ID code: '3NPN' 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' --------------------------------------------------------------------------------- 12 C1' G A 1 beta 7 13 10 35 C1' G A 2 beta 30 36 33 58 C1' A A 3 beta 53 59 56 80 C1' C A 4 beta 75 81 78 100 C1' G A 5 beta 95 101 98 123 C1' A A 6 beta 118 124 121 145 C1' G A 7 beta 140 146 143 168 C1' G A 8 beta 163 169 166 191 C1' A A 9 beta 186 192 189 213 C1' G A 10 beta 208 214 211 236 C1' C A 11 beta 231 237 234 256 C1' G A 12 beta 251 257 254 279 C1' U A 13 beta 274 280 277 299 C1' U A 14 beta 294 300 297 319 C1' G A 15 beta 314 320 317 342 C1' C A 16 beta 337 343 340 362 C1' A A 17 beta 357 363 360 384 C1' A A 18 beta 379 385 382 406 C1' G A 19 beta 401 407 404 429 C1' C A 20 beta 424 430 427 449 C1' G A 21 beta 444 450 447 472 C1' A A 22 beta 467 473 470 494 C1' A A 23 beta 489 495 492 516 C1' A A 24 beta 511 517 514 538 C1' G A 25 beta 533 539 536 561 C1' C A 26 beta 556 562 559 581 C1' C A 27 beta 576 582 579 601 C1' C A 28 beta 596 602 599 621 C1' A A 29 beta 616 622 619 643 C1' G A 30 beta 638 644 641 666 C1' G A 31 beta 661 667 664 689 C1' C A 32 beta 684 690 687 709 C1' U A 33 beta 704 710 707 729 C1' A A 34 beta 724 730 727 751 C1' G A 35 beta 746 752 749 774 C1' U A 36 beta 769 775 772 794 C1' C A 37 beta 789 795 792 814 C1' C A 38 beta 809 815 812 834 C1' G A 39 beta 829 835 832 857 C1' A A 44 beta 852 858 855 879 C1' A A 45 beta 874 880 877 901 C1' C A 46 beta 896 902 899 921 C1' G A 47 beta 916 922 919 944 C1' G A 48 beta 939 945 942 967 C1' C A 49 beta 962 968 965 987 C1' G A 50 beta 982 988 985 1010 C1' C A 51 beta 1005 1011 1008 1030 C1' U A 52 beta 1025 1031 1028 1050 C1' C A 53 beta 1045 1051 1048 1070 C1' A A 54 beta 1065 1071 1068 1097 C1' SAH A 55 beta 1092 1098 1095 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 1 OK 12 8 11 33 C2' G A 2 OK 35 31 34 56 C2' A A 3 OK 58 54 57 78 C2' C A 4 OK 80 76 79 98 C2' G A 5 OK 100 96 99 121 C2' A A 6 OK 123 119 122 143 C2' G A 7 OK 145 141 144 166 C2' G A 8 OK 168 164 167 189 C2' A A 9 OK 191 187 190 211 C2' G A 10 OK 213 209 212 234 C2' C A 11 OK 236 232 235 254 C2' G A 12 OK 256 252 255 277 C2' U A 13 OK 279 275 278 297 C2' U A 14 OK 299 295 298 317 C2' G A 15 OK 319 315 318 340 C2' C A 16 OK 342 338 341 360 C2' A A 17 OK 362 358 361 382 C2' A A 18 OK 384 380 383 404 C2' G A 19 OK 406 402 405 427 C2' C A 20 OK 429 425 428 447 C2' G A 21 OK 449 445 448 470 C2' A A 22 OK 472 468 471 492 C2' A A 23 OK 494 490 493 514 C2' A A 24 OK 516 512 515 536 C2' G A 25 OK 538 534 537 559 C2' C A 26 OK 561 557 560 579 C2' C A 27 OK 581 577 580 599 C2' C A 28 OK 601 597 600 619 C2' A A 29 OK 621 617 620 641 C2' G A 30 OK 643 639 642 664 C2' G A 31 OK 666 662 665 687 C2' C A 32 OK 689 685 688 707 C2' U A 33 OK 709 705 708 727 C2' A A 34 OK 729 725 728 749 C2' G A 35 OK 751 747 750 772 C2' U A 36 OK 774 770 773 792 C2' C A 37 OK 794 790 793 812 C2' C A 38 OK 814 810 813 832 C2' G A 39 OK 834 830 833 855 C2' A A 44 OK 857 853 856 877 C2' A A 45 OK 879 875 878 899 C2' C A 46 OK 901 897 900 919 C2' G A 47 OK 921 917 920 942 C2' G A 48 OK 944 940 943 965 C2' C A 49 OK 967 963 966 985 C2' G A 50 OK 987 983 986 1008 C2' C A 51 OK 1010 1006 1009 1028 C2' U A 52 OK 1030 1026 1029 1048 C2' C A 53 OK 1050 1046 1049 1068 C2' A A 54 OK 1070 1066 1069 1095 C2' SAH A 55 OK 1097 1093 1096 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 1 OK 6 9 10 31 C3' G A 2 OK 29 32 33 54 C3' A A 3 OK 52 55 56 76 C3' C A 4 OK 74 77 78 96 C3' G A 5 OK 94 97 98 119 C3' A A 6 OK 117 120 121 141 C3' G A 7 OK 139 142 143 164 C3' G A 8 OK 162 165 166 187 C3' A A 9 OK 185 188 189 209 C3' G A 10 OK 207 210 211 232 C3' C A 11 OK 230 233 234 252 C3' G A 12 OK 250 253 254 275 C3' U A 13 OK 273 276 277 295 C3' U A 14 OK 293 296 297 315 C3' G A 15 OK 313 316 317 338 C3' C A 16 OK 336 339 340 358 C3' A A 17 OK 356 359 360 380 C3' A A 18 OK 378 381 382 402 C3' G A 19 OK 400 403 404 425 C3' C A 20 OK 423 426 427 445 C3' G A 21 OK 443 446 447 468 C3' A A 22 OK 466 469 470 490 C3' A A 23 OK 488 491 492 512 C3' A A 24 OK 510 513 514 534 C3' G A 25 OK 532 535 536 557 C3' C A 26 OK 555 558 559 577 C3' C A 27 OK 575 578 579 597 C3' C A 28 OK 595 598 599 617 C3' A A 29 OK 615 618 619 639 C3' G A 30 OK 637 640 641 662 C3' G A 31 OK 660 663 664 685 C3' C A 32 OK 683 686 687 705 C3' U A 33 OK 703 706 707 725 C3' A A 34 OK 723 726 727 747 C3' G A 35 OK 745 748 749 770 C3' U A 36 OK 768 771 772 790 C3' C A 37 OK 788 791 792 810 C3' C A 38 OK 808 811 812 830 C3' G A 39 OK 828 831 832 853 C3' A A 44 OK 851 854 855 875 C3' A A 45 OK 873 876 877 897 C3' C A 46 OK 895 898 899 917 C3' G A 47 OK 915 918 919 940 C3' G A 48 OK 938 941 942 963 C3' C A 49 OK 961 964 965 983 C3' G A 50 OK 981 984 985 1006 C3' C A 51 OK 1004 1007 1008 1026 C3' U A 52 OK 1024 1027 1028 1046 C3' C A 53 OK 1044 1047 1048 1066 C3' A A 54 OK 1064 1067 1068 1093 C3' SAH A 55 OK 1091 1094 1095 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 1 OK 8 5 7 29 C4' G A 2 OK 31 28 30 52 C4' A A 3 OK 54 51 53 74 C4' C A 4 OK 76 73 75 94 C4' G A 5 OK 96 93 95 117 C4' A A 6 OK 119 116 118 139 C4' G A 7 OK 141 138 140 162 C4' G A 8 OK 164 161 163 185 C4' A A 9 OK 187 184 186 207 C4' G A 10 OK 209 206 208 230 C4' C A 11 OK 232 229 231 250 C4' G A 12 OK 252 249 251 273 C4' U A 13 OK 275 272 274 293 C4' U A 14 OK 295 292 294 313 C4' G A 15 OK 315 312 314 336 C4' C A 16 OK 338 335 337 356 C4' A A 17 OK 358 355 357 378 C4' A A 18 OK 380 377 379 400 C4' G A 19 OK 402 399 401 423 C4' C A 20 OK 425 422 424 443 C4' G A 21 OK 445 442 444 466 C4' A A 22 OK 468 465 467 488 C4' A A 23 OK 490 487 489 510 C4' A A 24 OK 512 509 511 532 C4' G A 25 OK 534 531 533 555 C4' C A 26 OK 557 554 556 575 C4' C A 27 OK 577 574 576 595 C4' C A 28 OK 597 594 596 615 C4' A A 29 OK 617 614 616 637 C4' G A 30 OK 639 636 638 660 C4' G A 31 OK 662 659 661 683 C4' C A 32 OK 685 682 684 703 C4' U A 33 OK 705 702 704 723 C4' A A 34 OK 725 722 724 745 C4' G A 35 OK 747 744 746 768 C4' U A 36 OK 770 767 769 788 C4' C A 37 OK 790 787 789 808 C4' C A 38 OK 810 807 809 828 C4' G A 39 OK 830 827 829 851 C4' A A 44 OK 853 850 852 873 C4' A A 45 OK 875 872 874 895 C4' C A 46 OK 897 894 896 915 C4' G A 47 OK 917 914 916 938 C4' G A 48 OK 940 937 939 961 C4' C A 49 OK 963 960 962 981 C4' G A 50 OK 983 980 982 1004 C4' C A 51 OK 1006 1003 1005 1024 C4' U A 52 OK 1026 1023 1025 1044 C4' C A 53 OK 1046 1043 1045 1064 C4' A A 54 OK 1066 1063 1065 1091 C4' SAH A 55 OK 1093 1090 1092 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 1 4 6 28 C5' G A 2 27 29 51 C5' A A 3 50 52 73 C5' C A 4 72 74 93 C5' G A 5 92 94 116 C5' A A 6 115 117 138 C5' G A 7 137 139 161 C5' G A 8 160 162 184 C5' A A 9 183 185 206 C5' G A 10 205 207 229 C5' C A 11 228 230 249 C5' G A 12 248 250 272 C5' U A 13 271 273 292 C5' U A 14 291 293 312 C5' G A 15 311 313 335 C5' C A 16 334 336 355 C5' A A 17 354 356 377 C5' A A 18 376 378 399 C5' G A 19 398 400 422 C5' C A 20 421 423 442 C5' G A 21 441 443 465 C5' A A 22 464 466 487 C5' A A 23 486 488 509 C5' A A 24 508 510 531 C5' G A 25 530 532 554 C5' C A 26 553 555 574 C5' C A 27 573 575 594 C5' C A 28 593 595 614 C5' A A 29 613 615 636 C5' G A 30 635 637 659 C5' G A 31 658 660 682 C5' C A 32 681 683 702 C5' U A 33 701 703 722 C5' A A 34 721 723 744 C5' G A 35 743 745 767 C5' U A 36 766 768 787 C5' C A 37 786 788 807 C5' C A 38 806 808 827 C5' G A 39 826 828 850 C5' A A 44 849 851 872 C5' A A 45 871 873 894 C5' C A 46 893 895 914 C5' G A 47 913 915 937 C5' G A 48 936 938 960 C5' C A 49 959 961 980 C5' G A 50 979 981 1003 C5' C A 51 1002 1004 1023 C5' U A 52 1022 1024 1043 C5' C A 53 1042 1044 1063 C5' A A 54 1062 1064 1090 C5' SAH A 55 1091 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 1 distorted distorted 2 3 4 24 P G A 2 distorted distorted 9 25 26 27 47 P A A 3 distorted distorted 32 48 49 50 69 P C A 4 distorted distorted 55 70 71 72 89 P G A 5 distorted distorted 77 90 91 92 112 P A A 6 distorted distorted 97 113 114 115 134 P G A 7 distorted distorted 120 135 136 137 157 P G A 8 distorted distorted 142 158 159 160 180 P A A 9 distorted distorted 165 181 182 183 202 P G A 10 distorted distorted 188 203 204 205 225 P C A 11 distorted distorted 210 226 227 228 245 P G A 12 distorted distorted 233 246 247 248 268 P U A 13 distorted distorted 253 269 270 271 288 P U A 14 distorted distorted 276 289 290 291 308 P G A 15 distorted distorted 296 309 310 311 331 P C A 16 distorted distorted 316 332 333 334 351 P A A 17 distorted distorted 339 352 353 354 373 P A A 18 distorted distorted 359 374 375 376 395 P G A 19 distorted distorted 381 396 397 398 418 P C A 20 distorted distorted 403 419 420 421 438 P G A 21 distorted distorted 426 439 440 441 461 P A A 22 distorted distorted 446 462 463 464 483 P A A 23 distorted distorted 469 484 485 486 505 P A A 24 distorted distorted 491 506 507 508 527 P G A 25 distorted distorted 513 528 529 530 550 P C A 26 distorted distorted 535 551 552 553 570 P C A 27 distorted distorted 558 571 572 573 590 P C A 28 distorted distorted 578 591 592 593 610 P A A 29 distorted distorted 598 611 612 613 632 P G A 30 distorted distorted 618 633 634 635 655 P G A 31 distorted distorted 640 656 657 658 678 P C A 32 distorted distorted 663 679 680 681 698 P U A 33 distorted distorted 686 699 700 701 718 P A A 34 distorted distorted 706 719 720 721 740 P G A 35 distorted distorted 726 741 742 743 763 P U A 36 distorted distorted 748 764 765 766 783 P C A 37 distorted distorted 771 784 785 786 803 P C A 38 distorted distorted 791 804 805 806 823 P G A 39 distorted distorted 811 824 825 826 846 P A A 44 distorted distorted 847 848 849 868 P A A 45 distorted distorted 854 869 870 871 890 P C A 46 distorted distorted 876 891 892 893 910 P G A 47 distorted distorted 898 911 912 913 933 P G A 48 distorted distorted 918 934 935 936 956 P C A 49 distorted distorted 941 957 958 959 976 P G A 50 distorted distorted 964 977 978 979 999 P C A 51 distorted distorted 984 1000 1001 1002 1019 P U A 52 distorted distorted 1007 1020 1021 1022 1039 P C A 53 distorted distorted 1027 1040 1041 1042 1059 P A A 54 distorted distorted 1047 1060 1061 1062 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