ID code: '2FK6' 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 R 1 beta 4 10 7 32 C1' C R 2 beta 27 33 30 52 C1' U R 3 beta 47 53 50 72 C1' U R 4 beta 67 73 70 92 C1' C R 5 beta 87 93 90 112 C1' C R 6 beta 107 113 110 132 C1' A R 7 beta 127 133 130 154 C1' U R 8 beta 149 155 152 174 C1' A R 9 beta 169 175 172 196 C1' G R 10 beta 191 197 194 219 C1' C R 11 beta 214 220 217 239 C1' U R 12 beta 234 240 237 259 C1' C R 13 beta 254 260 257 279 C1' A R 14 beta 274 280 277 301 C1' G R 15 beta 296 302 299 324 C1' C R 16 beta 319 325 322 344 C1' A R 17 beta 339 345 342 366 C1' G R 18 beta 361 367 364 389 C1' G R 19 beta 384 390 387 412 C1' U R 20 beta 407 413 410 432 C1' A R 21 beta 427 433 430 454 C1' G R 22 beta 449 455 452 477 C1' A R 23 beta 472 478 475 499 C1' G R 24 beta 494 500 497 522 C1' C R 25 beta 517 523 520 539 C1' G R 46 beta 534 540 537 562 C1' U R 47 beta 557 563 560 582 C1' C R 48 beta 577 583 580 602 C1' A R 49 beta 597 603 600 624 C1' G R 50 beta 619 625 622 647 C1' C R 51 beta 642 648 645 667 C1' G R 52 beta 662 668 665 690 C1' G R 53 beta 685 691 688 713 C1' U R 54 beta 708 714 711 733 C1' U R 55 beta 728 734 731 753 C1' C R 56 beta 748 754 751 773 C1' G R 57 beta 768 774 771 796 C1' A R 58 beta 791 797 794 818 C1' G R 59 beta 813 819 816 841 C1' C R 60 beta 836 842 839 861 C1' C R 61 beta 856 862 859 881 C1' C R 62 beta 876 882 879 901 C1' G R 63 beta 896 902 899 924 C1' C R 64 beta 919 925 922 944 C1' U R 65 beta 939 945 942 964 C1' U R 66 beta 959 965 962 984 C1' G R 67 beta 979 985 982 1007 C1' G R 68 beta 1002 1008 1005 1030 C1' A R 69 beta 1025 1031 1028 1052 C1' A R 70 beta 1047 1053 1050 1074 C1' G R 71 beta 1069 1075 1072 1097 C1' C R 72 beta 1092 1098 1095 1117 C1' U R 73 beta 1112 1118 1115 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G R 1 OK 9 5 8 30 C2' C R 2 OK 32 28 31 50 C2' U R 3 OK 52 48 51 70 C2' U R 4 OK 72 68 71 90 C2' C R 5 OK 92 88 91 110 C2' C R 6 OK 112 108 111 130 C2' A R 7 OK 132 128 131 152 C2' U R 8 OK 154 150 153 172 C2' A R 9 OK 174 170 173 194 C2' G R 10 OK 196 192 195 217 C2' C R 11 OK 219 215 218 237 C2' U R 12 OK 239 235 238 257 C2' C R 13 OK 259 255 258 277 C2' A R 14 OK 279 275 278 299 C2' G R 15 OK 301 297 300 322 C2' C R 16 OK 324 320 323 342 C2' A R 17 OK 344 340 343 364 C2' G R 18 OK 366 362 365 387 C2' G R 19 OK 389 385 388 410 C2' U R 20 OK 412 408 411 430 C2' A R 21 OK 432 428 431 452 C2' G R 22 OK 454 450 453 475 C2' A R 23 OK 477 473 476 497 C2' G R 24 OK 499 495 498 520 C2' C R 25 OK 522 518 521 537 C2' G R 46 OK 539 535 538 560 C2' U R 47 OK 562 558 561 580 C2' C R 48 OK 582 578 581 600 C2' A R 49 OK 602 598 601 622 C2' G R 50 OK 624 620 623 645 C2' C R 51 OK 647 643 646 665 C2' G R 52 OK 667 663 666 688 C2' G R 53 OK 690 686 689 711 C2' U R 54 OK 713 709 712 731 C2' U R 55 OK 733 729 732 751 C2' C R 56 OK 753 749 752 771 C2' G R 57 OK 773 769 772 794 C2' A R 58 OK 796 792 795 816 C2' G R 59 OK 818 814 817 839 C2' C R 60 OK 841 837 840 859 C2' C R 61 OK 861 857 860 879 C2' C R 62 OK 881 877 880 899 C2' G R 63 OK 901 897 900 922 C2' C R 64 OK 924 920 923 942 C2' U R 65 OK 944 940 943 962 C2' U R 66 OK 964 960 963 982 C2' G R 67 OK 984 980 983 1005 C2' G R 68 OK 1007 1003 1006 1028 C2' A R 69 OK 1030 1026 1029 1050 C2' A R 70 OK 1052 1048 1051 1072 C2' G R 71 OK 1074 1070 1073 1095 C2' C R 72 OK 1097 1093 1096 1115 C2' U R 73 OK 1117 1113 1116 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G R 1 OK 3 6 7 28 C3' C R 2 OK 26 29 30 48 C3' U R 3 OK 46 49 50 68 C3' U R 4 OK 66 69 70 88 C3' C R 5 OK 86 89 90 108 C3' C R 6 OK 106 109 110 128 C3' A R 7 OK 126 129 130 150 C3' U R 8 OK 148 151 152 170 C3' A R 9 OK 168 171 172 192 C3' G R 10 OK 190 193 194 215 C3' C R 11 OK 213 216 217 235 C3' U R 12 OK 233 236 237 255 C3' C R 13 OK 253 256 257 275 C3' A R 14 OK 273 276 277 297 C3' G R 15 OK 295 298 299 320 C3' C R 16 OK 318 321 322 340 C3' A R 17 OK 338 341 342 362 C3' G R 18 OK 360 363 364 385 C3' G R 19 OK 383 386 387 408 C3' U R 20 OK 406 409 410 428 C3' A R 21 OK 426 429 430 450 C3' G R 22 OK 448 451 452 473 C3' A R 23 OK 471 474 475 495 C3' G R 24 OK 493 496 497 518 C3' C R 25 OK 516 519 520 535 C3' G R 46 OK 533 536 537 558 C3' U R 47 OK 556 559 560 578 C3' C R 48 OK 576 579 580 598 C3' A R 49 OK 596 599 600 620 C3' G R 50 OK 618 621 622 643 C3' C R 51 OK 641 644 645 663 C3' G R 52 OK 661 664 665 686 C3' G R 53 OK 684 687 688 709 C3' U R 54 OK 707 710 711 729 C3' U R 55 OK 727 730 731 749 C3' C R 56 OK 747 750 751 769 C3' G R 57 OK 767 770 771 792 C3' A R 58 OK 790 793 794 814 C3' G R 59 OK 812 815 816 837 C3' C R 60 OK 835 838 839 857 C3' C R 61 OK 855 858 859 877 C3' C R 62 OK 875 878 879 897 C3' G R 63 OK 895 898 899 920 C3' C R 64 OK 918 921 922 940 C3' U R 65 OK 938 941 942 960 C3' U R 66 OK 958 961 962 980 C3' G R 67 OK 978 981 982 1003 C3' G R 68 OK 1001 1004 1005 1026 C3' A R 69 OK 1024 1027 1028 1048 C3' A R 70 OK 1046 1049 1050 1070 C3' G R 71 OK 1068 1071 1072 1093 C3' C R 72 OK 1091 1094 1095 1113 C3' U R 73 OK 1111 1114 1115 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G R 1 OK 5 2 4 26 C4' C R 2 OK 28 25 27 46 C4' U R 3 OK 48 45 47 66 C4' U R 4 OK 68 65 67 86 C4' C R 5 OK 88 85 87 106 C4' C R 6 OK 108 105 107 126 C4' A R 7 OK 128 125 127 148 C4' U R 8 OK 150 147 149 168 C4' A R 9 OK 170 167 169 190 C4' G R 10 OK 192 189 191 213 C4' C R 11 OK 215 212 214 233 C4' U R 12 OK 235 232 234 253 C4' C R 13 OK 255 252 254 273 C4' A R 14 OK 275 272 274 295 C4' G R 15 OK 297 294 296 318 C4' C R 16 OK 320 317 319 338 C4' A R 17 OK 340 337 339 360 C4' G R 18 OK 362 359 361 383 C4' G R 19 OK 385 382 384 406 C4' U R 20 OK 408 405 407 426 C4' A R 21 OK 428 425 427 448 C4' G R 22 OK 450 447 449 471 C4' A R 23 OK 473 470 472 493 C4' G R 24 OK 495 492 494 516 C4' C R 25 OK 518 515 517 533 C4' G R 46 OK 535 532 534 556 C4' U R 47 OK 558 555 557 576 C4' C R 48 OK 578 575 577 596 C4' A R 49 OK 598 595 597 618 C4' G R 50 OK 620 617 619 641 C4' C R 51 OK 643 640 642 661 C4' G R 52 OK 663 660 662 684 C4' G R 53 OK 686 683 685 707 C4' U R 54 OK 709 706 708 727 C4' U R 55 OK 729 726 728 747 C4' C R 56 OK 749 746 748 767 C4' G R 57 OK 769 766 768 790 C4' A R 58 OK 792 789 791 812 C4' G R 59 OK 814 811 813 835 C4' C R 60 OK 837 834 836 855 C4' C R 61 OK 857 854 856 875 C4' C R 62 OK 877 874 876 895 C4' G R 63 OK 897 894 896 918 C4' C R 64 OK 920 917 919 938 C4' U R 65 OK 940 937 939 958 C4' U R 66 OK 960 957 959 978 C4' G R 67 OK 980 977 979 1001 C4' G R 68 OK 1003 1000 1002 1024 C4' A R 69 OK 1026 1023 1025 1046 C4' A R 70 OK 1048 1045 1047 1068 C4' G R 71 OK 1070 1067 1069 1091 C4' C R 72 OK 1093 1090 1092 1111 C4' U R 73 OK 1113 1110 1112 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G R 1 1 3 25 C5' C R 2 24 26 45 C5' U R 3 44 46 65 C5' U R 4 64 66 85 C5' C R 5 84 86 105 C5' C R 6 104 106 125 C5' A R 7 124 126 147 C5' U R 8 146 148 167 C5' A R 9 166 168 189 C5' G R 10 188 190 212 C5' C R 11 211 213 232 C5' U R 12 231 233 252 C5' C R 13 251 253 272 C5' A R 14 271 273 294 C5' G R 15 293 295 317 C5' C R 16 316 318 337 C5' A R 17 336 338 359 C5' G R 18 358 360 382 C5' G R 19 381 383 405 C5' U R 20 404 406 425 C5' A R 21 424 426 447 C5' G R 22 446 448 470 C5' A R 23 469 471 492 C5' G R 24 491 493 515 C5' C R 25 514 516 532 C5' G R 46 531 533 555 C5' U R 47 554 556 575 C5' C R 48 574 576 595 C5' A R 49 594 596 617 C5' G R 50 616 618 640 C5' C R 51 639 641 660 C5' G R 52 659 661 683 C5' G R 53 682 684 706 C5' U R 54 705 707 726 C5' U R 55 725 727 746 C5' C R 56 745 747 766 C5' G R 57 765 767 789 C5' A R 58 788 790 811 C5' G R 59 810 812 834 C5' C R 60 833 835 854 C5' C R 61 853 855 874 C5' C R 62 873 875 894 C5' G R 63 893 895 917 C5' C R 64 916 918 937 C5' U R 65 936 938 957 C5' U R 66 956 958 977 C5' G R 67 976 978 1000 C5' G R 68 999 1001 1023 C5' A R 69 1022 1024 1045 C5' A R 70 1044 1046 1067 C5' G R 71 1066 1068 1090 C5' C R 72 1089 1091 1110 C5' U R 73 1109 1111 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P C R 2 distorted distorted 6 22 23 24 41 P U R 3 distorted distorted 29 42 43 44 61 P U R 4 distorted distorted 49 62 63 64 81 P C R 5 distorted distorted 69 82 83 84 101 P C R 6 distorted distorted 89 102 103 104 121 P A R 7 distorted distorted 109 122 123 124 143 P U R 8 distorted distorted 129 144 145 146 163 P A R 9 distorted distorted 151 164 165 166 185 P G R 10 distorted distorted 171 186 187 188 208 P C R 11 distorted distorted 193 209 210 211 228 P U R 12 distorted distorted 216 229 230 231 248 P C R 13 distorted distorted 236 249 250 251 268 P A R 14 distorted distorted 256 269 270 271 290 P G R 15 distorted distorted 276 291 292 293 313 P C R 16 distorted distorted 298 314 315 316 333 P A R 17 distorted distorted 321 334 335 336 355 P G R 18 distorted distorted 341 356 357 358 378 P G R 19 distorted distorted 363 379 380 381 401 P U R 20 distorted distorted 386 402 403 404 421 P A R 21 distorted distorted 409 422 423 424 443 P G R 22 distorted distorted 429 444 445 446 466 P A R 23 distorted distorted 451 467 468 469 488 P G R 24 distorted distorted 474 489 490 491 511 P C R 25 distorted distorted 496 512 513 514 551 P U R 47 distorted distorted 536 552 553 554 571 P C R 48 distorted distorted 559 572 573 574 591 P A R 49 distorted distorted 579 592 593 594 613 P G R 50 distorted distorted 599 614 615 616 636 P C R 51 distorted distorted 621 637 638 639 656 P G R 52 distorted distorted 644 657 658 659 679 P G R 53 distorted distorted 664 680 681 682 702 P U R 54 distorted distorted 687 703 704 705 722 P U R 55 distorted distorted 710 723 724 725 742 P C R 56 distorted distorted 730 743 744 745 762 P G R 57 distorted distorted 750 763 764 765 785 P A R 58 distorted distorted 770 786 787 788 807 P G R 59 distorted distorted 793 808 809 810 830 P C R 60 distorted distorted 815 831 832 833 850 P C R 61 distorted distorted 838 851 852 853 870 P C R 62 distorted distorted 858 871 872 873 890 P G R 63 distorted distorted 878 891 892 893 913 P C R 64 distorted distorted 898 914 915 916 933 P U R 65 distorted distorted 921 934 935 936 953 P U R 66 distorted distorted 941 954 955 956 973 P G R 67 distorted distorted 961 974 975 976 996 P G R 68 distorted distorted 981 997 998 999 1019 P A R 69 distorted distorted 1004 1020 1021 1022 1041 P A R 70 distorted distorted 1027 1042 1043 1044 1063 P G R 71 distorted distorted 1049 1064 1065 1066 1086 P C R 72 distorted distorted 1071 1087 1088 1089 1106 P U R 73 distorted distorted 1094 1107 1108 1109 ---------------------------------------------------------------------------------