ID code: '2KHY' 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' G A 3 alpha beta 73 96 79 76 112 C1' A A 4 alpha beta 107 129 113 110 145 C1' U A 5 alpha beta 140 160 146 143 175 C1' C A 6 alpha beta 170 190 176 173 206 C1' A A 7 alpha beta 201 223 207 204 239 C1' C A 8 alpha beta 234 254 240 237 270 C1' A A 9 alpha beta 265 287 271 268 303 C1' A A 10 alpha beta 298 320 304 301 336 C1' G A 11 alpha beta 331 354 337 334 370 C1' U A 12 alpha beta 365 385 371 368 400 C1' A A 13 alpha beta 395 417 401 398 433 C1' G A 14 alpha beta 428 451 434 431 467 C1' G A 15 alpha beta 462 485 468 465 501 C1' A A 16 alpha beta 496 518 502 499 534 C1' C A 17 alpha beta 529 549 535 532 565 C1' U A 18 alpha beta 560 580 566 563 595 C1' U A 19 alpha beta 590 610 596 593 625 C1' C A 20 alpha beta 620 640 626 623 656 C1' G A 21 alpha beta 651 674 657 654 690 C1' G A 22 alpha beta 685 708 691 688 724 C1' U A 23 alpha beta 719 739 725 722 754 C1' C A 24 alpha beta 749 769 755 752 785 C1' C A 25 alpha beta 780 800 786 783 816 C1' G A 26 alpha beta 811 834 817 814 850 C1' A A 27 alpha beta 845 867 851 848 883 C1' A A 28 alpha beta 878 900 884 881 916 C1' U A 29 alpha beta 911 931 917 914 946 C1' A A 30 alpha beta 941 963 947 944 979 C1' C A 31 alpha beta 974 994 980 977 1010 C1' A A 32 alpha beta 1005 1027 1011 1008 1043 C1' G A 33 alpha beta 1038 1061 1044 1041 1077 C1' A A 34 alpha beta 1072 1094 1078 1075 1110 C1' U A 35 alpha beta 1105 1125 1111 1108 1140 C1' C A 36 alpha beta 1135 1155 1141 1138 1171 C1' U A 37 alpha beta 1166 1186 1172 1169 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' G A 3 OK OK 78 74 94 77 110 C2' A A 4 OK OK 112 108 127 111 143 C2' U A 5 OK OK 145 141 158 144 173 C2' C A 6 OK OK 175 171 188 174 204 C2' A A 7 OK OK 206 202 221 205 237 C2' C A 8 OK OK 239 235 252 238 268 C2' A A 9 OK OK 270 266 285 269 301 C2' A A 10 OK OK 303 299 318 302 334 C2' G A 11 OK OK 336 332 352 335 368 C2' U A 12 OK OK 370 366 383 369 398 C2' A A 13 OK OK 400 396 415 399 431 C2' G A 14 OK OK 433 429 449 432 465 C2' G A 15 OK OK 467 463 483 466 499 C2' A A 16 OK OK 501 497 516 500 532 C2' C A 17 OK OK 534 530 547 533 563 C2' U A 18 OK OK 565 561 578 564 593 C2' U A 19 OK OK 595 591 608 594 623 C2' C A 20 OK OK 625 621 638 624 654 C2' G A 21 OK OK 656 652 672 655 688 C2' G A 22 OK OK 690 686 706 689 722 C2' U A 23 OK OK 724 720 737 723 752 C2' C A 24 OK OK 754 750 767 753 783 C2' C A 25 OK OK 785 781 798 784 814 C2' G A 26 OK OK 816 812 832 815 848 C2' A A 27 OK OK 850 846 865 849 881 C2' A A 28 OK OK 883 879 898 882 914 C2' U A 29 OK OK 916 912 929 915 944 C2' A A 30 OK OK 946 942 961 945 977 C2' C A 31 OK OK 979 975 992 978 1008 C2' A A 32 OK OK 1010 1006 1025 1009 1041 C2' G A 33 OK OK 1043 1039 1059 1042 1075 C2' A A 34 OK OK 1077 1073 1092 1076 1108 C2' U A 35 OK OK 1110 1106 1123 1109 1138 C2' C A 36 OK OK 1140 1136 1153 1139 1169 C2' U A 37 OK OK 1171 1167 1184 1170 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' G A 3 OK OK 72 93 75 76 108 C3' A A 4 OK OK 106 126 109 110 141 C3' U A 5 OK OK 139 157 142 143 171 C3' C A 6 OK OK 169 187 172 173 202 C3' A A 7 OK OK 200 220 203 204 235 C3' C A 8 OK OK 233 251 236 237 266 C3' A A 9 OK OK 264 284 267 268 299 C3' A A 10 OK OK 297 317 300 301 332 C3' G A 11 OK OK 330 351 333 334 366 C3' U A 12 OK OK 364 382 367 368 396 C3' A A 13 OK OK 394 414 397 398 429 C3' G A 14 OK OK 427 448 430 431 463 C3' G A 15 OK OK 461 482 464 465 497 C3' A A 16 OK OK 495 515 498 499 530 C3' C A 17 OK OK 528 546 531 532 561 C3' U A 18 OK OK 559 577 562 563 591 C3' U A 19 OK OK 589 607 592 593 621 C3' C A 20 OK OK 619 637 622 623 652 C3' G A 21 OK OK 650 671 653 654 686 C3' G A 22 OK OK 684 705 687 688 720 C3' U A 23 OK OK 718 736 721 722 750 C3' C A 24 OK OK 748 766 751 752 781 C3' C A 25 OK OK 779 797 782 783 812 C3' G A 26 OK OK 810 831 813 814 846 C3' A A 27 OK OK 844 864 847 848 879 C3' A A 28 OK OK 877 897 880 881 912 C3' U A 29 OK OK 910 928 913 914 942 C3' A A 30 OK OK 940 960 943 944 975 C3' C A 31 OK OK 973 991 976 977 1006 C3' A A 32 OK OK 1004 1024 1007 1008 1039 C3' G A 33 OK OK 1037 1058 1040 1041 1073 C3' A A 34 OK OK 1071 1091 1074 1075 1106 C3' U A 35 OK OK 1104 1122 1107 1108 1136 C3' C A 36 OK OK 1134 1152 1137 1138 1167 C3' U A 37 OK OK 1165 1183 1168 1169 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' G A 3 OK OK 74 92 71 73 106 C4' A A 4 OK OK 108 125 105 107 139 C4' U A 5 OK OK 141 156 138 140 169 C4' C A 6 OK OK 171 186 168 170 200 C4' A A 7 OK OK 202 219 199 201 233 C4' C A 8 OK OK 235 250 232 234 264 C4' A A 9 OK OK 266 283 263 265 297 C4' A A 10 OK OK 299 316 296 298 330 C4' G A 11 OK OK 332 350 329 331 364 C4' U A 12 OK OK 366 381 363 365 394 C4' A A 13 OK OK 396 413 393 395 427 C4' G A 14 OK OK 429 447 426 428 461 C4' G A 15 OK OK 463 481 460 462 495 C4' A A 16 OK OK 497 514 494 496 528 C4' C A 17 OK OK 530 545 527 529 559 C4' U A 18 OK OK 561 576 558 560 589 C4' U A 19 OK OK 591 606 588 590 619 C4' C A 20 OK OK 621 636 618 620 650 C4' G A 21 OK OK 652 670 649 651 684 C4' G A 22 OK OK 686 704 683 685 718 C4' U A 23 OK OK 720 735 717 719 748 C4' C A 24 OK OK 750 765 747 749 779 C4' C A 25 OK OK 781 796 778 780 810 C4' G A 26 OK OK 812 830 809 811 844 C4' A A 27 OK OK 846 863 843 845 877 C4' A A 28 OK OK 879 896 876 878 910 C4' U A 29 OK OK 912 927 909 911 940 C4' A A 30 OK OK 942 959 939 941 973 C4' C A 31 OK OK 975 990 972 974 1004 C4' A A 32 OK OK 1006 1023 1003 1005 1037 C4' G A 33 OK OK 1039 1057 1036 1038 1071 C4' A A 34 OK OK 1073 1090 1070 1072 1104 C4' U A 35 OK OK 1106 1121 1103 1105 1134 C4' C A 36 OK OK 1136 1151 1133 1135 1165 C4' U A 37 OK OK 1167 1182 1164 1166 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' G A 3 OK OK 70 90 91 72 105 C5' A A 4 OK OK 104 123 124 106 138 C5' U A 5 OK OK 137 154 155 139 168 C5' C A 6 OK OK 167 184 185 169 199 C5' A A 7 OK OK 198 217 218 200 232 C5' C A 8 OK OK 231 248 249 233 263 C5' A A 9 OK OK 262 281 282 264 296 C5' A A 10 OK OK 295 314 315 297 329 C5' G A 11 OK OK 328 348 349 330 363 C5' U A 12 OK OK 362 379 380 364 393 C5' A A 13 OK OK 392 411 412 394 426 C5' G A 14 OK OK 425 445 446 427 460 C5' G A 15 OK OK 459 479 480 461 494 C5' A A 16 OK OK 493 512 513 495 527 C5' C A 17 OK OK 526 543 544 528 558 C5' U A 18 OK OK 557 574 575 559 588 C5' U A 19 OK OK 587 604 605 589 618 C5' C A 20 OK OK 617 634 635 619 649 C5' G A 21 OK OK 648 668 669 650 683 C5' G A 22 OK OK 682 702 703 684 717 C5' U A 23 OK OK 716 733 734 718 747 C5' C A 24 OK OK 746 763 764 748 778 C5' C A 25 OK OK 777 794 795 779 809 C5' G A 26 OK OK 808 828 829 810 843 C5' A A 27 OK OK 842 861 862 844 876 C5' A A 28 OK OK 875 894 895 877 909 C5' U A 29 OK OK 908 925 926 910 939 C5' A A 30 OK OK 938 957 958 940 972 C5' C A 31 OK OK 971 988 989 973 1003 C5' A A 32 OK OK 1002 1021 1022 1004 1036 C5' G A 33 OK OK 1035 1055 1056 1037 1070 C5' A A 34 OK OK 1069 1088 1089 1071 1103 C5' U A 35 OK OK 1102 1119 1120 1104 1133 C5' C A 36 OK OK 1132 1149 1150 1134 1164 C5' U A 37 OK OK 1163 1180 1181 1165 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 G A 3 distorted distorted 41 68 69 70 101 P A A 4 distorted distorted 75 102 103 104 134 P U A 5 distorted distorted 109 135 136 137 164 P C A 6 distorted distorted 142 165 166 167 195 P A A 7 distorted distorted 172 196 197 198 228 P C A 8 distorted distorted 203 229 230 231 259 P A A 9 distorted distorted 236 260 261 262 292 P A A 10 distorted distorted 267 293 294 295 325 P G A 11 distorted distorted 300 326 327 328 359 P U A 12 distorted distorted 333 360 361 362 389 P A A 13 distorted distorted 367 390 391 392 422 P G A 14 distorted distorted 397 423 424 425 456 P G A 15 distorted distorted 430 457 458 459 490 P A A 16 distorted distorted 464 491 492 493 523 P C A 17 distorted distorted 498 524 525 526 554 P U A 18 distorted distorted 531 555 556 557 584 P U A 19 distorted distorted 562 585 586 587 614 P C A 20 distorted distorted 592 615 616 617 645 P G A 21 distorted distorted 622 646 647 648 679 P G A 22 distorted distorted 653 680 681 682 713 P U A 23 distorted distorted 687 714 715 716 743 P C A 24 distorted distorted 721 744 745 746 774 P C A 25 distorted distorted 751 775 776 777 805 P G A 26 distorted distorted 782 806 807 808 839 P A A 27 distorted distorted 813 840 841 842 872 P A A 28 distorted distorted 847 873 874 875 905 P U A 29 distorted distorted 880 906 907 908 935 P A A 30 distorted distorted 913 936 937 938 968 P C A 31 distorted distorted 943 969 970 971 999 P A A 32 distorted distorted 976 1000 1001 1002 1032 P G A 33 distorted distorted 1007 1033 1034 1035 1066 P A A 34 distorted distorted 1040 1067 1068 1069 1099 P U A 35 distorted distorted 1074 1100 1101 1102 1129 P C A 36 distorted distorted 1107 1130 1131 1132 1160 P U A 37 distorted distorted 1137 1161 1162 1163 1190 P C A 38 distorted distorted 1168 1191 1192 1193 ---------------------------------------------------------------------------------