ID code: '1HWQ' 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 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' U A 3 alpha beta 73 93 79 76 108 C1' G A 4 alpha beta 103 126 109 106 142 C1' C A 5 alpha beta 137 157 143 140 173 C1' G A 6 alpha beta 168 191 174 171 207 C1' A A 7 alpha beta 202 224 208 205 240 C1' A A 8 alpha beta 235 257 241 238 273 C1' G A 9 alpha beta 268 291 274 271 307 C1' G A 10 alpha beta 302 325 308 305 341 C1' G A 11 alpha beta 336 359 342 339 375 C1' C A 12 alpha beta 370 390 376 373 406 C1' G A 13 alpha beta 401 424 407 404 440 C1' U A 14 alpha beta 435 455 441 438 470 C1' C A 15 alpha beta 465 485 471 468 501 C1' G A 16 alpha beta 496 519 502 499 535 C1' U A 17 alpha beta 530 550 536 533 565 C1' C A 18 alpha beta 560 580 566 563 596 C1' G A 19 alpha beta 591 614 597 594 630 C1' C A 20 alpha beta 625 645 631 628 661 C1' C A 21 alpha beta 656 676 662 659 692 C1' C A 22 alpha beta 687 707 693 690 723 C1' C A 23 alpha beta 718 738 724 721 754 C1' G A 24 alpha beta 749 772 755 752 788 C1' A A 25 alpha beta 783 805 789 786 821 C1' G A 26 alpha beta 816 839 822 819 855 C1' C A 27 alpha beta 850 870 856 853 886 C1' G A 28 alpha beta 881 904 887 884 920 C1' C A 29 alpha beta 915 935 921 918 951 C1' C A 30 alpha beta 946 967 952 949 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' U A 3 OK OK 78 74 91 77 106 C2' G A 4 OK OK 108 104 124 107 140 C2' C A 5 OK OK 142 138 155 141 171 C2' G A 6 OK OK 173 169 189 172 205 C2' A A 7 OK OK 207 203 222 206 238 C2' A A 8 OK OK 240 236 255 239 271 C2' G A 9 OK OK 273 269 289 272 305 C2' G A 10 OK OK 307 303 323 306 339 C2' G A 11 OK OK 341 337 357 340 373 C2' C A 12 OK OK 375 371 388 374 404 C2' G A 13 OK OK 406 402 422 405 438 C2' U A 14 OK OK 440 436 453 439 468 C2' C A 15 OK OK 470 466 483 469 499 C2' G A 16 OK OK 501 497 517 500 533 C2' U A 17 OK OK 535 531 548 534 563 C2' C A 18 OK OK 565 561 578 564 594 C2' G A 19 OK OK 596 592 612 595 628 C2' C A 20 OK OK 630 626 643 629 659 C2' C A 21 OK OK 661 657 674 660 690 C2' C A 22 OK OK 692 688 705 691 721 C2' C A 23 OK OK 723 719 736 722 752 C2' G A 24 OK OK 754 750 770 753 786 C2' A A 25 OK OK 788 784 803 787 819 C2' G A 26 OK OK 821 817 837 820 853 C2' C A 27 OK OK 855 851 868 854 884 C2' G A 28 OK OK 886 882 902 885 918 C2' C A 29 OK OK 920 916 933 919 949 C2' C A 30 OK OK 951 947 965 950 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' U A 3 OK OK 72 90 75 76 104 C3' G A 4 OK OK 102 123 105 106 138 C3' C A 5 OK OK 136 154 139 140 169 C3' G A 6 OK OK 167 188 170 171 203 C3' A A 7 OK OK 201 221 204 205 236 C3' A A 8 OK OK 234 254 237 238 269 C3' G A 9 OK OK 267 288 270 271 303 C3' G A 10 OK OK 301 322 304 305 337 C3' G A 11 OK OK 335 356 338 339 371 C3' C A 12 OK OK 369 387 372 373 402 C3' G A 13 OK OK 400 421 403 404 436 C3' U A 14 OK OK 434 452 437 438 466 C3' C A 15 OK OK 464 482 467 468 497 C3' G A 16 OK OK 495 516 498 499 531 C3' U A 17 OK OK 529 547 532 533 561 C3' C A 18 OK OK 559 577 562 563 592 C3' G A 19 OK OK 590 611 593 594 626 C3' C A 20 OK OK 624 642 627 628 657 C3' C A 21 OK OK 655 673 658 659 688 C3' C A 22 OK OK 686 704 689 690 719 C3' C A 23 OK OK 717 735 720 721 750 C3' G A 24 OK OK 748 769 751 752 784 C3' A A 25 OK OK 782 802 785 786 817 C3' G A 26 OK OK 815 836 818 819 851 C3' C A 27 OK OK 849 867 852 853 882 C3' G A 28 OK OK 880 901 883 884 916 C3' C A 29 OK OK 914 932 917 918 947 C3' C A 30 OK OK 945 963 948 949 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' U A 3 OK OK 74 89 71 73 102 C4' G A 4 OK OK 104 122 101 103 136 C4' C A 5 OK OK 138 153 135 137 167 C4' G A 6 OK OK 169 187 166 168 201 C4' A A 7 OK OK 203 220 200 202 234 C4' A A 8 OK OK 236 253 233 235 267 C4' G A 9 OK OK 269 287 266 268 301 C4' G A 10 OK OK 303 321 300 302 335 C4' G A 11 OK OK 337 355 334 336 369 C4' C A 12 OK OK 371 386 368 370 400 C4' G A 13 OK OK 402 420 399 401 434 C4' U A 14 OK OK 436 451 433 435 464 C4' C A 15 OK OK 466 481 463 465 495 C4' G A 16 OK OK 497 515 494 496 529 C4' U A 17 OK OK 531 546 528 530 559 C4' C A 18 OK OK 561 576 558 560 590 C4' G A 19 OK OK 592 610 589 591 624 C4' C A 20 OK OK 626 641 623 625 655 C4' C A 21 OK OK 657 672 654 656 686 C4' C A 22 OK OK 688 703 685 687 717 C4' C A 23 OK OK 719 734 716 718 748 C4' G A 24 OK OK 750 768 747 749 782 C4' A A 25 OK OK 784 801 781 783 815 C4' G A 26 OK OK 817 835 814 816 849 C4' C A 27 OK OK 851 866 848 850 880 C4' G A 28 OK OK 882 900 879 881 914 C4' C A 29 OK OK 916 931 913 915 945 C4' C A 30 OK OK 947 962 944 946 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' U A 3 OK OK 70 87 88 72 101 C5' G A 4 OK OK 100 120 121 102 135 C5' C A 5 OK OK 134 151 152 136 166 C5' G A 6 OK OK 165 185 186 167 200 C5' A A 7 OK OK 199 218 219 201 233 C5' A A 8 OK OK 232 251 252 234 266 C5' G A 9 OK OK 265 285 286 267 300 C5' G A 10 OK OK 299 319 320 301 334 C5' G A 11 OK OK 333 353 354 335 368 C5' C A 12 OK OK 367 384 385 369 399 C5' G A 13 OK OK 398 418 419 400 433 C5' U A 14 OK OK 432 449 450 434 463 C5' C A 15 OK OK 462 479 480 464 494 C5' G A 16 OK OK 493 513 514 495 528 C5' U A 17 OK OK 527 544 545 529 558 C5' C A 18 OK OK 557 574 575 559 589 C5' G A 19 OK OK 588 608 609 590 623 C5' C A 20 OK OK 622 639 640 624 654 C5' C A 21 OK OK 653 670 671 655 685 C5' C A 22 OK OK 684 701 702 686 716 C5' C A 23 OK OK 715 732 733 717 747 C5' G A 24 OK OK 746 766 767 748 781 C5' A A 25 OK OK 780 799 800 782 814 C5' G A 26 OK OK 813 833 834 815 848 C5' C A 27 OK OK 847 864 865 849 879 C5' G A 28 OK OK 878 898 899 880 913 C5' C A 29 OK OK 912 929 930 914 944 C5' C A 30 OK OK 943 960 961 945 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P U A 3 distorted distorted 41 68 69 70 97 P G A 4 distorted distorted 75 98 99 100 131 P C A 5 distorted distorted 105 132 133 134 162 P G A 6 distorted distorted 139 163 164 165 196 P A A 7 distorted distorted 170 197 198 199 229 P A A 8 distorted distorted 204 230 231 232 262 P G A 9 distorted distorted 237 263 264 265 296 P G A 10 distorted distorted 270 297 298 299 330 P G A 11 distorted distorted 304 331 332 333 364 P C A 12 distorted distorted 338 365 366 367 395 P G A 13 distorted distorted 372 396 397 398 429 P U A 14 distorted distorted 403 430 431 432 459 P C A 15 distorted distorted 437 460 461 462 490 P G A 16 distorted distorted 467 491 492 493 524 P U A 17 distorted distorted 498 525 526 527 554 P C A 18 distorted distorted 532 555 556 557 585 P G A 19 distorted distorted 562 586 587 588 619 P C A 20 distorted distorted 593 620 621 622 650 P C A 21 distorted distorted 627 651 652 653 681 P C A 22 distorted distorted 658 682 683 684 712 P C A 23 distorted distorted 689 713 714 715 743 P G A 24 distorted distorted 720 744 745 746 777 P A A 25 distorted distorted 751 778 779 780 810 P G A 26 distorted distorted 785 811 812 813 844 P C A 27 distorted distorted 818 845 846 847 875 P G A 28 distorted distorted 852 876 877 878 909 P C A 29 distorted distorted 883 910 911 912 940 P C A 30 distorted distorted 917 941 942 943 ---------------------------------------------------------------------------------