ID code: '1B36' 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' U A 3 alpha beta 73 93 79 76 108 C1' G A 4 alpha beta 103 126 109 106 142 C1' C A 5 alpha beta 137 157 143 140 173 C1' A A 6 alpha beta 168 190 174 171 206 C1' G A 7 alpha beta 201 224 207 204 240 C1' A A 8 alpha beta 235 257 241 238 273 C1' A A 9 alpha beta 268 290 274 271 306 C1' A A 10 alpha beta 301 323 307 304 339 C1' C A 11 alpha beta 334 354 340 337 370 C1' A A 12 alpha beta 365 387 371 368 403 C1' G A 13 alpha beta 398 421 404 401 437 C1' C A 14 alpha beta 432 452 438 435 468 C1' G A 15 alpha beta 463 486 469 466 502 C1' C A 16 alpha beta 497 517 503 500 533 C1' U A 17 alpha beta 528 548 534 531 563 C1' U A 18 alpha beta 558 578 564 561 593 C1' C A 19 alpha beta 588 608 594 591 624 C1' G A 20 alpha beta 619 642 625 622 658 C1' G A 21 alpha beta 653 676 659 656 692 C1' C A 22 alpha beta 687 707 693 690 723 C1' G A 23 alpha beta 718 741 724 721 757 C1' C A 24 alpha beta 752 772 758 755 788 C1' G A 25 alpha beta 783 806 789 786 822 C1' U A 26 alpha beta 817 837 823 820 852 C1' A A 27 alpha beta 847 869 853 850 885 C1' U A 28 alpha beta 880 900 886 883 915 C1' A A 29 alpha beta 910 932 916 913 948 C1' U A 30 alpha beta 943 963 949 946 978 C1' U A 31 alpha beta 973 993 979 976 1008 C1' A A 32 alpha beta 1003 1025 1009 1006 1041 C1' C A 33 alpha beta 1036 1056 1042 1039 1072 C1' G A 34 alpha beta 1067 1090 1073 1070 1106 C1' C A 35 alpha beta 1101 1121 1107 1104 1137 C1' A A 36 alpha beta 1132 1154 1138 1135 1170 C1' C A 37 alpha beta 1165 1185 1171 1168 1201 C1' C A 38 alpha beta 1196 1217 1202 1199 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U A 3 OK OK 78 74 91 77 106 C2' G A 4 OK OK 108 104 124 107 140 C2' C A 5 OK OK 142 138 155 141 171 C2' A A 6 OK OK 173 169 188 172 204 C2' G A 7 OK OK 206 202 222 205 238 C2' A A 8 OK OK 240 236 255 239 271 C2' A A 9 OK OK 273 269 288 272 304 C2' A A 10 OK OK 306 302 321 305 337 C2' C A 11 OK OK 339 335 352 338 368 C2' A A 12 OK OK 370 366 385 369 401 C2' G A 13 OK OK 403 399 419 402 435 C2' C A 14 OK OK 437 433 450 436 466 C2' G A 15 OK OK 468 464 484 467 500 C2' C A 16 OK OK 502 498 515 501 531 C2' U A 17 OK OK 533 529 546 532 561 C2' U A 18 OK OK 563 559 576 562 591 C2' C A 19 OK OK 593 589 606 592 622 C2' G A 20 OK OK 624 620 640 623 656 C2' G A 21 OK OK 658 654 674 657 690 C2' C A 22 OK OK 692 688 705 691 721 C2' G A 23 OK OK 723 719 739 722 755 C2' C A 24 OK OK 757 753 770 756 786 C2' G A 25 OK OK 788 784 804 787 820 C2' U A 26 OK OK 822 818 835 821 850 C2' A A 27 OK OK 852 848 867 851 883 C2' U A 28 OK OK 885 881 898 884 913 C2' A A 29 OK OK 915 911 930 914 946 C2' U A 30 OK OK 948 944 961 947 976 C2' U A 31 OK OK 978 974 991 977 1006 C2' A A 32 OK OK 1008 1004 1023 1007 1039 C2' C A 33 OK OK 1041 1037 1054 1040 1070 C2' G A 34 OK OK 1072 1068 1088 1071 1104 C2' C A 35 OK OK 1106 1102 1119 1105 1135 C2' A A 36 OK OK 1137 1133 1152 1136 1168 C2' C A 37 OK OK 1170 1166 1183 1169 1199 C2' C A 38 OK OK 1201 1197 1215 1200 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK OK 72 90 75 76 104 C3' G A 4 OK OK 102 123 105 106 138 C3' C A 5 OK OK 136 154 139 140 169 C3' A A 6 OK OK 167 187 170 171 202 C3' G A 7 OK OK 200 221 203 204 236 C3' A A 8 OK OK 234 254 237 238 269 C3' A A 9 OK OK 267 287 270 271 302 C3' A A 10 OK OK 300 320 303 304 335 C3' C A 11 OK OK 333 351 336 337 366 C3' A A 12 OK OK 364 384 367 368 399 C3' G A 13 OK OK 397 418 400 401 433 C3' C A 14 OK OK 431 449 434 435 464 C3' G A 15 OK OK 462 483 465 466 498 C3' C A 16 OK OK 496 514 499 500 529 C3' U A 17 OK OK 527 545 530 531 559 C3' U A 18 OK OK 557 575 560 561 589 C3' C A 19 OK OK 587 605 590 591 620 C3' G A 20 OK OK 618 639 621 622 654 C3' G A 21 OK OK 652 673 655 656 688 C3' C A 22 OK OK 686 704 689 690 719 C3' G A 23 OK OK 717 738 720 721 753 C3' C A 24 OK OK 751 769 754 755 784 C3' G A 25 OK OK 782 803 785 786 818 C3' U A 26 OK OK 816 834 819 820 848 C3' A A 27 OK OK 846 866 849 850 881 C3' U A 28 OK OK 879 897 882 883 911 C3' A A 29 OK OK 909 929 912 913 944 C3' U A 30 OK OK 942 960 945 946 974 C3' U A 31 OK OK 972 990 975 976 1004 C3' A A 32 OK OK 1002 1022 1005 1006 1037 C3' C A 33 OK OK 1035 1053 1038 1039 1068 C3' G A 34 OK OK 1066 1087 1069 1070 1102 C3' C A 35 OK OK 1100 1118 1103 1104 1133 C3' A A 36 OK OK 1131 1151 1134 1135 1166 C3' C A 37 OK OK 1164 1182 1167 1168 1197 C3' C A 38 OK OK 1195 1213 1198 1199 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK OK 74 89 71 73 102 C4' G A 4 OK OK 104 122 101 103 136 C4' C A 5 OK OK 138 153 135 137 167 C4' A A 6 OK OK 169 186 166 168 200 C4' G A 7 OK OK 202 220 199 201 234 C4' A A 8 OK OK 236 253 233 235 267 C4' A A 9 OK OK 269 286 266 268 300 C4' A A 10 OK OK 302 319 299 301 333 C4' C A 11 OK OK 335 350 332 334 364 C4' A A 12 OK OK 366 383 363 365 397 C4' G A 13 OK OK 399 417 396 398 431 C4' C A 14 OK OK 433 448 430 432 462 C4' G A 15 OK OK 464 482 461 463 496 C4' C A 16 OK OK 498 513 495 497 527 C4' U A 17 OK OK 529 544 526 528 557 C4' U A 18 OK OK 559 574 556 558 587 C4' C A 19 OK OK 589 604 586 588 618 C4' G A 20 OK OK 620 638 617 619 652 C4' G A 21 OK OK 654 672 651 653 686 C4' C A 22 OK OK 688 703 685 687 717 C4' G A 23 OK OK 719 737 716 718 751 C4' C A 24 OK OK 753 768 750 752 782 C4' G A 25 OK OK 784 802 781 783 816 C4' U A 26 OK OK 818 833 815 817 846 C4' A A 27 OK OK 848 865 845 847 879 C4' U A 28 OK OK 881 896 878 880 909 C4' A A 29 OK OK 911 928 908 910 942 C4' U A 30 OK OK 944 959 941 943 972 C4' U A 31 OK OK 974 989 971 973 1002 C4' A A 32 OK OK 1004 1021 1001 1003 1035 C4' C A 33 OK OK 1037 1052 1034 1036 1066 C4' G A 34 OK OK 1068 1086 1065 1067 1100 C4' C A 35 OK OK 1102 1117 1099 1101 1131 C4' A A 36 OK OK 1133 1150 1130 1132 1164 C4' C A 37 OK OK 1166 1181 1163 1165 1195 C4' C A 38 OK OK 1197 1212 1194 1196 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK OK 70 87 88 72 101 C5' G A 4 OK OK 100 120 121 102 135 C5' C A 5 OK OK 134 151 152 136 166 C5' A A 6 OK OK 165 184 185 167 199 C5' G A 7 OK OK 198 218 219 200 233 C5' A A 8 OK OK 232 251 252 234 266 C5' A A 9 OK OK 265 284 285 267 299 C5' A A 10 OK OK 298 317 318 300 332 C5' C A 11 OK OK 331 348 349 333 363 C5' A A 12 OK OK 362 381 382 364 396 C5' G A 13 OK OK 395 415 416 397 430 C5' C A 14 OK OK 429 446 447 431 461 C5' G A 15 OK OK 460 480 481 462 495 C5' C A 16 OK OK 494 511 512 496 526 C5' U A 17 OK OK 525 542 543 527 556 C5' U A 18 OK OK 555 572 573 557 586 C5' C A 19 OK OK 585 602 603 587 617 C5' G A 20 OK OK 616 636 637 618 651 C5' G A 21 OK OK 650 670 671 652 685 C5' C A 22 OK OK 684 701 702 686 716 C5' G A 23 OK OK 715 735 736 717 750 C5' C A 24 OK OK 749 766 767 751 781 C5' G A 25 OK OK 780 800 801 782 815 C5' U A 26 OK OK 814 831 832 816 845 C5' A A 27 OK OK 844 863 864 846 878 C5' U A 28 OK OK 877 894 895 879 908 C5' A A 29 OK OK 907 926 927 909 941 C5' U A 30 OK OK 940 957 958 942 971 C5' U A 31 OK OK 970 987 988 972 1001 C5' A A 32 OK OK 1000 1019 1020 1002 1034 C5' C A 33 OK OK 1033 1050 1051 1035 1065 C5' G A 34 OK OK 1064 1084 1085 1066 1099 C5' C A 35 OK OK 1098 1115 1116 1100 1130 C5' A A 36 OK OK 1129 1148 1149 1131 1163 C5' C A 37 OK OK 1162 1179 1180 1164 1194 C5' C A 38 OK OK 1193 1210 1211 1195 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P U A 3 distorted distorted 41 68 69 70 97 P G A 4 distorted distorted 75 98 99 100 131 P C A 5 distorted distorted 105 132 133 134 162 P A A 6 distorted distorted 139 163 164 165 195 P G A 7 distorted distorted 170 196 197 198 229 P A A 8 distorted distorted 203 230 231 232 262 P A A 9 distorted distorted 237 263 264 265 295 P A A 10 distorted distorted 270 296 297 298 328 P C A 11 distorted distorted 303 329 330 331 359 P A A 12 distorted distorted 336 360 361 362 392 P G A 13 distorted distorted 367 393 394 395 426 P C A 14 distorted distorted 400 427 428 429 457 P G A 15 distorted distorted 434 458 459 460 491 P C A 16 distorted distorted 465 492 493 494 522 P U A 17 distorted distorted 499 523 524 525 552 P U A 18 distorted distorted 530 553 554 555 582 P C A 19 distorted distorted 560 583 584 585 613 P G A 20 distorted distorted 590 614 615 616 647 P G A 21 distorted distorted 621 648 649 650 681 P C A 22 distorted distorted 655 682 683 684 712 P G A 23 distorted distorted 689 713 714 715 746 P C A 24 distorted distorted 720 747 748 749 777 P G A 25 distorted distorted 754 778 779 780 811 P U A 26 distorted distorted 785 812 813 814 841 P A A 27 distorted distorted 819 842 843 844 874 P U A 28 distorted distorted 849 875 876 877 904 P A A 29 distorted distorted 882 905 906 907 937 P U A 30 distorted distorted 912 938 939 940 967 P U A 31 distorted distorted 945 968 969 970 997 P A A 32 distorted distorted 975 998 999 1000 1030 P C A 33 distorted distorted 1005 1031 1032 1033 1061 P G A 34 distorted distorted 1038 1062 1063 1064 1095 P C A 35 distorted distorted 1069 1096 1097 1098 1126 P A A 36 distorted distorted 1103 1127 1128 1129 1159 P C A 37 distorted distorted 1134 1160 1161 1162 1190 P C A 38 distorted distorted 1167 1191 1192 1193 ---------------------------------------------------------------------------------