8 beta 585 590 588 608 C1' A H 9 beta 604 609 607 629 C1' A H 10 beta 625 630 628 650 C1' C H 11 beta 646 651 649 669 C1' T H 12 beta 665 670 668 689 C1' T H 13 beta 685 690 688 709 C1' T H 14 beta 705 710 708 729 C1' A H 15 beta 725 730 728 750 C1' T H 16 beta 746 751 749 770 C1' G H 17 beta 766 771 769 792 C1' A H 18 beta 788 793 791 813 C1' C H 19 beta 809 814 812 832 C1' A H 20 beta 828 833 831 853 C1' G H 21 beta 849 854 852 875 C1' C H 22 beta 871 876 874 894 C1' T H 23 beta 890 895 893 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' A G 2 11 8 31 C2' G G 3 32 29 53 C2' C G 4 54 51 72 C2' T G 5 73 70 92 C2' G G 6 93 90 114 C2' T G 7 115 112 134 C2' C G 8 135 132 153 C2' A G 9 154 151 174 C2' T G 10 175 172 194 C2' A G 11 195 192 215 C2' A G 12 216 213 236 C2' A G 13 237 234 257 C2' G G 14 258 255 279 C2' T G 15 280 277 299 C2' T G 16 300 297 319 C2' G G 17 320 317 341 C2' T G 18 342 339 361 C2' C G 19 362 359 380 C2' A G 20 381 378 401 C2' C G 21 402 399 420 C2' G G 22 421 418 442 C2' G G 23 443 440 465 C2' C H 2 466 463 484 C2' C H 3 485 482 503 C2' G H 4 504 501 525 C2' T H 5 526 523 545 C2' G H 6 546 543 567 C2' A H 7 568 565 588 C2' C H 8 589 586 607 C2' A H 9 608 605 628 C2' A H 10 629 626 649 C2' C H 11 650 647 668 C2' T H 12 669 666 688 C2' T H 13 689 686 708 C2' T H 14 709 706 728 C2' A H 15 729 726 749 C2' T H 16 750 747 769 C2' G H 17 770 767 791 C2' A H 18 792 789 812 C2' C H 19 813 810 831 C2' A H 20 832 829 852 C2' G H 21 853 850 874 C2' C H 22 875 872 893 C2' T H 23 894 891 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A G 2 OK 6 9 10 29 C3' G G 3 OK 27 30 31 51 C3' C G 4 OK 49 52 53 70 C3' T G 5 OK 68 71 72 90 C3' G G 6 OK 88 91 92 112 C3' T G 7 OK 110 113 114 132 C3' C G 8 OK 130 133 134 151 C3' A G 9 OK 149 152 153 172 C3' T G 10 OK 170 173 174 192 C3' A G 11 OK 190 193 194 213 C3' A G 12 OK 211 214 215 234 C3' A G 13 OK 232 235 236 255 C3' G G 14 OK 253 256 257 277 C3' T G 15 OK 275 278 279 297 C3' T G 16 OK 295 298 299 317 C3' G G 17 OK 315 318 319 339 C3' T G 18 OK 337 340 341 359 C3' C G 19 OK 357 360 361 378 C3' A G 20 OK 376 379 380 399 C3' C G 21 OK 397 400 401 418 C3' G G 22 OK 416 419 420 440 C3' G G 23 OK 438 441 442 463 C3' C H 2 OK 461 464 465 482 C3' C H 3 OK 480 483 484 501 C3' G H 4 OK 499 502 503 523 C3' T H 5 OK 521 524 525 543 C3' G H 6 OK 541 544 545 565 C3' A H 7 OK 563 566 567 586 C3' C H 8 OK 584 587 588 605 C3' A H 9 OK 603 606 607 626 C3' A H 10 OK 624 627 628 647 C3' C H 11 OK 645 648 649 666 C3' T H 12 OK 664 667 668 686 C3' T H 13 OK 684 687 688 706 C3' T H 14 OK 704 707 708 726 C3' A H 15 OK 724 727 728 747 C3' T H 16 OK 745 748 749 767 C3' G H 17 OK 765 768 769 789 C3' A H 18 OK 787 790 791 810 C3' C H 19 OK 808 811 812 829 C3' A H 20 OK 827 830 831 850 C3' G H 21 OK 848 851 852 872 C3' C H 22 OK 870 873 874 891 C3' T H 23 OK 889 892 893 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A G 2 OK 8 5 7 27 C4' G G 3 OK 29 26 28 49 C4' C G 4 OK 51 48 50 68 C4' T G 5 OK 70 67 69 88 C4' G G 6 OK 90 87 89 110 C4' T G 7 OK 112 109 111 130 C4' C G 8 OK 132 129 131 149 C4' A G 9 OK 151 148 150 170 C4' T G 10 OK 172 169 171 190 C4' A G 11 OK 192 189 191 211 C4' A G 12 OK 213 210 212 232 C4' A G 13 OK 234 231 233 253 C4' G G 14 OK 255 252 254 275 C4' T G 15 OK 277 274 276 295 C4' T G 16 OK 297 294 296 315 C4' G G 17 OK 317 314 316 337 C4' T G 18 OK 339 336 338 357 C4' C G 19 OK 359 356 358 376 C4' A G 20 OK 378 375 377 397 C4' C G 21 OK 399 396 398 416 C4' G G 22 OK 418 415 417 438 C4' G G 23 OK 440 437 439 461 C4' C H 2 OK 463 460 462 480 C4' C H 3 OK 482 479 481 499 C4' G H 4 OK 501 498 500 521 C4' T H 5 OK 523 520 522 541 C4' G H 6 OK 543 540 542 563 C4' A H 7 OK 565 562 564 584 C4' C H 8 OK 586 583 585 603 C4' A H 9 OK 605 602 604 624 C4' A H 10 OK 626 623 625 645 C4' C H 11 OK 647 644 646 664 C4' T H 12 OK 666 663 665 684 C4' T H 13 OK 686 683 685 704 C4' T H 14 OK 706 703 705 724 C4' A H 15 OK 726 723 725 745 C4' T H 16 OK 747 744 746 765 C4' G H 17 OK 767 764 766 787 C4' A H 18 OK 789 786 788 808 C4' C H 19 OK 810 807 809 827 C4' A H 20 OK 829 826 828 848 C4' G H 21 OK 850 847 849 870 C4' C H 22 OK 872 869 871 889 C4' T H 23 OK 891 888 890 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A G 2 4 6 26 C5' G G 3 25 27 48 C5' C G 4 47 49 67 C5' T G 5 66 68 87 C5' G G 6 86 88 109 C5' T G 7 108 110 129 C5' C G 8 128 130 148 C5' A G 9 147 149 169 C5' T G 10 168 170 189 C5' A G 11 188 190 210 C5' A G 12 209 211 231 C5' A G 13 230 232 252 C5' G G 14 251 253 274 C5' T G 15 273 275 294 C5' T G 16 293 295 314 C5' G G 17 313 315 336 C5' T G 18 335 337 356 C5' C G 19 355 357 375 C5' A G 20 374 376 396 C5' C G 21 395 397 415 C5' G G 22 414 416 437 C5' G G 23 436 438 460 C5' C H 2 459 461 479 C5' C H 3 478 480 498 C5' G H 4 497 499 520 C5' T H 5 519 521 540 C5' G H 6 539 541 562 C5' A H 7 561 563 583 C5' C H 8 582 584 602 C5' A H 9 601 603 623 C5' A H 10 622 624 644 C5' C H 11 643 645 663 C5' T H 12 662 664 683 C5' T H 13 682 684 703 C5' T H 14 702 704 723 C5' A H 15 722 724 744 C5' T H 16 743 745 764 C5' G H 17 763 765 786 C5' A H 18 785 787 807 C5' C H 19 806 808 826 C5' A H 20 825 827 847 C5' G H 21 846 848 869 C5' C H 22 868 870 888 C5' T H 23 887 889 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A G 2 distorted distorted 2 3 4 22 P G G 3 distorted distorted 9 23 24 25 44 P C G 4 distorted distorted 30 45 46 47 63 P T G 5 distorted distorted 52 64 65 66 83 P G G 6 distorted distorted 71 84 85 86 105 P T G 7 distorted distorted 91 106 107 108 125 P C G 8 distorted distorted 113 126 127 128 144 P A G 9 distorted distorted 133 145 146 147 165 P T G 10 distorted distorted 152 166 167 168 185 P A G 11 distorted distorted 173 186 187 188 206 P A G 12 distorted distorted 193 207 208 209 227 P A G 13 distorted distorted 214 228 229 230 248 P G G 14 distorted distorted 235 249 250 251 270 P T G 15 distorted distorted 256 271 272 273 290 P T G 16 distorted distorted 278 291 292 293 310 P G G 17 distorted distorted 298 311 312 313 332 P T G 18 distorted distorted 318 333 334 335 352 P C G 19 distorted distorted 340 353 354 355 371 P A G 20 distorted distorted 360 372 373 374 392 P C G 21 distorted distorted 379 393 394 395 411 P G G 22 distorted distorted 400 412 413 414 433 P G G 23 distorted distorted 419 434 435 436 456 P C H 2 distorted distorted 457 458 459 475 P C H 3 distorted distorted 464 476 477 478 494 P G H 4 distorted distorted 483 495 496 497 516 P T H 5 distorted distorted 502 517 518 519 536 P G H 6 distorted distorted 524 537 538 539 558 P A H 7 distorted distorted 544 559 560 561 579 P C H 8 distorted distorted 566 580 581 582 598 P A H 9 distorted distorted 587 599 600 601 619 P A H 10 distorted distorted 606 620 621 622 640 P C H 11 distorted distorted 627 641 642 643 659 P T H 12 distorted distorted 648 660 661 662 679 P T H 13 distorted distorted 667 680 681 682 699 P T H 14 distorted distorted 687 700 701 702 719 P A H 15 distorted distorted 707 720 721 722 740 P T H 16 distorted distorted 727 741 742 743 760 P G H 17 distorted distorted 748 761 762 763 782 P A H 18 distorted distorted 768 783 784 785 803 P C H 19 distorted distorted 790 804 805 806 822 P A H 20 distorted distorted 811 823 824 825 843 P G H 21 distorted distorted 830 844 845 846 865 P C H 22 distorted distorted 851 866 867 868 884 P T H 23 distorted distorted 873 885 886 887 ---------------------------------------------------------------------------------