ID code: '2LUP' 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' A A 4 alpha beta 107 129 113 110 145 C1' U A 5 alpha beta 140 160 146 143 175 C1' A A 6 alpha beta 170 192 176 173 208 C1' C A 7 alpha beta 203 223 209 206 239 C1' C A 8 alpha beta 234 254 240 237 270 C1' A A 9 alpha beta 265 287 271 268 303 C1' U A 10 alpha beta 298 318 304 301 333 C1' G A 11 alpha beta 328 351 334 331 367 C1' U A 12 alpha beta 362 382 368 365 397 C1' U A 13 alpha beta 392 412 398 395 427 C1' C A 14 alpha beta 422 442 428 425 458 C1' A A 15 alpha beta 453 475 459 456 491 C1' G A 16 alpha beta 486 509 492 489 525 C1' A A 17 alpha beta 520 542 526 523 558 C1' A A 18 alpha beta 553 575 559 556 591 C1' G A 19 alpha beta 586 609 592 589 625 C1' A A 20 alpha beta 620 642 626 623 658 C1' A A 21 alpha beta 653 675 659 656 691 C1' C A 22 alpha beta 686 706 692 689 722 C1' G A 23 alpha beta 717 740 723 720 756 C1' U A 24 alpha beta 751 771 757 754 786 C1' G A 25 alpha beta 781 804 787 784 820 C1' G A 26 alpha beta 815 838 821 818 854 C1' U A 27 alpha beta 849 869 855 852 884 C1' A A 28 alpha beta 879 901 885 882 917 C1' U A 29 alpha beta 912 932 918 915 947 C1' C A 30 alpha beta 942 962 948 945 978 C1' U A 31 alpha beta 973 993 979 976 1008 C1' C A 32 alpha beta 1003 1024 1009 1006 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 4 OK OK 112 108 127 111 143 C2' U A 5 OK OK 145 141 158 144 173 C2' A A 6 OK OK 175 171 190 174 206 C2' C A 7 OK OK 208 204 221 207 237 C2' C A 8 OK OK 239 235 252 238 268 C2' A A 9 OK OK 270 266 285 269 301 C2' U A 10 OK OK 303 299 316 302 331 C2' G A 11 OK OK 333 329 349 332 365 C2' U A 12 OK OK 367 363 380 366 395 C2' U A 13 OK OK 397 393 410 396 425 C2' C A 14 OK OK 427 423 440 426 456 C2' A A 15 OK OK 458 454 473 457 489 C2' G A 16 OK OK 491 487 507 490 523 C2' A A 17 OK OK 525 521 540 524 556 C2' A A 18 OK OK 558 554 573 557 589 C2' G A 19 OK OK 591 587 607 590 623 C2' A A 20 OK OK 625 621 640 624 656 C2' A A 21 OK OK 658 654 673 657 689 C2' C A 22 OK OK 691 687 704 690 720 C2' G A 23 OK OK 722 718 738 721 754 C2' U A 24 OK OK 756 752 769 755 784 C2' G A 25 OK OK 786 782 802 785 818 C2' G A 26 OK OK 820 816 836 819 852 C2' U A 27 OK OK 854 850 867 853 882 C2' A A 28 OK OK 884 880 899 883 915 C2' U A 29 OK OK 917 913 930 916 945 C2' C A 30 OK OK 947 943 960 946 976 C2' U A 31 OK OK 978 974 991 977 1006 C2' C A 32 OK OK 1008 1004 1022 1007 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 4 OK OK 106 126 109 110 141 C3' U A 5 OK OK 139 157 142 143 171 C3' A A 6 OK OK 169 189 172 173 204 C3' C A 7 OK OK 202 220 205 206 235 C3' C A 8 OK OK 233 251 236 237 266 C3' A A 9 OK OK 264 284 267 268 299 C3' U A 10 OK OK 297 315 300 301 329 C3' G A 11 OK OK 327 348 330 331 363 C3' U A 12 OK OK 361 379 364 365 393 C3' U A 13 OK OK 391 409 394 395 423 C3' C A 14 OK OK 421 439 424 425 454 C3' A A 15 OK OK 452 472 455 456 487 C3' G A 16 OK OK 485 506 488 489 521 C3' A A 17 OK OK 519 539 522 523 554 C3' A A 18 OK OK 552 572 555 556 587 C3' G A 19 OK OK 585 606 588 589 621 C3' A A 20 OK OK 619 639 622 623 654 C3' A A 21 OK OK 652 672 655 656 687 C3' C A 22 OK OK 685 703 688 689 718 C3' G A 23 OK OK 716 737 719 720 752 C3' U A 24 OK OK 750 768 753 754 782 C3' G A 25 OK OK 780 801 783 784 816 C3' G A 26 OK OK 814 835 817 818 850 C3' U A 27 OK OK 848 866 851 852 880 C3' A A 28 OK OK 878 898 881 882 913 C3' U A 29 OK OK 911 929 914 915 943 C3' C A 30 OK OK 941 959 944 945 974 C3' U A 31 OK OK 972 990 975 976 1004 C3' C A 32 OK OK 1002 1020 1005 1006 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 4 OK OK 108 125 105 107 139 C4' U A 5 OK OK 141 156 138 140 169 C4' A A 6 OK OK 171 188 168 170 202 C4' C A 7 OK OK 204 219 201 203 233 C4' C A 8 OK OK 235 250 232 234 264 C4' A A 9 OK OK 266 283 263 265 297 C4' U A 10 OK OK 299 314 296 298 327 C4' G A 11 OK OK 329 347 326 328 361 C4' U A 12 OK OK 363 378 360 362 391 C4' U A 13 OK OK 393 408 390 392 421 C4' C A 14 OK OK 423 438 420 422 452 C4' A A 15 OK OK 454 471 451 453 485 C4' G A 16 OK OK 487 505 484 486 519 C4' A A 17 OK OK 521 538 518 520 552 C4' A A 18 OK OK 554 571 551 553 585 C4' G A 19 OK OK 587 605 584 586 619 C4' A A 20 OK OK 621 638 618 620 652 C4' A A 21 OK OK 654 671 651 653 685 C4' C A 22 OK OK 687 702 684 686 716 C4' G A 23 OK OK 718 736 715 717 750 C4' U A 24 OK OK 752 767 749 751 780 C4' G A 25 OK OK 782 800 779 781 814 C4' G A 26 OK OK 816 834 813 815 848 C4' U A 27 OK OK 850 865 847 849 878 C4' A A 28 OK OK 880 897 877 879 911 C4' U A 29 OK OK 913 928 910 912 941 C4' C A 30 OK OK 943 958 940 942 972 C4' U A 31 OK OK 974 989 971 973 1002 C4' C A 32 OK OK 1004 1019 1001 1003 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 4 OK OK 104 123 124 106 138 C5' U A 5 OK OK 137 154 155 139 168 C5' A A 6 OK OK 167 186 187 169 201 C5' C A 7 OK OK 200 217 218 202 232 C5' C A 8 OK OK 231 248 249 233 263 C5' A A 9 OK OK 262 281 282 264 296 C5' U A 10 OK OK 295 312 313 297 326 C5' G A 11 OK OK 325 345 346 327 360 C5' U A 12 OK OK 359 376 377 361 390 C5' U A 13 OK OK 389 406 407 391 420 C5' C A 14 OK OK 419 436 437 421 451 C5' A A 15 OK OK 450 469 470 452 484 C5' G A 16 OK OK 483 503 504 485 518 C5' A A 17 OK OK 517 536 537 519 551 C5' A A 18 OK OK 550 569 570 552 584 C5' G A 19 OK OK 583 603 604 585 618 C5' A A 20 OK OK 617 636 637 619 651 C5' A A 21 OK OK 650 669 670 652 684 C5' C A 22 OK OK 683 700 701 685 715 C5' G A 23 OK OK 714 734 735 716 749 C5' U A 24 OK OK 748 765 766 750 779 C5' G A 25 OK OK 778 798 799 780 813 C5' G A 26 OK OK 812 832 833 814 847 C5' U A 27 OK OK 846 863 864 848 877 C5' A A 28 OK OK 876 895 896 878 910 C5' U A 29 OK OK 909 926 927 911 940 C5' C A 30 OK OK 939 956 957 941 971 C5' U A 31 OK OK 970 987 988 972 1001 C5' C A 32 OK OK 1000 1017 1018 1002 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 A A 4 distorted distorted 75 102 103 104 134 P U A 5 distorted distorted 109 135 136 137 164 P A A 6 distorted distorted 142 165 166 167 197 P C A 7 distorted distorted 172 198 199 200 228 P C A 8 distorted distorted 205 229 230 231 259 P A A 9 distorted distorted 236 260 261 262 292 P U A 10 distorted distorted 267 293 294 295 322 P G A 11 distorted distorted 300 323 324 325 356 P U A 12 distorted distorted 330 357 358 359 386 P U A 13 distorted distorted 364 387 388 389 416 P C A 14 distorted distorted 394 417 418 419 447 P A A 15 distorted distorted 424 448 449 450 480 P G A 16 distorted distorted 455 481 482 483 514 P A A 17 distorted distorted 488 515 516 517 547 P A A 18 distorted distorted 522 548 549 550 580 P G A 19 distorted distorted 555 581 582 583 614 P A A 20 distorted distorted 588 615 616 617 647 P A A 21 distorted distorted 622 648 649 650 680 P C A 22 distorted distorted 655 681 682 683 711 P G A 23 distorted distorted 688 712 713 714 745 P U A 24 distorted distorted 719 746 747 748 775 P G A 25 distorted distorted 753 776 777 778 809 P G A 26 distorted distorted 783 810 811 812 843 P U A 27 distorted distorted 817 844 845 846 873 P A A 28 distorted distorted 851 874 875 876 906 P U A 29 distorted distorted 881 907 908 909 936 P C A 30 distorted distorted 914 937 938 939 967 P U A 31 distorted distorted 944 968 969 970 997 P C A 32 distorted distorted 975 998 999 1000 ---------------------------------------------------------------------------------