ID code: '2NC0' 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 681 alpha beta 4 27 10 7 44 C1' G A 682 alpha beta 39 62 45 42 78 C1' G A 683 alpha beta 73 96 79 76 112 C1' C A 684 alpha beta 107 127 113 110 143 C1' U A 685 alpha beta 138 158 144 141 173 C1' G A 686 alpha beta 168 191 174 171 207 C1' A A 687 alpha beta 202 224 208 205 240 C1' A A 688 alpha beta 235 257 241 238 273 C1' G A 689 alpha beta 268 291 274 271 307 C1' G A 690 alpha beta 302 325 308 305 341 C1' A A 691 alpha beta 336 358 342 339 374 C1' U A 692 alpha beta 369 389 375 372 404 C1' G A 693 alpha beta 399 422 405 402 438 C1' G A 694 alpha beta 433 456 439 436 472 C1' A A 695 alpha beta 467 489 473 470 505 C1' G A 696 alpha beta 500 523 506 503 539 C1' A A 697 alpha beta 534 556 540 537 572 C1' C A 776 alpha beta 567 587 573 570 603 C1' G A 777 alpha beta 598 621 604 601 637 C1' U A 778 alpha beta 632 652 638 635 667 C1' C A 779 alpha beta 662 682 668 665 698 C1' U A 780 alpha beta 693 713 699 696 728 C1' A A 781 alpha beta 723 745 729 726 761 C1' G A 782 alpha beta 756 779 762 759 795 C1' G A 783 alpha beta 790 813 796 793 829 C1' C A 784 alpha beta 824 844 830 827 860 C1' C A 785 alpha beta 855 875 861 858 891 C1' C A 786 alpha beta 886 906 892 889 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 681 OK OK 9 5 25 8 42 C2' G A 682 OK OK 44 40 60 43 76 C2' G A 683 OK OK 78 74 94 77 110 C2' C A 684 OK OK 112 108 125 111 141 C2' U A 685 OK OK 143 139 156 142 171 C2' G A 686 OK OK 173 169 189 172 205 C2' A A 687 OK OK 207 203 222 206 238 C2' A A 688 OK OK 240 236 255 239 271 C2' G A 689 OK OK 273 269 289 272 305 C2' G A 690 OK OK 307 303 323 306 339 C2' A A 691 OK OK 341 337 356 340 372 C2' U A 692 OK OK 374 370 387 373 402 C2' G A 693 OK OK 404 400 420 403 436 C2' G A 694 OK OK 438 434 454 437 470 C2' A A 695 OK OK 472 468 487 471 503 C2' G A 696 OK OK 505 501 521 504 537 C2' A A 697 OK OK 539 535 554 538 570 C2' C A 776 OK OK 572 568 585 571 601 C2' G A 777 OK OK 603 599 619 602 635 C2' U A 778 OK OK 637 633 650 636 665 C2' C A 779 OK OK 667 663 680 666 696 C2' U A 780 OK OK 698 694 711 697 726 C2' A A 781 OK OK 728 724 743 727 759 C2' G A 782 OK OK 761 757 777 760 793 C2' G A 783 OK OK 795 791 811 794 827 C2' C A 784 OK OK 829 825 842 828 858 C2' C A 785 OK OK 860 856 873 859 889 C2' C A 786 OK OK 891 887 904 890 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 681 OK OK 3 24 6 7 40 C3' G A 682 OK OK 38 59 41 42 74 C3' G A 683 OK OK 72 93 75 76 108 C3' C A 684 OK OK 106 124 109 110 139 C3' U A 685 OK OK 137 155 140 141 169 C3' G A 686 OK OK 167 188 170 171 203 C3' A A 687 OK OK 201 221 204 205 236 C3' A A 688 OK OK 234 254 237 238 269 C3' G A 689 OK OK 267 288 270 271 303 C3' G A 690 OK OK 301 322 304 305 337 C3' A A 691 OK OK 335 355 338 339 370 C3' U A 692 OK OK 368 386 371 372 400 C3' G A 693 OK OK 398 419 401 402 434 C3' G A 694 OK OK 432 453 435 436 468 C3' A A 695 OK OK 466 486 469 470 501 C3' G A 696 OK OK 499 520 502 503 535 C3' A A 697 OK OK 533 553 536 537 568 C3' C A 776 OK OK 566 584 569 570 599 C3' G A 777 OK OK 597 618 600 601 633 C3' U A 778 OK OK 631 649 634 635 663 C3' C A 779 OK OK 661 679 664 665 694 C3' U A 780 OK OK 692 710 695 696 724 C3' A A 781 OK OK 722 742 725 726 757 C3' G A 782 OK OK 755 776 758 759 791 C3' G A 783 OK OK 789 810 792 793 825 C3' C A 784 OK OK 823 841 826 827 856 C3' C A 785 OK OK 854 872 857 858 887 C3' C A 786 OK OK 885 903 888 889 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 681 OK OK 5 23 2 4 38 C4' G A 682 OK OK 40 58 37 39 72 C4' G A 683 OK OK 74 92 71 73 106 C4' C A 684 OK OK 108 123 105 107 137 C4' U A 685 OK OK 139 154 136 138 167 C4' G A 686 OK OK 169 187 166 168 201 C4' A A 687 OK OK 203 220 200 202 234 C4' A A 688 OK OK 236 253 233 235 267 C4' G A 689 OK OK 269 287 266 268 301 C4' G A 690 OK OK 303 321 300 302 335 C4' A A 691 OK OK 337 354 334 336 368 C4' U A 692 OK OK 370 385 367 369 398 C4' G A 693 OK OK 400 418 397 399 432 C4' G A 694 OK OK 434 452 431 433 466 C4' A A 695 OK OK 468 485 465 467 499 C4' G A 696 OK OK 501 519 498 500 533 C4' A A 697 OK OK 535 552 532 534 566 C4' C A 776 OK OK 568 583 565 567 597 C4' G A 777 OK OK 599 617 596 598 631 C4' U A 778 OK OK 633 648 630 632 661 C4' C A 779 OK OK 663 678 660 662 692 C4' U A 780 OK OK 694 709 691 693 722 C4' A A 781 OK OK 724 741 721 723 755 C4' G A 782 OK OK 757 775 754 756 789 C4' G A 783 OK OK 791 809 788 790 823 C4' C A 784 OK OK 825 840 822 824 854 C4' C A 785 OK OK 856 871 853 855 885 C4' C A 786 OK OK 887 902 884 886 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 681 OK OK 1 21 22 3 37 C5' G A 682 OK OK 36 56 57 38 71 C5' G A 683 OK OK 70 90 91 72 105 C5' C A 684 OK OK 104 121 122 106 136 C5' U A 685 OK OK 135 152 153 137 166 C5' G A 686 OK OK 165 185 186 167 200 C5' A A 687 distorted OK 199 251 219 201 233 C5' A A 688 OK OK 232 251 252 234 266 C5' G A 689 OK OK 265 285 286 267 300 C5' G A 690 OK OK 299 319 320 301 334 C5' A A 691 OK OK 333 352 353 335 367 C5' U A 692 OK OK 366 383 384 368 397 C5' G A 693 OK OK 396 416 417 398 431 C5' G A 694 OK OK 430 450 451 432 465 C5' A A 695 OK OK 464 483 484 466 498 C5' G A 696 OK OK 497 517 518 499 532 C5' A A 697 OK OK 531 550 551 533 565 C5' C A 776 OK OK 564 581 582 566 596 C5' G A 777 OK OK 595 615 616 597 630 C5' U A 778 OK OK 629 646 647 631 660 C5' C A 779 OK OK 659 676 677 661 691 C5' U A 780 OK OK 690 707 708 692 721 C5' A A 781 OK OK 720 739 740 722 754 C5' G A 782 OK OK 753 773 774 755 788 C5' G A 783 OK OK 787 807 808 789 822 C5' C A 784 OK OK 821 838 839 823 853 C5' C A 785 OK OK 852 869 870 854 884 C5' C A 786 OK OK 883 900 901 885 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 682 distorted distorted 6 34 35 36 67 P G A 683 distorted distorted 41 68 69 70 101 P C A 684 distorted distorted 75 102 103 104 132 P U A 685 distorted distorted 109 133 134 135 162 P G A 686 distorted distorted 140 163 164 165 196 P A A 687 distorted distorted 170 197 198 199 229 P A A 688 distorted distorted 204 230 231 232 262 P G A 689 distorted distorted 237 263 264 265 296 P G A 690 distorted distorted 270 297 298 299 330 P A A 691 distorted distorted 304 331 332 333 363 P U A 692 distorted distorted 338 364 365 366 393 P G A 693 distorted distorted 371 394 395 396 427 P G A 694 distorted distorted 401 428 429 430 461 P A A 695 distorted distorted 435 462 463 464 494 P G A 696 distorted distorted 469 495 496 497 528 P A A 697 distorted distorted 502 529 530 531 561 P C A 776 distorted distorted 536 562 563 564 592 P G A 777 distorted distorted 569 593 594 595 626 P U A 778 distorted distorted 600 627 628 629 656 P C A 779 distorted distorted 634 657 658 659 687 P U A 780 distorted distorted 664 688 689 690 717 P A A 781 distorted distorted 695 718 719 720 750 P G A 782 distorted distorted 725 751 752 753 784 P G A 783 distorted distorted 758 785 786 787 818 P C A 784 distorted distorted 792 819 820 821 849 P C A 785 distorted distorted 826 850 851 852 880 P C A 786 distorted distorted 857 881 882 883 ---------------------------------------------------------------------------------