ID code: '2LUN' 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' G A 3 alpha beta 73 96 79 76 112 C1' C A 4 alpha beta 107 127 113 110 143 C1' A A 5 alpha beta 138 160 144 141 176 C1' G A 6 alpha beta 171 194 177 174 210 C1' U A 7 alpha beta 205 225 211 208 240 C1' G A 8 alpha beta 235 258 241 238 274 C1' A A 9 alpha beta 269 291 275 272 307 C1' U A 10 alpha beta 302 322 308 305 337 C1' G A 11 alpha beta 332 355 338 335 371 C1' C A 12 alpha beta 366 386 372 369 402 C1' U A 13 alpha beta 397 417 403 400 432 C1' U A 14 alpha beta 427 447 433 430 462 C1' C A 15 alpha beta 457 477 463 460 493 C1' G A 16 alpha beta 488 511 494 491 527 C1' G A 17 alpha beta 522 545 528 525 561 C1' C A 18 alpha beta 556 576 562 559 592 C1' A A 19 alpha beta 587 609 593 590 625 C1' U A 20 alpha beta 620 640 626 623 655 C1' A A 21 alpha beta 650 672 656 653 688 C1' U A 22 alpha beta 683 703 689 686 718 C1' C A 23 alpha beta 713 733 719 716 749 C1' A A 24 alpha beta 744 766 750 747 782 C1' G A 25 alpha beta 777 800 783 780 816 C1' C A 26 alpha beta 811 831 817 814 847 C1' C A 27 alpha beta 842 862 848 845 878 C1' C A 28 alpha beta 873 894 879 876 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 3 OK OK 78 74 94 77 110 C2' C A 4 OK OK 112 108 125 111 141 C2' A A 5 OK OK 143 139 158 142 174 C2' G A 6 OK OK 176 172 192 175 208 C2' U A 7 OK OK 210 206 223 209 238 C2' G A 8 OK OK 240 236 256 239 272 C2' A A 9 OK OK 274 270 289 273 305 C2' U A 10 OK OK 307 303 320 306 335 C2' G A 11 OK OK 337 333 353 336 369 C2' C A 12 OK OK 371 367 384 370 400 C2' U A 13 OK OK 402 398 415 401 430 C2' U A 14 OK OK 432 428 445 431 460 C2' C A 15 OK OK 462 458 475 461 491 C2' G A 16 OK OK 493 489 509 492 525 C2' G A 17 OK OK 527 523 543 526 559 C2' C A 18 OK OK 561 557 574 560 590 C2' A A 19 OK OK 592 588 607 591 623 C2' U A 20 OK OK 625 621 638 624 653 C2' A A 21 OK OK 655 651 670 654 686 C2' U A 22 OK OK 688 684 701 687 716 C2' C A 23 OK OK 718 714 731 717 747 C2' A A 24 OK OK 749 745 764 748 780 C2' G A 25 OK OK 782 778 798 781 814 C2' C A 26 OK OK 816 812 829 815 845 C2' C A 27 OK OK 847 843 860 846 876 C2' C A 28 OK OK 878 874 892 877 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 72 93 75 76 108 C3' C A 4 OK OK 106 124 109 110 139 C3' A A 5 OK OK 137 157 140 141 172 C3' G A 6 OK OK 170 191 173 174 206 C3' U A 7 OK OK 204 222 207 208 236 C3' G A 8 OK OK 234 255 237 238 270 C3' A A 9 OK OK 268 288 271 272 303 C3' U A 10 OK OK 301 319 304 305 333 C3' G A 11 OK OK 331 352 334 335 367 C3' C A 12 OK OK 365 383 368 369 398 C3' U A 13 OK OK 396 414 399 400 428 C3' U A 14 OK OK 426 444 429 430 458 C3' C A 15 OK OK 456 474 459 460 489 C3' G A 16 OK OK 487 508 490 491 523 C3' G A 17 OK OK 521 542 524 525 557 C3' C A 18 OK OK 555 573 558 559 588 C3' A A 19 OK OK 586 606 589 590 621 C3' U A 20 OK OK 619 637 622 623 651 C3' A A 21 OK OK 649 669 652 653 684 C3' U A 22 OK OK 682 700 685 686 714 C3' C A 23 OK OK 712 730 715 716 745 C3' A A 24 OK OK 743 763 746 747 778 C3' G A 25 OK OK 776 797 779 780 812 C3' C A 26 OK OK 810 828 813 814 843 C3' C A 27 OK OK 841 859 844 845 874 C3' C A 28 OK OK 872 890 875 876 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 74 92 71 73 106 C4' C A 4 OK OK 108 123 105 107 137 C4' A A 5 OK OK 139 156 136 138 170 C4' G A 6 OK OK 172 190 169 171 204 C4' U A 7 OK OK 206 221 203 205 234 C4' G A 8 OK OK 236 254 233 235 268 C4' A A 9 OK OK 270 287 267 269 301 C4' U A 10 OK OK 303 318 300 302 331 C4' G A 11 OK OK 333 351 330 332 365 C4' C A 12 OK OK 367 382 364 366 396 C4' U A 13 OK OK 398 413 395 397 426 C4' U A 14 OK OK 428 443 425 427 456 C4' C A 15 OK OK 458 473 455 457 487 C4' G A 16 OK OK 489 507 486 488 521 C4' G A 17 OK OK 523 541 520 522 555 C4' C A 18 OK OK 557 572 554 556 586 C4' A A 19 OK OK 588 605 585 587 619 C4' U A 20 OK OK 621 636 618 620 649 C4' A A 21 OK OK 651 668 648 650 682 C4' U A 22 OK OK 684 699 681 683 712 C4' C A 23 OK OK 714 729 711 713 743 C4' A A 24 OK OK 745 762 742 744 776 C4' G A 25 OK OK 778 796 775 777 810 C4' C A 26 OK OK 812 827 809 811 841 C4' C A 27 OK OK 843 858 840 842 872 C4' C A 28 OK OK 874 889 871 873 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 3 OK OK 70 90 91 72 105 C5' C A 4 OK OK 104 121 122 106 136 C5' A A 5 OK OK 135 154 155 137 169 C5' G A 6 OK OK 168 188 189 170 203 C5' U A 7 OK OK 202 219 220 204 233 C5' G A 8 OK OK 232 252 253 234 267 C5' A A 9 OK OK 266 285 286 268 300 C5' U A 10 OK OK 299 316 317 301 330 C5' G A 11 OK OK 329 349 350 331 364 C5' C A 12 OK OK 363 380 381 365 395 C5' U A 13 OK OK 394 411 412 396 425 C5' U A 14 OK OK 424 441 442 426 455 C5' C A 15 OK OK 454 471 472 456 486 C5' G A 16 OK OK 485 505 506 487 520 C5' G A 17 OK OK 519 539 540 521 554 C5' C A 18 OK OK 553 570 571 555 585 C5' A A 19 OK OK 584 603 604 586 618 C5' U A 20 OK OK 617 634 635 619 648 C5' A A 21 OK OK 647 666 667 649 681 C5' U A 22 OK OK 680 697 698 682 711 C5' C A 23 OK OK 710 727 728 712 742 C5' A A 24 OK OK 741 760 761 743 775 C5' G A 25 OK OK 774 794 795 776 809 C5' C A 26 OK OK 808 825 826 810 840 C5' C A 27 OK OK 839 856 857 841 871 C5' C A 28 OK OK 870 887 888 872 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P G A 3 distorted distorted 41 68 69 70 101 P C A 4 distorted distorted 75 102 103 104 132 P A A 5 distorted distorted 109 133 134 135 165 P G A 6 distorted distorted 140 166 167 168 199 P U A 7 distorted distorted 173 200 201 202 229 P G A 8 distorted distorted 207 230 231 232 263 P A A 9 distorted distorted 237 264 265 266 296 P U A 10 distorted distorted 271 297 298 299 326 P G A 11 distorted distorted 304 327 328 329 360 P C A 12 distorted distorted 334 361 362 363 391 P U A 13 distorted distorted 368 392 393 394 421 P U A 14 distorted distorted 399 422 423 424 451 P C A 15 distorted distorted 429 452 453 454 482 P G A 16 distorted distorted 459 483 484 485 516 P G A 17 distorted distorted 490 517 518 519 550 P C A 18 distorted distorted 524 551 552 553 581 P A A 19 distorted distorted 558 582 583 584 614 P U A 20 distorted distorted 589 615 616 617 644 P A A 21 distorted distorted 622 645 646 647 677 P U A 22 distorted distorted 652 678 679 680 707 P C A 23 distorted distorted 685 708 709 710 738 P A A 24 distorted distorted 715 739 740 741 771 P G A 25 distorted distorted 746 772 773 774 805 P C A 26 distorted distorted 779 806 807 808 836 P C A 27 distorted distorted 813 837 838 839 867 P C A 28 distorted distorted 844 868 869 870 ---------------------------------------------------------------------------------