ID code: '1KIS' 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' A A 2 alpha beta 39 61 45 42 77 C1' G A 3 alpha beta 72 95 78 75 111 C1' C A 4 alpha beta 106 126 112 109 142 C1' C A 5 alpha beta 137 157 143 140 173 C1' C A 6 alpha beta 168 188 174 171 204 C1' U A 7 alpha beta 199 219 205 202 234 C1' G A 8 alpha beta 229 252 235 232 268 C1' G A 9 alpha beta 263 286 269 266 302 C1' G A 10 alpha beta 297 320 303 300 336 C1' A A 11 alpha beta 331 353 337 334 369 C1' G A 12 alpha beta 364 387 370 367 403 C1' G A 13 alpha beta 398 421 404 401 437 C1' C A 14 alpha beta 432 452 438 435 468 C1' U A 15 alpha beta 463 483 469 466 498 C1' C A 16 alpha beta 493 514 499 496 528 C1' G B 17 alpha beta 523 546 529 526 563 C1' C B 18 alpha beta 558 578 564 561 594 C1' U B 19 alpha beta 589 609 595 592 624 C1' G B 20 alpha beta 619 642 625 622 658 C1' U B 21 alpha beta 653 673 659 656 688 C1' U B 22 alpha beta 683 703 689 686 718 C1' C B 23 alpha beta 713 733 719 716 749 C1' C B 24 alpha beta 744 764 750 747 780 C1' C B 25 alpha beta 775 795 781 778 811 C1' A B 26 alpha beta 806 828 812 809 844 C1' G B 27 alpha beta 839 862 845 842 878 C1' A B 28 alpha beta 873 895 879 876 911 C1' C B 29 alpha beta 906 926 912 909 942 C1' A B 30 alpha beta 937 959 943 940 975 C1' G B 31 alpha beta 970 993 976 973 1009 C1' C B 32 alpha beta 1004 1025 1010 1007 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 2 OK OK 44 40 59 43 75 C2' G A 3 OK OK 77 73 93 76 109 C2' C A 4 OK OK 111 107 124 110 140 C2' C A 5 OK OK 142 138 155 141 171 C2' C A 6 OK OK 173 169 186 172 202 C2' U A 7 OK OK 204 200 217 203 232 C2' G A 8 OK OK 234 230 250 233 266 C2' G A 9 OK OK 268 264 284 267 300 C2' G A 10 OK OK 302 298 318 301 334 C2' A A 11 OK OK 336 332 351 335 367 C2' G A 12 OK OK 369 365 385 368 401 C2' G A 13 OK OK 403 399 419 402 435 C2' C A 14 OK OK 437 433 450 436 466 C2' U A 15 OK OK 468 464 481 467 496 C2' C A 16 OK OK 498 494 512 497 526 C2' G B 17 OK OK 528 524 544 527 561 C2' C B 18 OK OK 563 559 576 562 592 C2' U B 19 OK OK 594 590 607 593 622 C2' G B 20 OK OK 624 620 640 623 656 C2' U B 21 OK OK 658 654 671 657 686 C2' U B 22 OK OK 688 684 701 687 716 C2' C B 23 OK OK 718 714 731 717 747 C2' C B 24 OK OK 749 745 762 748 778 C2' C B 25 OK OK 780 776 793 779 809 C2' A B 26 OK OK 811 807 826 810 842 C2' G B 27 OK OK 844 840 860 843 876 C2' A B 28 OK OK 878 874 893 877 909 C2' C B 29 OK OK 911 907 924 910 940 C2' A B 30 OK OK 942 938 957 941 973 C2' G B 31 OK OK 975 971 991 974 1007 C2' C B 32 OK OK 1009 1005 1023 1008 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' A A 2 OK OK 38 58 41 42 73 C3' G A 3 OK OK 71 92 74 75 107 C3' C A 4 OK OK 105 123 108 109 138 C3' C A 5 OK OK 136 154 139 140 169 C3' C A 6 OK OK 167 185 170 171 200 C3' U A 7 OK OK 198 216 201 202 230 C3' G A 8 OK OK 228 249 231 232 264 C3' G A 9 OK OK 262 283 265 266 298 C3' G A 10 OK OK 296 317 299 300 332 C3' A A 11 OK OK 330 350 333 334 365 C3' G A 12 OK OK 363 384 366 367 399 C3' G A 13 OK OK 397 418 400 401 433 C3' C A 14 OK OK 431 449 434 435 464 C3' U A 15 OK OK 462 480 465 466 494 C3' C A 16 OK OK 492 510 495 496 524 C3' G B 17 OK OK 522 543 525 526 559 C3' C B 18 OK OK 557 575 560 561 590 C3' U B 19 OK OK 588 606 591 592 620 C3' G B 20 OK OK 618 639 621 622 654 C3' U B 21 OK OK 652 670 655 656 684 C3' U B 22 OK OK 682 700 685 686 714 C3' C B 23 OK OK 712 730 715 716 745 C3' C B 24 OK OK 743 761 746 747 776 C3' C B 25 OK OK 774 792 777 778 807 C3' A B 26 OK OK 805 825 808 809 840 C3' G B 27 OK OK 838 859 841 842 874 C3' A B 28 OK OK 872 892 875 876 907 C3' C B 29 OK OK 905 923 908 909 938 C3' A B 30 OK OK 936 956 939 940 971 C3' G B 31 OK OK 969 990 972 973 1005 C3' C B 32 OK OK 1003 1021 1006 1007 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' A A 2 OK OK 40 57 37 39 71 C4' G A 3 OK OK 73 91 70 72 105 C4' C A 4 OK OK 107 122 104 106 136 C4' C A 5 OK OK 138 153 135 137 167 C4' C A 6 OK OK 169 184 166 168 198 C4' U A 7 OK OK 200 215 197 199 228 C4' G A 8 OK OK 230 248 227 229 262 C4' G A 9 OK OK 264 282 261 263 296 C4' G A 10 OK OK 298 316 295 297 330 C4' A A 11 OK OK 332 349 329 331 363 C4' G A 12 OK OK 365 383 362 364 397 C4' G A 13 OK OK 399 417 396 398 431 C4' C A 14 OK OK 433 448 430 432 462 C4' U A 15 OK OK 464 479 461 463 492 C4' C A 16 OK OK 494 509 491 493 522 C4' G B 17 OK OK 524 542 521 523 557 C4' C B 18 OK OK 559 574 556 558 588 C4' U B 19 OK OK 590 605 587 589 618 C4' G B 20 OK OK 620 638 617 619 652 C4' U B 21 OK OK 654 669 651 653 682 C4' U B 22 OK OK 684 699 681 683 712 C4' C B 23 OK OK 714 729 711 713 743 C4' C B 24 OK OK 745 760 742 744 774 C4' C B 25 OK OK 776 791 773 775 805 C4' A B 26 OK OK 807 824 804 806 838 C4' G B 27 OK OK 840 858 837 839 872 C4' A B 28 OK OK 874 891 871 873 905 C4' C B 29 OK OK 907 922 904 906 936 C4' A B 30 OK OK 938 955 935 937 969 C4' G B 31 OK OK 971 989 968 970 1003 C4' C B 32 OK OK 1005 1020 1002 1004 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 2 OK OK 36 55 56 38 70 C5' G A 3 OK OK 69 89 90 71 104 C5' C A 4 OK OK 103 120 121 105 135 C5' C A 5 OK OK 134 151 152 136 166 C5' C A 6 OK OK 165 182 183 167 197 C5' U A 7 OK OK 196 213 214 198 227 C5' G A 8 OK OK 226 246 247 228 261 C5' G A 9 OK OK 260 280 281 262 295 C5' G A 10 OK OK 294 314 315 296 329 C5' A A 11 OK OK 328 347 348 330 362 C5' G A 12 OK OK 361 381 382 363 396 C5' G A 13 OK OK 395 415 416 397 430 C5' C A 14 OK OK 429 446 447 431 461 C5' U A 15 OK OK 460 477 478 462 491 C5' C A 16 OK OK 490 507 508 492 521 C5' G B 17 OK OK 520 540 541 522 556 C5' C B 18 OK OK 555 572 573 557 587 C5' U B 19 OK OK 586 603 604 588 617 C5' G B 20 OK OK 616 636 637 618 651 C5' U B 21 OK OK 650 667 668 652 681 C5' U B 22 OK OK 680 697 698 682 711 C5' C B 23 OK OK 710 727 728 712 742 C5' C B 24 OK OK 741 758 759 743 773 C5' C B 25 OK OK 772 789 790 774 804 C5' A B 26 OK OK 803 822 823 805 837 C5' G B 27 OK OK 836 856 857 838 871 C5' A B 28 OK OK 870 889 890 872 904 C5' C B 29 OK OK 903 920 921 905 935 C5' A B 30 OK OK 934 953 954 936 968 C5' G B 31 OK OK 967 987 988 969 1002 C5' C B 32 OK OK 1001 1018 1019 1003 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P A A 2 distorted distorted 6 34 35 36 66 P G A 3 distorted distorted 41 67 68 69 100 P C A 4 distorted distorted 74 101 102 103 131 P C A 5 distorted distorted 108 132 133 134 162 P C A 6 distorted distorted 139 163 164 165 193 P U A 7 distorted distorted 170 194 195 196 223 P G A 8 distorted distorted 201 224 225 226 257 P G A 9 distorted distorted 231 258 259 260 291 P G A 10 distorted distorted 265 292 293 294 325 P A A 11 distorted distorted 299 326 327 328 358 P G A 12 distorted distorted 333 359 360 361 392 P G A 13 distorted distorted 366 393 394 395 426 P C A 14 distorted distorted 400 427 428 429 457 P U A 15 distorted distorted 434 458 459 460 487 P C A 16 distorted distorted 465 488 489 490 552 P C B 18 distorted distorted 525 553 554 555 583 P U B 19 distorted distorted 560 584 585 586 613 P G B 20 distorted distorted 591 614 615 616 647 P U B 21 distorted distorted 621 648 649 650 677 P U B 22 distorted distorted 655 678 679 680 707 P C B 23 distorted distorted 685 708 709 710 738 P C B 24 distorted distorted 715 739 740 741 769 P C B 25 distorted distorted 746 770 771 772 800 P A B 26 distorted distorted 777 801 802 803 833 P G B 27 distorted distorted 808 834 835 836 867 P A B 28 distorted distorted 841 868 869 870 900 P C B 29 distorted distorted 875 901 902 903 931 P A B 30 distorted distorted 908 932 933 934 964 P G B 31 distorted distorted 939 965 966 967 998 P C B 32 distorted distorted 972 999 1000 1001 ---------------------------------------------------------------------------------