ID code: '3S49' 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 beta 4 10 7 32 C1' U A 2 beta 27 33 30 52 C1' A A 3 beta 47 53 50 74 C1' U A 4 beta 69 75 72 94 C1' A A 5 beta 89 95 92 114 C1' RUS A 6 beta 122 106 116 136 C1' A A 7 beta 131 137 134 158 C1' C A 8 beta 153 159 156 176 C1' G B 9 beta 171 177 174 199 C1' U B 10 beta 194 200 197 219 C1' A B 11 beta 214 220 217 241 C1' U B 12 beta 236 242 239 261 C1' A B 13 beta 256 262 259 281 C1' RUS B 14 beta 289 273 283 303 C1' A B 15 beta 298 304 301 325 C1' C B 16 beta 320 326 323 343 C1' G C 1 beta 338 344 341 366 C1' U C 2 beta 361 367 364 386 C1' A C 3 beta 381 387 384 408 C1' U C 4 beta 403 409 406 428 C1' A C 5 beta 423 429 426 448 C1' RUS C 6 beta 456 440 450 470 C1' A C 7 beta 465 471 468 492 C1' C C 8 beta 487 493 490 510 C1' G D 9 beta 505 511 508 533 C1' U D 10 beta 528 534 531 553 C1' A D 11 beta 548 554 551 575 C1' U D 12 beta 570 576 573 595 C1' A D 13 beta 590 596 593 615 C1' RUS D 14 beta 623 607 617 637 C1' A D 15 beta 632 638 635 659 C1' C D 16 beta 654 660 657 677 C1' G E 1 beta 672 678 675 700 C1' U E 2 beta 695 701 698 720 C1' A E 3 beta 715 721 718 742 C1' U E 4 beta 737 743 740 762 C1' A E 5 beta 757 763 760 782 C1' RUS E 6 beta 790 774 784 804 C1' A E 7 beta 799 805 802 826 C1' C E 8 beta 821 827 824 844 C1' G F 9 beta 839 845 842 867 C1' U F 10 beta 862 868 865 887 C1' A F 11 beta 882 888 885 909 C1' U F 12 beta 904 910 907 929 C1' A F 13 beta 924 930 927 949 C1' RUS F 14 beta 957 941 951 971 C1' A F 15 beta 966 972 969 993 C1' C F 16 beta 988 994 991 1011 C1' G G 1 beta 1006 1012 1009 1034 C1' U G 2 beta 1029 1035 1032 1054 C1' A G 3 beta 1049 1055 1052 1076 C1' U G 4 beta 1071 1077 1074 1096 C1' A G 5 beta 1091 1097 1094 1116 C1' RUS G 6 beta 1124 1108 1118 1138 C1' A G 7 beta 1133 1139 1136 1160 C1' C G 8 beta 1155 1161 1158 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 9 5 8 30 C2' U A 2 OK 32 28 31 50 C2' A A 3 OK 52 48 51 72 C2' U A 4 OK 74 70 73 92 C2' A A 5 OK 94 90 93 116 C2' RUS A 6 OK 114 119 117 134 C2' A A 7 OK 136 132 135 156 C2' C A 8 OK 158 154 157 174 C2' G B 9 OK 176 172 175 197 C2' U B 10 OK 199 195 198 217 C2' A B 11 OK 219 215 218 239 C2' U B 12 OK 241 237 240 259 C2' A B 13 OK 261 257 260 283 C2' RUS B 14 OK 281 286 284 301 C2' A B 15 OK 303 299 302 323 C2' C B 16 OK 325 321 324 341 C2' G C 1 OK 343 339 342 364 C2' U C 2 OK 366 362 365 384 C2' A C 3 OK 386 382 385 406 C2' U C 4 OK 408 404 407 426 C2' A C 5 OK 428 424 427 450 C2' RUS C 6 OK 448 453 451 468 C2' A C 7 OK 470 466 469 490 C2' C C 8 OK 492 488 491 508 C2' G D 9 OK 510 506 509 531 C2' U D 10 OK 533 529 532 551 C2' A D 11 OK 553 549 552 573 C2' U D 12 OK 575 571 574 593 C2' A D 13 OK 595 591 594 617 C2' RUS D 14 OK 615 620 618 635 C2' A D 15 OK 637 633 636 657 C2' C D 16 OK 659 655 658 675 C2' G E 1 OK 677 673 676 698 C2' U E 2 OK 700 696 699 718 C2' A E 3 OK 720 716 719 740 C2' U E 4 OK 742 738 741 760 C2' A E 5 OK 762 758 761 784 C2' RUS E 6 OK 782 787 785 802 C2' A E 7 OK 804 800 803 824 C2' C E 8 OK 826 822 825 842 C2' G F 9 OK 844 840 843 865 C2' U F 10 OK 867 863 866 885 C2' A F 11 OK 887 883 886 907 C2' U F 12 OK 909 905 908 927 C2' A F 13 OK 929 925 928 951 C2' RUS F 14 OK 949 954 952 969 C2' A F 15 OK 971 967 970 991 C2' C F 16 OK 993 989 992 1009 C2' G G 1 OK 1011 1007 1010 1032 C2' U G 2 OK 1034 1030 1033 1052 C2' A G 3 OK 1054 1050 1053 1074 C2' U G 4 OK 1076 1072 1075 1094 C2' A G 5 OK 1096 1092 1095 1118 C2' RUS G 6 OK 1116 1121 1119 1136 C2' A G 7 OK 1138 1134 1137 1158 C2' C G 8 OK 1160 1156 1159 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 28 C3' U A 2 OK 26 29 30 48 C3' A A 3 OK 46 49 50 70 C3' U A 4 OK 68 71 72 90 C3' A A 5 OK 88 91 92 119 C3' RUS A 6 OK 121 120 116 132 C3' A A 7 OK 130 133 134 154 C3' C A 8 OK 152 155 156 172 C3' G B 9 OK 170 173 174 195 C3' U B 10 OK 193 196 197 215 C3' A B 11 OK 213 216 217 237 C3' U B 12 OK 235 238 239 257 C3' A B 13 OK 255 258 259 286 C3' RUS B 14 OK 288 287 283 299 C3' A B 15 OK 297 300 301 321 C3' C B 16 OK 319 322 323 339 C3' G C 1 OK 337 340 341 362 C3' U C 2 OK 360 363 364 382 C3' A C 3 OK 380 383 384 404 C3' U C 4 OK 402 405 406 424 C3' A C 5 OK 422 425 426 453 C3' RUS C 6 OK 455 454 450 466 C3' A C 7 OK 464 467 468 488 C3' C C 8 OK 486 489 490 506 C3' G D 9 OK 504 507 508 529 C3' U D 10 OK 527 530 531 549 C3' A D 11 OK 547 550 551 571 C3' U D 12 OK 569 572 573 591 C3' A D 13 OK 589 592 593 620 C3' RUS D 14 OK 622 621 617 633 C3' A D 15 OK 631 634 635 655 C3' C D 16 OK 653 656 657 673 C3' G E 1 OK 671 674 675 696 C3' U E 2 OK 694 697 698 716 C3' A E 3 OK 714 717 718 738 C3' U E 4 OK 736 739 740 758 C3' A E 5 OK 756 759 760 787 C3' RUS E 6 OK 789 788 784 800 C3' A E 7 OK 798 801 802 822 C3' C E 8 OK 820 823 824 840 C3' G F 9 OK 838 841 842 863 C3' U F 10 OK 861 864 865 883 C3' A F 11 OK 881 884 885 905 C3' U F 12 OK 903 906 907 925 C3' A F 13 OK 923 926 927 954 C3' RUS F 14 OK 956 955 951 967 C3' A F 15 OK 965 968 969 989 C3' C F 16 OK 987 990 991 1007 C3' G G 1 OK 1005 1008 1009 1030 C3' U G 2 OK 1028 1031 1032 1050 C3' A G 3 OK 1048 1051 1052 1072 C3' U G 4 OK 1070 1073 1074 1092 C3' A G 5 OK 1090 1093 1094 1121 C3' RUS G 6 OK 1123 1122 1118 1134 C3' A G 7 OK 1132 1135 1136 1156 C3' C G 8 OK 1154 1157 1158 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 26 C4' U A 2 OK 28 25 27 46 C4' A A 3 OK 48 45 47 68 C4' U A 4 OK 70 67 69 88 C4' A A 5 OK 90 87 89 121 C4' RUS A 6 OK 119 123 122 130 C4' A A 7 OK 132 129 131 152 C4' C A 8 OK 154 151 153 170 C4' G B 9 OK 172 169 171 193 C4' U B 10 OK 195 192 194 213 C4' A B 11 OK 215 212 214 235 C4' U B 12 OK 237 234 236 255 C4' A B 13 OK 257 254 256 288 C4' RUS B 14 OK 286 290 289 297 C4' A B 15 OK 299 296 298 319 C4' C B 16 OK 321 318 320 337 C4' G C 1 OK 339 336 338 360 C4' U C 2 OK 362 359 361 380 C4' A C 3 OK 382 379 381 402 C4' U C 4 OK 404 401 403 422 C4' A C 5 OK 424 421 423 455 C4' RUS C 6 OK 453 457 456 464 C4' A C 7 OK 466 463 465 486 C4' C C 8 OK 488 485 487 504 C4' G D 9 OK 506 503 505 527 C4' U D 10 OK 529 526 528 547 C4' A D 11 OK 549 546 548 569 C4' U D 12 OK 571 568 570 589 C4' A D 13 OK 591 588 590 622 C4' RUS D 14 OK 620 624 623 631 C4' A D 15 OK 633 630 632 653 C4' C D 16 OK 655 652 654 671 C4' G E 1 OK 673 670 672 694 C4' U E 2 OK 696 693 695 714 C4' A E 3 OK 716 713 715 736 C4' U E 4 OK 738 735 737 756 C4' A E 5 OK 758 755 757 789 C4' RUS E 6 OK 787 791 790 798 C4' A E 7 OK 800 797 799 820 C4' C E 8 OK 822 819 821 838 C4' G F 9 OK 840 837 839 861 C4' U F 10 OK 863 860 862 881 C4' A F 11 OK 883 880 882 903 C4' U F 12 OK 905 902 904 923 C4' A F 13 OK 925 922 924 956 C4' RUS F 14 OK 954 958 957 965 C4' A F 15 OK 967 964 966 987 C4' C F 16 OK 989 986 988 1005 C4' G G 1 OK 1007 1004 1006 1028 C4' U G 2 OK 1030 1027 1029 1048 C4' A G 3 OK 1050 1047 1049 1070 C4' U G 4 OK 1072 1069 1071 1090 C4' A G 5 OK 1092 1089 1091 1123 C4' RUS G 6 OK 1121 1125 1124 1132 C4' A G 7 OK 1134 1131 1133 1154 C4' C G 8 OK 1156 1153 1155 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 25 C5' U A 2 24 26 45 C5' A A 3 44 46 67 C5' U A 4 66 68 87 C5' A A 5 86 88 123 C5' RUS A 6 124 121 129 C5' A A 7 128 130 151 C5' C A 8 150 152 169 C5' G B 9 168 170 192 C5' U B 10 191 193 212 C5' A B 11 211 213 234 C5' U B 12 233 235 254 C5' A B 13 253 255 290 C5' RUS B 14 291 288 296 C5' A B 15 295 297 318 C5' C B 16 317 319 336 C5' G C 1 335 337 359 C5' U C 2 358 360 379 C5' A C 3 378 380 401 C5' U C 4 400 402 421 C5' A C 5 420 422 457 C5' RUS C 6 458 455 463 C5' A C 7 462 464 485 C5' C C 8 484 486 503 C5' G D 9 502 504 526 C5' U D 10 525 527 546 C5' A D 11 545 547 568 C5' U D 12 567 569 588 C5' A D 13 587 589 624 C5' RUS D 14 625 622 630 C5' A D 15 629 631 652 C5' C D 16 651 653 670 C5' G E 1 669 671 693 C5' U E 2 692 694 713 C5' A E 3 712 714 735 C5' U E 4 734 736 755 C5' A E 5 754 756 791 C5' RUS E 6 792 789 797 C5' A E 7 796 798 819 C5' C E 8 818 820 837 C5' G F 9 836 838 860 C5' U F 10 859 861 880 C5' A F 11 879 881 902 C5' U F 12 901 903 922 C5' A F 13 921 923 958 C5' RUS F 14 959 956 964 C5' A F 15 963 965 986 C5' C F 16 985 987 1004 C5' G G 1 1003 1005 1027 C5' U G 2 1026 1028 1047 C5' A G 3 1046 1048 1069 C5' U G 4 1068 1070 1089 C5' A G 5 1088 1090 1125 C5' RUS G 6 1126 1123 1131 C5' A G 7 1130 1132 1153 C5' C G 8 1152 1154 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P U A 2 distorted distorted 6 22 23 24 41 P A A 3 distorted distorted 29 42 43 44 63 P U A 4 distorted distorted 49 64 65 66 83 P A A 5 distorted distorted 71 84 85 86 105 P RUS A 6 distorted distorted 91 115 118 124 125 P A A 7 distorted distorted 120 126 127 128 147 P C A 8 distorted distorted 133 148 149 150 188 P U B 10 distorted distorted 173 189 190 191 208 P A B 11 distorted distorted 196 209 210 211 230 P U B 12 distorted distorted 216 231 232 233 250 P A B 13 distorted distorted 238 251 252 253 272 P RUS B 14 distorted distorted 258 282 285 291 292 P A B 15 distorted distorted 287 293 294 295 314 P C B 16 distorted distorted 300 315 316 317 355 P U C 2 distorted distorted 340 356 357 358 375 P A C 3 distorted distorted 363 376 377 378 397 P U C 4 distorted distorted 383 398 399 400 417 P A C 5 distorted distorted 405 418 419 420 439 P RUS C 6 distorted distorted 425 449 452 458 459 P A C 7 distorted distorted 454 460 461 462 481 P C C 8 distorted distorted 467 482 483 484 522 P U D 10 distorted distorted 507 523 524 525 542 P A D 11 distorted distorted 530 543 544 545 564 P U D 12 distorted distorted 550 565 566 567 584 P A D 13 distorted distorted 572 585 586 587 606 P RUS D 14 distorted distorted 592 616 619 625 626 P A D 15 distorted distorted 621 627 628 629 648 P C D 16 distorted distorted 634 649 650 651 689 P U E 2 distorted distorted 674 690 691 692 709 P A E 3 distorted distorted 697 710 711 712 731 P U E 4 distorted distorted 717 732 733 734 751 P A E 5 distorted distorted 739 752 753 754 773 P RUS E 6 distorted distorted 759 783 786 792 793 P A E 7 distorted distorted 788 794 795 796 815 P C E 8 distorted distorted 801 816 817 818 856 P U F 10 distorted distorted 841 857 858 859 876 P A F 11 distorted distorted 864 877 878 879 898 P U F 12 distorted distorted 884 899 900 901 918 P A F 13 distorted distorted 906 919 920 921 940 P RUS F 14 distorted distorted 926 950 953 959 960 P A F 15 distorted distorted 955 961 962 963 982 P C F 16 distorted distorted 968 983 984 985 1023 P U G 2 distorted distorted 1008 1024 1025 1026 1043 P A G 3 distorted distorted 1031 1044 1045 1046 1065 P U G 4 distorted distorted 1051 1066 1067 1068 1085 P A G 5 distorted distorted 1073 1086 1087 1088 1107 P RUS G 6 distorted distorted 1093 1117 1120 1126 1127 P A G 7 distorted distorted 1122 1128 1129 1130 1149 P C G 8 distorted distorted 1135 1150 1151 1152 ---------------------------------------------------------------------------------