ID code: '3BNP' 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' C A 1 beta 4 10 7 29 C1' G A 2 beta 24 30 27 52 C1' C A 3 beta 47 53 50 72 C1' G A 4 beta 67 73 70 95 C1' U A 5 beta 90 96 93 115 C1' C A 6 beta 110 116 113 135 C1' A A 7 beta 130 136 133 157 C1' C A 8 beta 152 158 155 177 C1' C A 9 beta 172 178 175 197 C1' C A 10 beta 192 198 195 217 C1' C A 11 beta 212 218 215 237 C1' G A 12 beta 232 238 235 260 C1' G A 13 beta 255 261 258 283 C1' G A 14 beta 278 284 281 306 C1' C A 15 beta 301 307 304 326 C1' A A 16 beta 321 327 324 348 C1' A A 17 beta 343 349 346 370 C1' G A 18 beta 365 371 368 393 C1' U A 19 beta 388 394 391 413 C1' C A 20 beta 408 414 411 433 C1' G A 21 beta 428 434 431 456 C1' C A 22 beta 451 457 454 474 C1' G B 1 beta 469 475 472 497 C1' C B 2 beta 492 498 495 517 C1' G B 3 beta 512 518 515 540 C1' U B 4 beta 535 541 538 560 C1' C B 5 beta 555 561 558 580 C1' A B 6 beta 575 581 578 602 C1' C B 7 beta 597 603 600 622 C1' C B 8 beta 617 623 620 642 C1' C B 9 beta 637 643 640 662 C1' C B 10 beta 657 663 660 682 C1' G B 11 beta 677 683 680 705 C1' G B 12 beta 700 706 703 728 C1' G B 13 beta 723 729 726 751 C1' C B 14 beta 746 752 749 771 C1' A B 15 beta 766 772 769 793 C1' A B 16 beta 788 794 791 815 C1' G B 17 beta 810 816 813 838 C1' U B 18 beta 833 839 836 858 C1' C B 19 beta 853 859 856 878 C1' G B 20 beta 873 879 876 901 C1' C B 21 beta 896 902 899 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 1 OK 9 5 8 27 C2' G A 2 OK 29 25 28 50 C2' C A 3 OK 52 48 51 70 C2' G A 4 OK 72 68 71 93 C2' U A 5 OK 95 91 94 113 C2' C A 6 OK 115 111 114 133 C2' A A 7 OK 135 131 134 155 C2' C A 8 OK 157 153 156 175 C2' C A 9 OK 177 173 176 195 C2' C A 10 OK 197 193 196 215 C2' C A 11 OK 217 213 216 235 C2' G A 12 OK 237 233 236 258 C2' G A 13 OK 260 256 259 281 C2' G A 14 OK 283 279 282 304 C2' C A 15 OK 306 302 305 324 C2' A A 16 OK 326 322 325 346 C2' A A 17 OK 348 344 347 368 C2' G A 18 OK 370 366 369 391 C2' U A 19 OK 393 389 392 411 C2' C A 20 OK 413 409 412 431 C2' G A 21 OK 433 429 432 454 C2' C A 22 OK 456 452 455 472 C2' G B 1 OK 474 470 473 495 C2' C B 2 OK 497 493 496 515 C2' G B 3 OK 517 513 516 538 C2' U B 4 OK 540 536 539 558 C2' C B 5 OK 560 556 559 578 C2' A B 6 OK 580 576 579 600 C2' C B 7 OK 602 598 601 620 C2' C B 8 OK 622 618 621 640 C2' C B 9 OK 642 638 641 660 C2' C B 10 OK 662 658 661 680 C2' G B 11 OK 682 678 681 703 C2' G B 12 OK 705 701 704 726 C2' G B 13 OK 728 724 727 749 C2' C B 14 OK 751 747 750 769 C2' A B 15 OK 771 767 770 791 C2' A B 16 OK 793 789 792 813 C2' G B 17 OK 815 811 814 836 C2' U B 18 OK 838 834 837 856 C2' C B 19 OK 858 854 857 876 C2' G B 20 OK 878 874 877 899 C2' C B 21 OK 901 897 900 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK 3 6 7 25 C3' G A 2 OK 23 26 27 48 C3' C A 3 OK 46 49 50 68 C3' G A 4 OK 66 69 70 91 C3' U A 5 OK 89 92 93 111 C3' C A 6 OK 109 112 113 131 C3' A A 7 OK 129 132 133 153 C3' C A 8 OK 151 154 155 173 C3' C A 9 OK 171 174 175 193 C3' C A 10 OK 191 194 195 213 C3' C A 11 OK 211 214 215 233 C3' G A 12 OK 231 234 235 256 C3' G A 13 OK 254 257 258 279 C3' G A 14 OK 277 280 281 302 C3' C A 15 OK 300 303 304 322 C3' A A 16 OK 320 323 324 344 C3' A A 17 OK 342 345 346 366 C3' G A 18 OK 364 367 368 389 C3' U A 19 OK 387 390 391 409 C3' C A 20 OK 407 410 411 429 C3' G A 21 OK 427 430 431 452 C3' C A 22 OK 450 453 454 470 C3' G B 1 OK 468 471 472 493 C3' C B 2 OK 491 494 495 513 C3' G B 3 OK 511 514 515 536 C3' U B 4 OK 534 537 538 556 C3' C B 5 OK 554 557 558 576 C3' A B 6 OK 574 577 578 598 C3' C B 7 OK 596 599 600 618 C3' C B 8 OK 616 619 620 638 C3' C B 9 OK 636 639 640 658 C3' C B 10 OK 656 659 660 678 C3' G B 11 OK 676 679 680 701 C3' G B 12 OK 699 702 703 724 C3' G B 13 OK 722 725 726 747 C3' C B 14 OK 745 748 749 767 C3' A B 15 OK 765 768 769 789 C3' A B 16 OK 787 790 791 811 C3' G B 17 OK 809 812 813 834 C3' U B 18 OK 832 835 836 854 C3' C B 19 OK 852 855 856 874 C3' G B 20 OK 872 875 876 897 C3' C B 21 OK 895 898 899 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK 5 2 4 23 C4' G A 2 OK 25 22 24 46 C4' C A 3 OK 48 45 47 66 C4' G A 4 OK 68 65 67 89 C4' U A 5 OK 91 88 90 109 C4' C A 6 OK 111 108 110 129 C4' A A 7 OK 131 128 130 151 C4' C A 8 OK 153 150 152 171 C4' C A 9 OK 173 170 172 191 C4' C A 10 OK 193 190 192 211 C4' C A 11 OK 213 210 212 231 C4' G A 12 OK 233 230 232 254 C4' G A 13 OK 256 253 255 277 C4' G A 14 OK 279 276 278 300 C4' C A 15 OK 302 299 301 320 C4' A A 16 OK 322 319 321 342 C4' A A 17 OK 344 341 343 364 C4' G A 18 OK 366 363 365 387 C4' U A 19 OK 389 386 388 407 C4' C A 20 OK 409 406 408 427 C4' G A 21 OK 429 426 428 450 C4' C A 22 OK 452 449 451 468 C4' G B 1 OK 470 467 469 491 C4' C B 2 OK 493 490 492 511 C4' G B 3 OK 513 510 512 534 C4' U B 4 OK 536 533 535 554 C4' C B 5 OK 556 553 555 574 C4' A B 6 OK 576 573 575 596 C4' C B 7 OK 598 595 597 616 C4' C B 8 OK 618 615 617 636 C4' C B 9 OK 638 635 637 656 C4' C B 10 OK 658 655 657 676 C4' G B 11 OK 678 675 677 699 C4' G B 12 OK 701 698 700 722 C4' G B 13 OK 724 721 723 745 C4' C B 14 OK 747 744 746 765 C4' A B 15 OK 767 764 766 787 C4' A B 16 OK 789 786 788 809 C4' G B 17 OK 811 808 810 832 C4' U B 18 OK 834 831 833 852 C4' C B 19 OK 854 851 853 872 C4' G B 20 OK 874 871 873 895 C4' C B 21 OK 897 894 896 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 1 3 22 C5' G A 2 21 23 45 C5' C A 3 44 46 65 C5' G A 4 64 66 88 C5' U A 5 87 89 108 C5' C A 6 107 109 128 C5' A A 7 127 129 150 C5' C A 8 149 151 170 C5' C A 9 169 171 190 C5' C A 10 189 191 210 C5' C A 11 209 211 230 C5' G A 12 229 231 253 C5' G A 13 252 254 276 C5' G A 14 275 277 299 C5' C A 15 298 300 319 C5' A A 16 318 320 341 C5' A A 17 340 342 363 C5' G A 18 362 364 386 C5' U A 19 385 387 406 C5' C A 20 405 407 426 C5' G A 21 425 427 449 C5' C A 22 448 450 467 C5' G B 1 466 468 490 C5' C B 2 489 491 510 C5' G B 3 509 511 533 C5' U B 4 532 534 553 C5' C B 5 552 554 573 C5' A B 6 572 574 595 C5' C B 7 594 596 615 C5' C B 8 614 616 635 C5' C B 9 634 636 655 C5' C B 10 654 656 675 C5' G B 11 674 676 698 C5' G B 12 697 699 721 C5' G B 13 720 722 744 C5' C B 14 743 745 764 C5' A B 15 763 765 786 C5' A B 16 785 787 808 C5' G B 17 807 809 831 C5' U B 18 830 832 851 C5' C B 19 850 852 871 C5' G B 20 870 872 894 C5' C B 21 893 895 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P G A 2 distorted distorted 6 19 20 21 41 P C A 3 distorted distorted 26 42 43 44 61 P G A 4 distorted distorted 49 62 63 64 84 P U A 5 distorted distorted 69 85 86 87 104 P C A 6 distorted distorted 92 105 106 107 124 P A A 7 distorted distorted 112 125 126 127 146 P C A 8 distorted distorted 132 147 148 149 166 P C A 9 distorted distorted 154 167 168 169 186 P C A 10 distorted distorted 174 187 188 189 206 P C A 11 distorted distorted 194 207 208 209 226 P G A 12 distorted distorted 214 227 228 229 249 P G A 13 distorted distorted 234 250 251 252 272 P G A 14 distorted distorted 257 273 274 275 295 P C A 15 distorted distorted 280 296 297 298 315 P A A 16 distorted distorted 303 316 317 318 337 P A A 17 distorted distorted 323 338 339 340 359 P G A 18 distorted distorted 345 360 361 362 382 P U A 19 distorted distorted 367 383 384 385 402 P C A 20 distorted distorted 390 403 404 405 422 P G A 21 distorted distorted 410 423 424 425 445 P C A 22 distorted distorted 430 446 447 448 486 P C B 2 distorted distorted 471 487 488 489 506 P G B 3 distorted distorted 494 507 508 509 529 P U B 4 distorted distorted 514 530 531 532 549 P C B 5 distorted distorted 537 550 551 552 569 P A B 6 distorted distorted 557 570 571 572 591 P C B 7 distorted distorted 577 592 593 594 611 P C B 8 distorted distorted 599 612 613 614 631 P C B 9 distorted distorted 619 632 633 634 651 P C B 10 distorted distorted 639 652 653 654 671 P G B 11 distorted distorted 659 672 673 674 694 P G B 12 distorted distorted 679 695 696 697 717 P G B 13 distorted distorted 702 718 719 720 740 P C B 14 distorted distorted 725 741 742 743 760 P A B 15 distorted distorted 748 761 762 763 782 P A B 16 distorted distorted 768 783 784 785 804 P G B 17 distorted distorted 790 805 806 807 827 P U B 18 distorted distorted 812 828 829 830 847 P C B 19 distorted distorted 835 848 849 850 867 P G B 20 distorted distorted 855 868 869 870 890 P C B 21 distorted distorted 875 891 892 893 ---------------------------------------------------------------------------------