ID code: '4PKD' 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' --------------------------------------------------------------------------------- 21 C1' GTP V 59 beta 16 22 19 44 C1' G V 60 beta 39 45 42 67 C1' A V 61 beta 62 68 65 89 C1' U V 62 beta 84 90 87 109 C1' C V 63 beta 104 110 107 129 C1' C V 64 beta 124 130 127 149 C1' A V 65 beta 144 150 147 171 C1' U V 66 beta 166 172 169 191 C1' U V 67 beta 186 192 189 211 C1' G V 68 beta 206 212 209 234 C1' C V 69 beta 229 235 232 254 C1' A V 70 beta 249 255 252 276 C1' C V 71 beta 271 277 274 296 C1' U V 72 beta 291 297 294 316 C1' C V 73 beta 311 317 314 336 C1' C V 74 beta 331 337 334 356 C1' G V 75 beta 351 357 354 379 C1' G V 76 beta 374 380 377 402 C1' A V 77 beta 397 403 400 424 C1' U V 78 beta 419 425 422 444 C1' C V 79 beta 439 445 442 464 C1' C V 80 beta 459 465 462 484 C1' A V 81 beta 479 485 482 506 C1' G V 82 beta 501 507 504 529 C1' G V 83 beta 524 530 527 552 C1' A V 84 beta 547 553 550 574 C1' G V 85 beta 569 575 572 597 C1' A V 86 beta 592 598 595 619 C1' U V 87 beta 614 620 617 639 C1' A V 88 beta 634 640 637 661 C1' C V 89 beta 656 662 659 681 C1' C V 90 beta 676 682 679 701 C1' A V 91 beta 696 702 699 723 C1' U V 92 beta 718 724 721 743 C1' G V 93 beta 738 744 741 766 C1' A V 94 beta 761 767 764 788 C1' U V 95 beta 783 789 786 808 C1' C V 96 beta 803 809 806 828 C1' A V 97 beta 823 829 826 850 C1' C V 98 beta 845 851 848 870 C1' G V 99 beta 865 871 868 893 C1' A V 100 beta 888 894 891 915 C1' A V 101 beta 910 916 913 937 C1' G V 102 beta 932 938 935 960 C1' G V 103 beta 955 961 958 983 C1' U V 104 beta 978 984 981 1003 C1' G V 105 beta 998 1004 1001 1026 C1' G V 106 beta 1021 1027 1024 1049 C1' U V 107 beta 1044 1050 1047 1069 C1' U V 108 beta 1064 1070 1067 1089 C1' U V 109 beta 1084 1090 1087 1109 C1' U V 110 beta 1104 1110 1107 1129 C1' C V 111 beta 1124 1130 1127 1149 C1' C V 112 beta 1144 1150 1147 1169 C1' U V 113 beta 1164 1170 1167 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 19 C2' GTP V 59 OK 21 17 20 42 C2' G V 60 OK 44 40 43 65 C2' A V 61 OK 67 63 66 87 C2' U V 62 OK 89 85 88 107 C2' C V 63 OK 109 105 108 127 C2' C V 64 OK 129 125 128 147 C2' A V 65 OK 149 145 148 169 C2' U V 66 OK 171 167 170 189 C2' U V 67 OK 191 187 190 209 C2' G V 68 OK 211 207 210 232 C2' C V 69 OK 234 230 233 252 C2' A V 70 OK 254 250 253 274 C2' C V 71 OK 276 272 275 294 C2' U V 72 OK 296 292 295 314 C2' C V 73 OK 316 312 315 334 C2' C V 74 OK 336 332 335 354 C2' G V 75 OK 356 352 355 377 C2' G V 76 OK 379 375 378 400 C2' A V 77 OK 402 398 401 422 C2' U V 78 OK 424 420 423 442 C2' C V 79 OK 444 440 443 462 C2' C V 80 OK 464 460 463 482 C2' A V 81 OK 484 480 483 504 C2' G V 82 OK 506 502 505 527 C2' G V 83 OK 529 525 528 550 C2' A V 84 OK 552 548 551 572 C2' G V 85 OK 574 570 573 595 C2' A V 86 OK 597 593 596 617 C2' U V 87 OK 619 615 618 637 C2' A V 88 OK 639 635 638 659 C2' C V 89 OK 661 657 660 679 C2' C V 90 OK 681 677 680 699 C2' A V 91 OK 701 697 700 721 C2' U V 92 OK 723 719 722 741 C2' G V 93 OK 743 739 742 764 C2' A V 94 OK 766 762 765 786 C2' U V 95 OK 788 784 787 806 C2' C V 96 OK 808 804 807 826 C2' A V 97 OK 828 824 827 848 C2' C V 98 OK 850 846 849 868 C2' G V 99 OK 870 866 869 891 C2' A V 100 OK 893 889 892 913 C2' A V 101 OK 915 911 914 935 C2' G V 102 OK 937 933 936 958 C2' G V 103 OK 960 956 959 981 C2' U V 104 OK 983 979 982 1001 C2' G V 105 OK 1003 999 1002 1024 C2' G V 106 OK 1026 1022 1025 1047 C2' U V 107 OK 1049 1045 1048 1067 C2' U V 108 OK 1069 1065 1068 1087 C2' U V 109 OK 1089 1085 1088 1107 C2' U V 110 OK 1109 1105 1108 1127 C2' C V 111 OK 1129 1125 1128 1147 C2' C V 112 OK 1149 1145 1148 1167 C2' U V 113 OK 1169 1165 1168 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 17 C3' GTP V 59 OK 15 18 19 40 C3' G V 60 OK 38 41 42 63 C3' A V 61 OK 61 64 65 85 C3' U V 62 OK 83 86 87 105 C3' C V 63 OK 103 106 107 125 C3' C V 64 OK 123 126 127 145 C3' A V 65 OK 143 146 147 167 C3' U V 66 OK 165 168 169 187 C3' U V 67 OK 185 188 189 207 C3' G V 68 OK 205 208 209 230 C3' C V 69 OK 228 231 232 250 C3' A V 70 OK 248 251 252 272 C3' C V 71 OK 270 273 274 292 C3' U V 72 OK 290 293 294 312 C3' C V 73 OK 310 313 314 332 C3' C V 74 OK 330 333 334 352 C3' G V 75 OK 350 353 354 375 C3' G V 76 OK 373 376 377 398 C3' A V 77 OK 396 399 400 420 C3' U V 78 OK 418 421 422 440 C3' C V 79 OK 438 441 442 460 C3' C V 80 OK 458 461 462 480 C3' A V 81 OK 478 481 482 502 C3' G V 82 OK 500 503 504 525 C3' G V 83 OK 523 526 527 548 C3' A V 84 OK 546 549 550 570 C3' G V 85 OK 568 571 572 593 C3' A V 86 OK 591 594 595 615 C3' U V 87 OK 613 616 617 635 C3' A V 88 OK 633 636 637 657 C3' C V 89 OK 655 658 659 677 C3' C V 90 OK 675 678 679 697 C3' A V 91 OK 695 698 699 719 C3' U V 92 OK 717 720 721 739 C3' G V 93 OK 737 740 741 762 C3' A V 94 OK 760 763 764 784 C3' U V 95 OK 782 785 786 804 C3' C V 96 OK 802 805 806 824 C3' A V 97 OK 822 825 826 846 C3' C V 98 OK 844 847 848 866 C3' G V 99 OK 864 867 868 889 C3' A V 100 OK 887 890 891 911 C3' A V 101 OK 909 912 913 933 C3' G V 102 OK 931 934 935 956 C3' G V 103 OK 954 957 958 979 C3' U V 104 OK 977 980 981 999 C3' G V 105 OK 997 1000 1001 1022 C3' G V 106 OK 1020 1023 1024 1045 C3' U V 107 OK 1043 1046 1047 1065 C3' U V 108 OK 1063 1066 1067 1085 C3' U V 109 OK 1083 1086 1087 1105 C3' U V 110 OK 1103 1106 1107 1125 C3' C V 111 OK 1123 1126 1127 1145 C3' C V 112 OK 1143 1146 1147 1165 C3' U V 113 OK 1163 1166 1167 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 15 C4' GTP V 59 OK 17 14 16 38 C4' G V 60 OK 40 37 39 61 C4' A V 61 OK 63 60 62 83 C4' U V 62 OK 85 82 84 103 C4' C V 63 OK 105 102 104 123 C4' C V 64 OK 125 122 124 143 C4' A V 65 OK 145 142 144 165 C4' U V 66 OK 167 164 166 185 C4' U V 67 OK 187 184 186 205 C4' G V 68 OK 207 204 206 228 C4' C V 69 OK 230 227 229 248 C4' A V 70 OK 250 247 249 270 C4' C V 71 OK 272 269 271 290 C4' U V 72 OK 292 289 291 310 C4' C V 73 OK 312 309 311 330 C4' C V 74 OK 332 329 331 350 C4' G V 75 OK 352 349 351 373 C4' G V 76 OK 375 372 374 396 C4' A V 77 OK 398 395 397 418 C4' U V 78 OK 420 417 419 438 C4' C V 79 OK 440 437 439 458 C4' C V 80 OK 460 457 459 478 C4' A V 81 OK 480 477 479 500 C4' G V 82 OK 502 499 501 523 C4' G V 83 OK 525 522 524 546 C4' A V 84 OK 548 545 547 568 C4' G V 85 OK 570 567 569 591 C4' A V 86 OK 593 590 592 613 C4' U V 87 OK 615 612 614 633 C4' A V 88 OK 635 632 634 655 C4' C V 89 OK 657 654 656 675 C4' C V 90 OK 677 674 676 695 C4' A V 91 OK 697 694 696 717 C4' U V 92 OK 719 716 718 737 C4' G V 93 OK 739 736 738 760 C4' A V 94 OK 762 759 761 782 C4' U V 95 OK 784 781 783 802 C4' C V 96 OK 804 801 803 822 C4' A V 97 OK 824 821 823 844 C4' C V 98 OK 846 843 845 864 C4' G V 99 OK 866 863 865 887 C4' A V 100 OK 889 886 888 909 C4' A V 101 OK 911 908 910 931 C4' G V 102 OK 933 930 932 954 C4' G V 103 OK 956 953 955 977 C4' U V 104 OK 979 976 978 997 C4' G V 105 OK 999 996 998 1020 C4' G V 106 OK 1022 1019 1021 1043 C4' U V 107 OK 1045 1042 1044 1063 C4' U V 108 OK 1065 1062 1064 1083 C4' U V 109 OK 1085 1082 1084 1103 C4' U V 110 OK 1105 1102 1104 1123 C4' C V 111 OK 1125 1122 1124 1143 C4' C V 112 OK 1145 1142 1144 1163 C4' U V 113 OK 1165 1162 1164 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 14 C5' GTP V 59 13 15 37 C5' G V 60 36 38 60 C5' A V 61 59 61 82 C5' U V 62 81 83 102 C5' C V 63 101 103 122 C5' C V 64 121 123 142 C5' A V 65 141 143 164 C5' U V 66 163 165 184 C5' U V 67 183 185 204 C5' G V 68 203 205 227 C5' C V 69 226 228 247 C5' A V 70 246 248 269 C5' C V 71 268 270 289 C5' U V 72 288 290 309 C5' C V 73 308 310 329 C5' C V 74 328 330 349 C5' G V 75 348 350 372 C5' G V 76 371 373 395 C5' A V 77 394 396 417 C5' U V 78 416 418 437 C5' C V 79 436 438 457 C5' C V 80 456 458 477 C5' A V 81 476 478 499 C5' G V 82 498 500 522 C5' G V 83 521 523 545 C5' A V 84 544 546 567 C5' G V 85 566 568 590 C5' A V 86 589 591 612 C5' U V 87 611 613 632 C5' A V 88 631 633 654 C5' C V 89 653 655 674 C5' C V 90 673 675 694 C5' A V 91 693 695 716 C5' U V 92 715 717 736 C5' G V 93 735 737 759 C5' A V 94 758 760 781 C5' U V 95 780 782 801 C5' C V 96 800 802 821 C5' A V 97 820 822 843 C5' C V 98 842 844 863 C5' G V 99 862 864 886 C5' A V 100 885 887 908 C5' A V 101 907 909 930 C5' G V 102 929 931 953 C5' G V 103 952 954 976 C5' U V 104 975 977 996 C5' G V 105 995 997 1019 C5' G V 106 1018 1020 1042 C5' U V 107 1041 1043 1062 C5' U V 108 1061 1063 1082 C5' U V 109 1081 1083 1102 C5' U V 110 1101 1103 1122 C5' C V 111 1121 1123 1142 C5' C V 112 1141 1143 1162 C5' U V 113 1161 1163 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G V 60 distorted distorted 18 34 35 36 56 P A V 61 distorted distorted 41 57 58 59 78 P U V 62 distorted distorted 64 79 80 81 98 P C V 63 distorted distorted 86 99 100 101 118 P C V 64 distorted distorted 106 119 120 121 138 P A V 65 distorted distorted 126 139 140 141 160 P U V 66 distorted distorted 146 161 162 163 180 P U V 67 distorted distorted 168 181 182 183 200 P G V 68 distorted distorted 188 201 202 203 223 P C V 69 distorted distorted 208 224 225 226 243 P A V 70 distorted distorted 231 244 245 246 265 P C V 71 distorted distorted 251 266 267 268 285 P U V 72 distorted distorted 273 286 287 288 305 P C V 73 distorted distorted 293 306 307 308 325 P C V 74 distorted distorted 313 326 327 328 345 P G V 75 distorted distorted 333 346 347 348 368 P G V 76 distorted distorted 353 369 370 371 391 P A V 77 distorted distorted 376 392 393 394 413 P U V 78 distorted distorted 399 414 415 416 433 P C V 79 distorted distorted 421 434 435 436 453 P C V 80 distorted distorted 441 454 455 456 473 P A V 81 distorted distorted 461 474 475 476 495 P G V 82 distorted distorted 481 496 497 498 518 P G V 83 distorted distorted 503 519 520 521 541 P A V 84 distorted distorted 526 542 543 544 563 P G V 85 distorted distorted 549 564 565 566 586 P A V 86 distorted distorted 571 587 588 589 608 P U V 87 distorted distorted 594 609 610 611 628 P A V 88 distorted distorted 616 629 630 631 650 P C V 89 distorted distorted 636 651 652 653 670 P C V 90 distorted distorted 658 671 672 673 690 P A V 91 distorted distorted 678 691 692 693 712 P U V 92 distorted distorted 698 713 714 715 732 P G V 93 distorted distorted 720 733 734 735 755 P A V 94 distorted distorted 740 756 757 758 777 P U V 95 distorted distorted 763 778 779 780 797 P C V 96 distorted distorted 785 798 799 800 817 P A V 97 distorted distorted 805 818 819 820 839 P C V 98 distorted distorted 825 840 841 842 859 P G V 99 distorted distorted 847 860 861 862 882 P A V 100 distorted distorted 867 883 884 885 904 P A V 101 distorted distorted 890 905 906 907 926 P G V 102 distorted distorted 912 927 928 929 949 P G V 103 distorted distorted 934 950 951 952 972 P U V 104 distorted distorted 957 973 974 975 992 P G V 105 distorted distorted 980 993 994 995 1015 P G V 106 distorted distorted 1000 1016 1017 1018 1038 P U V 107 distorted distorted 1023 1039 1040 1041 1058 P U V 108 distorted distorted 1046 1059 1060 1061 1078 P U V 109 distorted distorted 1066 1079 1080 1081 1098 P U V 110 distorted distorted 1086 1099 1100 1101 1118 P C V 111 distorted distorted 1106 1119 1120 1121 1138 P C V 112 distorted distorted 1126 1139 1140 1141 1158 P U V 113 distorted distorted 1146 1159 1160 1161 ---------------------------------------------------------------------------------