ID code: '2KX5' 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' --------------------------------------------------------------------------------- 13 C1' G A 17 alpha beta 8 31 14 11 48 C1' G A 18 alpha beta 43 66 49 46 82 C1' C A 19 alpha beta 77 97 83 80 113 C1' A A 20 alpha beta 108 130 114 111 146 C1' G A 21 alpha beta 141 164 147 144 180 C1' A A 22 alpha beta 175 197 181 178 213 C1' U A 23 alpha beta 208 228 214 211 243 C1' C A 24 alpha beta 238 258 244 241 274 C1' U A 25 alpha beta 269 289 275 272 304 C1' G A 26 alpha beta 299 322 305 302 338 C1' A A 27 alpha beta 333 355 339 336 371 C1' G A 28 alpha beta 366 389 372 369 405 C1' C A 29 alpha beta 400 420 406 403 436 C1' C A 30 alpha beta 431 451 437 434 467 C1' U A 31 alpha beta 462 482 468 465 497 C1' G A 32 alpha beta 492 515 498 495 531 C1' G A 33 alpha beta 526 549 532 529 565 C1' G A 34 alpha beta 560 583 566 563 599 C1' A A 35 alpha beta 594 616 600 597 632 C1' G A 36 alpha beta 627 650 633 630 666 C1' C A 37 alpha beta 661 681 667 664 697 C1' U A 38 alpha beta 692 712 698 695 727 C1' C A 39 alpha beta 722 742 728 725 758 C1' U A 40 alpha beta 753 773 759 756 788 C1' C A 41 alpha beta 783 803 789 786 819 C1' U A 42 alpha beta 814 834 820 817 849 C1' G A 43 alpha beta 844 867 850 847 883 C1' C A 44 alpha beta 878 898 884 881 914 C1' C A 45 alpha beta 909 930 915 912 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G A 17 OK OK 13 9 29 12 46 C2' G A 18 OK OK 48 44 64 47 80 C2' C A 19 OK OK 82 78 95 81 111 C2' A A 20 OK OK 113 109 128 112 144 C2' G A 21 OK OK 146 142 162 145 178 C2' A A 22 OK OK 180 176 195 179 211 C2' U A 23 OK OK 213 209 226 212 241 C2' C A 24 OK OK 243 239 256 242 272 C2' U A 25 OK OK 274 270 287 273 302 C2' G A 26 OK OK 304 300 320 303 336 C2' A A 27 OK OK 338 334 353 337 369 C2' G A 28 OK OK 371 367 387 370 403 C2' C A 29 OK OK 405 401 418 404 434 C2' C A 30 OK OK 436 432 449 435 465 C2' U A 31 OK OK 467 463 480 466 495 C2' G A 32 OK OK 497 493 513 496 529 C2' G A 33 OK OK 531 527 547 530 563 C2' G A 34 OK OK 565 561 581 564 597 C2' A A 35 OK OK 599 595 614 598 630 C2' G A 36 OK OK 632 628 648 631 664 C2' C A 37 OK OK 666 662 679 665 695 C2' U A 38 OK OK 697 693 710 696 725 C2' C A 39 OK OK 727 723 740 726 756 C2' U A 40 OK OK 758 754 771 757 786 C2' C A 41 OK OK 788 784 801 787 817 C2' U A 42 OK OK 819 815 832 818 847 C2' G A 43 OK OK 849 845 865 848 881 C2' C A 44 OK OK 883 879 896 882 912 C2' C A 45 OK OK 914 910 928 913 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G A 17 OK OK 7 28 10 11 44 C3' G A 18 OK OK 42 63 45 46 78 C3' C A 19 OK OK 76 94 79 80 109 C3' A A 20 OK OK 107 127 110 111 142 C3' G A 21 OK OK 140 161 143 144 176 C3' A A 22 OK OK 174 194 177 178 209 C3' U A 23 OK OK 207 225 210 211 239 C3' C A 24 OK OK 237 255 240 241 270 C3' U A 25 OK OK 268 286 271 272 300 C3' G A 26 OK OK 298 319 301 302 334 C3' A A 27 OK OK 332 352 335 336 367 C3' G A 28 OK OK 365 386 368 369 401 C3' C A 29 OK OK 399 417 402 403 432 C3' C A 30 OK OK 430 448 433 434 463 C3' U A 31 OK OK 461 479 464 465 493 C3' G A 32 OK OK 491 512 494 495 527 C3' G A 33 OK OK 525 546 528 529 561 C3' G A 34 OK OK 559 580 562 563 595 C3' A A 35 OK OK 593 613 596 597 628 C3' G A 36 OK OK 626 647 629 630 662 C3' C A 37 OK OK 660 678 663 664 693 C3' U A 38 OK OK 691 709 694 695 723 C3' C A 39 OK OK 721 739 724 725 754 C3' U A 40 OK OK 752 770 755 756 784 C3' C A 41 OK OK 782 800 785 786 815 C3' U A 42 OK OK 813 831 816 817 845 C3' G A 43 OK OK 843 864 846 847 879 C3' C A 44 OK OK 877 895 880 881 910 C3' C A 45 OK OK 908 926 911 912 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G A 17 OK OK 9 27 6 8 42 C4' G A 18 OK OK 44 62 41 43 76 C4' C A 19 OK OK 78 93 75 77 107 C4' A A 20 OK OK 109 126 106 108 140 C4' G A 21 OK OK 142 160 139 141 174 C4' A A 22 OK OK 176 193 173 175 207 C4' U A 23 OK OK 209 224 206 208 237 C4' C A 24 OK OK 239 254 236 238 268 C4' U A 25 OK OK 270 285 267 269 298 C4' G A 26 OK OK 300 318 297 299 332 C4' A A 27 OK OK 334 351 331 333 365 C4' G A 28 OK OK 367 385 364 366 399 C4' C A 29 OK OK 401 416 398 400 430 C4' C A 30 OK OK 432 447 429 431 461 C4' U A 31 OK OK 463 478 460 462 491 C4' G A 32 OK OK 493 511 490 492 525 C4' G A 33 OK OK 527 545 524 526 559 C4' G A 34 OK OK 561 579 558 560 593 C4' A A 35 OK OK 595 612 592 594 626 C4' G A 36 OK OK 628 646 625 627 660 C4' C A 37 OK OK 662 677 659 661 691 C4' U A 38 OK OK 693 708 690 692 721 C4' C A 39 OK OK 723 738 720 722 752 C4' U A 40 OK OK 754 769 751 753 782 C4' C A 41 OK OK 784 799 781 783 813 C4' U A 42 OK OK 815 830 812 814 843 C4' G A 43 OK OK 845 863 842 844 877 C4' C A 44 OK OK 879 894 876 878 908 C4' C A 45 OK OK 910 925 907 909 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G A 17 OK OK 5 25 26 7 41 C5' G A 18 OK OK 40 60 61 42 75 C5' C A 19 OK OK 74 91 92 76 106 C5' A A 20 OK OK 105 124 125 107 139 C5' G A 21 OK OK 138 158 159 140 173 C5' A A 22 OK OK 172 191 192 174 206 C5' U A 23 OK OK 205 222 223 207 236 C5' C A 24 OK OK 235 252 253 237 267 C5' U A 25 OK OK 266 283 284 268 297 C5' G A 26 OK OK 296 316 317 298 331 C5' A A 27 OK OK 330 349 350 332 364 C5' G A 28 OK OK 363 383 384 365 398 C5' C A 29 OK OK 397 414 415 399 429 C5' C A 30 OK OK 428 445 446 430 460 C5' U A 31 OK OK 459 476 477 461 490 C5' G A 32 OK OK 489 509 510 491 524 C5' G A 33 OK OK 523 543 544 525 558 C5' G A 34 OK OK 557 577 578 559 592 C5' A A 35 OK OK 591 610 611 593 625 C5' G A 36 OK OK 624 644 645 626 659 C5' C A 37 OK OK 658 675 676 660 690 C5' U A 38 OK OK 689 706 707 691 720 C5' C A 39 OK OK 719 736 737 721 751 C5' U A 40 OK OK 750 767 768 752 781 C5' C A 41 OK OK 780 797 798 782 812 C5' U A 42 OK OK 811 828 829 813 842 C5' G A 43 OK OK 841 861 862 843 876 C5' C A 44 OK OK 875 892 893 877 907 C5' C A 45 OK OK 906 923 924 908 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G A 17 distorted distorted 3 4 5 37 P G A 18 distorted distorted 10 38 39 40 71 P C A 19 distorted distorted 45 72 73 74 102 P A A 20 distorted distorted 79 103 104 105 135 P G A 21 distorted distorted 110 136 137 138 169 P A A 22 distorted distorted 143 170 171 172 202 P U A 23 distorted distorted 177 203 204 205 232 P C A 24 distorted distorted 210 233 234 235 263 P U A 25 distorted distorted 240 264 265 266 293 P G A 26 distorted distorted 271 294 295 296 327 P A A 27 distorted distorted 301 328 329 330 360 P G A 28 distorted distorted 335 361 362 363 394 P C A 29 distorted distorted 368 395 396 397 425 P C A 30 distorted distorted 402 426 427 428 456 P U A 31 distorted distorted 433 457 458 459 486 P G A 32 distorted distorted 464 487 488 489 520 P G A 33 distorted distorted 494 521 522 523 554 P G A 34 distorted distorted 528 555 556 557 588 P A A 35 distorted distorted 562 589 590 591 621 P G A 36 distorted distorted 596 622 623 624 655 P C A 37 distorted distorted 629 656 657 658 686 P U A 38 distorted distorted 663 687 688 689 716 P C A 39 distorted distorted 694 717 718 719 747 P U A 40 distorted distorted 724 748 749 750 777 P C A 41 distorted distorted 755 778 779 780 808 P U A 42 distorted distorted 785 809 810 811 838 P G A 43 distorted distorted 816 839 840 841 872 P C A 44 distorted distorted 846 873 874 875 903 P C A 45 distorted distorted 880 904 905 906 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