ID code: '1EBS' 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' G A 5 alpha beta 137 160 143 140 176 C1' G A 6 alpha beta 171 194 177 174 210 C1' C A 7 alpha beta 205 225 211 208 241 C1' G A 8 alpha beta 236 259 242 239 275 C1' C A 9 alpha beta 270 290 276 273 306 C1' A A 10 alpha beta 301 323 307 304 339 C1' G A 11 alpha beta 334 357 340 337 373 C1' C A 12 alpha beta 368 388 374 371 404 C1' U A 13 alpha beta 399 419 405 402 434 C1' U A 14 alpha beta 429 449 435 432 464 C1' C A 15 alpha beta 459 479 465 462 495 C1' G A 16 alpha beta 490 513 496 493 529 C1' G A 17 alpha beta 524 547 530 527 563 C1' C A 18 alpha beta 558 578 564 561 594 C1' U A 19 alpha beta 589 609 595 592 624 C1' G A 20 alpha beta 619 642 625 622 658 C1' C A 21 alpha beta 653 673 659 656 689 C1' G A 22 alpha beta 684 707 690 687 723 C1' G A 23 alpha beta 718 741 724 721 757 C1' U A 24 alpha beta 752 772 758 755 787 C1' A A 25 alpha beta 782 804 788 785 820 C1' C A 26 alpha beta 815 835 821 818 851 C1' A A 27 alpha beta 846 868 852 849 884 C1' C A 28 alpha beta 879 899 885 882 915 C1' C A 29 alpha beta 910 931 916 913 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 5 OK OK 142 138 158 141 174 C2' G A 6 OK OK 176 172 192 175 208 C2' C A 7 OK OK 210 206 223 209 239 C2' G A 8 OK OK 241 237 257 240 273 C2' C A 9 OK OK 275 271 288 274 304 C2' A A 10 OK OK 306 302 321 305 337 C2' G A 11 OK OK 339 335 355 338 371 C2' C A 12 OK OK 373 369 386 372 402 C2' U A 13 OK OK 404 400 417 403 432 C2' U A 14 OK OK 434 430 447 433 462 C2' C A 15 OK OK 464 460 477 463 493 C2' G A 16 OK OK 495 491 511 494 527 C2' G A 17 OK OK 529 525 545 528 561 C2' C A 18 OK OK 563 559 576 562 592 C2' U A 19 OK OK 594 590 607 593 622 C2' G A 20 OK OK 624 620 640 623 656 C2' C A 21 OK OK 658 654 671 657 687 C2' G A 22 OK OK 689 685 705 688 721 C2' G A 23 OK OK 723 719 739 722 755 C2' U A 24 OK OK 757 753 770 756 785 C2' A A 25 OK OK 787 783 802 786 818 C2' C A 26 OK OK 820 816 833 819 849 C2' A A 27 OK OK 851 847 866 850 882 C2' C A 28 OK OK 884 880 897 883 913 C2' C A 29 OK OK 915 911 929 914 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 5 OK OK 136 157 139 140 172 C3' G A 6 OK OK 170 191 173 174 206 C3' C A 7 OK OK 204 222 207 208 237 C3' G A 8 OK OK 235 256 238 239 271 C3' C A 9 OK OK 269 287 272 273 302 C3' A A 10 OK OK 300 320 303 304 335 C3' G A 11 OK OK 333 354 336 337 369 C3' C A 12 OK OK 367 385 370 371 400 C3' U A 13 OK OK 398 416 401 402 430 C3' U A 14 OK OK 428 446 431 432 460 C3' C A 15 OK OK 458 476 461 462 491 C3' G A 16 OK OK 489 510 492 493 525 C3' G A 17 OK OK 523 544 526 527 559 C3' C A 18 OK OK 557 575 560 561 590 C3' U A 19 OK OK 588 606 591 592 620 C3' G A 20 OK OK 618 639 621 622 654 C3' C A 21 OK OK 652 670 655 656 685 C3' G A 22 OK OK 683 704 686 687 719 C3' G A 23 OK OK 717 738 720 721 753 C3' U A 24 OK OK 751 769 754 755 783 C3' A A 25 OK OK 781 801 784 785 816 C3' C A 26 OK OK 814 832 817 818 847 C3' A A 27 OK OK 845 865 848 849 880 C3' C A 28 OK OK 878 896 881 882 911 C3' C A 29 OK OK 909 927 912 913 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 5 OK OK 138 156 135 137 170 C4' G A 6 OK OK 172 190 169 171 204 C4' C A 7 OK OK 206 221 203 205 235 C4' G A 8 OK OK 237 255 234 236 269 C4' C A 9 OK OK 271 286 268 270 300 C4' A A 10 OK OK 302 319 299 301 333 C4' G A 11 OK OK 335 353 332 334 367 C4' C A 12 OK OK 369 384 366 368 398 C4' U A 13 OK OK 400 415 397 399 428 C4' U A 14 OK OK 430 445 427 429 458 C4' C A 15 OK OK 460 475 457 459 489 C4' G A 16 OK OK 491 509 488 490 523 C4' G A 17 OK OK 525 543 522 524 557 C4' C A 18 OK OK 559 574 556 558 588 C4' U A 19 OK OK 590 605 587 589 618 C4' G A 20 OK OK 620 638 617 619 652 C4' C A 21 OK OK 654 669 651 653 683 C4' G A 22 OK OK 685 703 682 684 717 C4' G A 23 OK OK 719 737 716 718 751 C4' U A 24 OK OK 753 768 750 752 781 C4' A A 25 OK OK 783 800 780 782 814 C4' C A 26 OK OK 816 831 813 815 845 C4' A A 27 OK OK 847 864 844 846 878 C4' C A 28 OK OK 880 895 877 879 909 C4' C A 29 OK OK 911 926 908 910 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 5 OK OK 134 154 155 136 169 C5' G A 6 OK OK 168 188 189 170 203 C5' C A 7 OK OK 202 219 220 204 234 C5' G A 8 OK OK 233 253 254 235 268 C5' C A 9 OK OK 267 284 285 269 299 C5' A A 10 OK OK 298 317 318 300 332 C5' G A 11 OK OK 331 351 352 333 366 C5' C A 12 OK OK 365 382 383 367 397 C5' U A 13 OK OK 396 413 414 398 427 C5' U A 14 OK OK 426 443 444 428 457 C5' C A 15 OK OK 456 473 474 458 488 C5' G A 16 OK OK 487 507 508 489 522 C5' G A 17 OK OK 521 541 542 523 556 C5' C A 18 OK OK 555 572 573 557 587 C5' U A 19 OK OK 586 603 604 588 617 C5' G A 20 OK OK 616 636 637 618 651 C5' C A 21 OK OK 650 667 668 652 682 C5' G A 22 OK OK 681 701 702 683 716 C5' G A 23 OK OK 715 735 736 717 750 C5' U A 24 OK OK 749 766 767 751 780 C5' A A 25 OK OK 779 798 799 781 813 C5' C A 26 OK OK 812 829 830 814 844 C5' A A 27 OK OK 843 862 863 845 877 C5' C A 28 OK OK 876 893 894 878 908 C5' C A 29 OK OK 907 924 925 909 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 G A 5 distorted distorted 105 132 133 134 165 P G A 6 distorted distorted 139 166 167 168 199 P C A 7 distorted distorted 173 200 201 202 230 P G A 8 distorted distorted 207 231 232 233 264 P C A 9 distorted distorted 238 265 266 267 295 P A A 10 distorted distorted 272 296 297 298 328 P G A 11 distorted distorted 303 329 330 331 362 P C A 12 distorted distorted 336 363 364 365 393 P U A 13 distorted distorted 370 394 395 396 423 P U A 14 distorted distorted 401 424 425 426 453 P C A 15 distorted distorted 431 454 455 456 484 P G A 16 distorted distorted 461 485 486 487 518 P G A 17 distorted distorted 492 519 520 521 552 P C A 18 distorted distorted 526 553 554 555 583 P U A 19 distorted distorted 560 584 585 586 613 P G A 20 distorted distorted 591 614 615 616 647 P C A 21 distorted distorted 621 648 649 650 678 P G A 22 distorted distorted 655 679 680 681 712 P G A 23 distorted distorted 686 713 714 715 746 P U A 24 distorted distorted 720 747 748 749 776 P A A 25 distorted distorted 754 777 778 779 809 P C A 26 distorted distorted 784 810 811 812 840 P A A 27 distorted distorted 817 841 842 843 873 P C A 28 distorted distorted 848 874 875 876 904 P C A 29 distorted distorted 881 905 906 907 ---------------------------------------------------------------------------------