ID code: '1A9L' 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' U A 4 alpha beta 107 127 113 110 142 C1' G A 5 alpha beta 137 160 143 140 176 C1' A A 6 alpha beta 171 193 177 174 209 C1' C A 7 alpha beta 204 224 210 207 240 C1' U A 8 alpha beta 235 255 241 238 270 C1' C A 9 alpha beta 265 285 271 268 301 C1' C A 10 alpha beta 296 316 302 299 332 C1' A A 11 alpha beta 327 349 333 330 365 C1' G A 12 alpha beta 360 383 366 363 399 C1' A A 13 alpha beta 394 416 400 397 432 C1' G A 14 alpha beta 427 450 433 430 466 C1' G A 15 alpha beta 461 484 467 464 500 C1' U A 16 alpha beta 495 515 501 498 530 C1' C A 17 alpha beta 525 545 531 528 561 C1' G A 18 alpha beta 556 579 562 559 595 C1' A A 19 alpha beta 590 612 596 593 628 C1' G A 20 alpha beta 623 646 629 626 662 C1' A A 21 alpha beta 657 679 663 660 695 C1' G A 22 alpha beta 690 713 696 693 729 C1' A A 23 alpha beta 724 746 730 727 762 C1' C A 24 alpha beta 757 777 763 760 793 C1' C A 25 alpha beta 788 808 794 791 824 C1' G A 26 alpha beta 819 842 825 822 858 C1' G A 27 alpha beta 853 876 859 856 892 C1' A A 28 alpha beta 887 909 893 890 925 C1' G A 29 alpha beta 920 943 926 923 959 C1' A A 30 alpha beta 954 976 960 957 992 C1' U A 31 alpha beta 987 1007 993 990 1022 C1' A A 32 alpha beta 1017 1039 1023 1020 1055 C1' U A 33 alpha beta 1050 1070 1056 1053 1085 C1' C A 34 alpha beta 1080 1100 1086 1083 1116 C1' A A 35 alpha beta 1111 1133 1117 1114 1149 C1' C A 36 alpha beta 1144 1164 1150 1147 1180 C1' C A 37 alpha beta 1175 1195 1181 1178 1211 C1' C A 38 alpha beta 1206 1227 1212 1209 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U A 4 OK OK 112 108 125 111 140 C2' G A 5 OK OK 142 138 158 141 174 C2' A A 6 OK OK 176 172 191 175 207 C2' C A 7 OK OK 209 205 222 208 238 C2' U A 8 OK OK 240 236 253 239 268 C2' C A 9 OK OK 270 266 283 269 299 C2' C A 10 OK OK 301 297 314 300 330 C2' A A 11 OK OK 332 328 347 331 363 C2' G A 12 OK OK 365 361 381 364 397 C2' A A 13 OK OK 399 395 414 398 430 C2' G A 14 OK OK 432 428 448 431 464 C2' G A 15 OK OK 466 462 482 465 498 C2' U A 16 OK OK 500 496 513 499 528 C2' C A 17 OK OK 530 526 543 529 559 C2' G A 18 OK OK 561 557 577 560 593 C2' A A 19 OK OK 595 591 610 594 626 C2' G A 20 OK OK 628 624 644 627 660 C2' A A 21 OK OK 662 658 677 661 693 C2' G A 22 OK OK 695 691 711 694 727 C2' A A 23 OK OK 729 725 744 728 760 C2' C A 24 OK OK 762 758 775 761 791 C2' C A 25 OK OK 793 789 806 792 822 C2' G A 26 OK OK 824 820 840 823 856 C2' G A 27 OK OK 858 854 874 857 890 C2' A A 28 OK OK 892 888 907 891 923 C2' G A 29 OK OK 925 921 941 924 957 C2' A A 30 OK OK 959 955 974 958 990 C2' U A 31 OK OK 992 988 1005 991 1020 C2' A A 32 OK OK 1022 1018 1037 1021 1053 C2' U A 33 OK OK 1055 1051 1068 1054 1083 C2' C A 34 OK OK 1085 1081 1098 1084 1114 C2' A A 35 OK OK 1116 1112 1131 1115 1147 C2' C A 36 OK OK 1149 1145 1162 1148 1178 C2' C A 37 OK OK 1180 1176 1193 1179 1209 C2' C A 38 OK OK 1211 1207 1225 1210 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 4 OK OK 106 124 109 110 138 C3' G A 5 OK OK 136 157 139 140 172 C3' A A 6 OK OK 170 190 173 174 205 C3' C A 7 OK OK 203 221 206 207 236 C3' U A 8 OK OK 234 252 237 238 266 C3' C A 9 OK OK 264 282 267 268 297 C3' C A 10 OK OK 295 313 298 299 328 C3' A A 11 OK OK 326 346 329 330 361 C3' G A 12 OK OK 359 380 362 363 395 C3' A A 13 OK OK 393 413 396 397 428 C3' G A 14 OK OK 426 447 429 430 462 C3' G A 15 OK OK 460 481 463 464 496 C3' U A 16 OK OK 494 512 497 498 526 C3' C A 17 OK OK 524 542 527 528 557 C3' G A 18 OK OK 555 576 558 559 591 C3' A A 19 OK OK 589 609 592 593 624 C3' G A 20 OK OK 622 643 625 626 658 C3' A A 21 OK OK 656 676 659 660 691 C3' G A 22 OK OK 689 710 692 693 725 C3' A A 23 OK OK 723 743 726 727 758 C3' C A 24 OK OK 756 774 759 760 789 C3' C A 25 OK OK 787 805 790 791 820 C3' G A 26 OK OK 818 839 821 822 854 C3' G A 27 OK OK 852 873 855 856 888 C3' A A 28 OK OK 886 906 889 890 921 C3' G A 29 OK OK 919 940 922 923 955 C3' A A 30 OK OK 953 973 956 957 988 C3' U A 31 OK OK 986 1004 989 990 1018 C3' A A 32 OK OK 1016 1036 1019 1020 1051 C3' U A 33 OK OK 1049 1067 1052 1053 1081 C3' C A 34 OK OK 1079 1097 1082 1083 1112 C3' A A 35 OK OK 1110 1130 1113 1114 1145 C3' C A 36 OK OK 1143 1161 1146 1147 1176 C3' C A 37 OK OK 1174 1192 1177 1178 1207 C3' C A 38 OK OK 1205 1223 1208 1209 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 4 OK OK 108 123 105 107 136 C4' G A 5 OK OK 138 156 135 137 170 C4' A A 6 OK OK 172 189 169 171 203 C4' C A 7 OK OK 205 220 202 204 234 C4' U A 8 OK OK 236 251 233 235 264 C4' C A 9 OK OK 266 281 263 265 295 C4' C A 10 OK OK 297 312 294 296 326 C4' A A 11 OK OK 328 345 325 327 359 C4' G A 12 OK OK 361 379 358 360 393 C4' A A 13 OK OK 395 412 392 394 426 C4' G A 14 OK OK 428 446 425 427 460 C4' G A 15 OK OK 462 480 459 461 494 C4' U A 16 OK OK 496 511 493 495 524 C4' C A 17 OK OK 526 541 523 525 555 C4' G A 18 OK OK 557 575 554 556 589 C4' A A 19 OK OK 591 608 588 590 622 C4' G A 20 OK OK 624 642 621 623 656 C4' A A 21 OK OK 658 675 655 657 689 C4' G A 22 OK OK 691 709 688 690 723 C4' A A 23 OK OK 725 742 722 724 756 C4' C A 24 OK OK 758 773 755 757 787 C4' C A 25 OK OK 789 804 786 788 818 C4' G A 26 OK OK 820 838 817 819 852 C4' G A 27 OK OK 854 872 851 853 886 C4' A A 28 OK OK 888 905 885 887 919 C4' G A 29 OK OK 921 939 918 920 953 C4' A A 30 OK OK 955 972 952 954 986 C4' U A 31 OK OK 988 1003 985 987 1016 C4' A A 32 OK OK 1018 1035 1015 1017 1049 C4' U A 33 OK OK 1051 1066 1048 1050 1079 C4' C A 34 OK OK 1081 1096 1078 1080 1110 C4' A A 35 OK OK 1112 1129 1109 1111 1143 C4' C A 36 OK OK 1145 1160 1142 1144 1174 C4' C A 37 OK OK 1176 1191 1173 1175 1205 C4' C A 38 OK OK 1207 1222 1204 1206 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 4 OK OK 104 121 122 106 135 C5' G A 5 OK OK 134 154 155 136 169 C5' A A 6 OK OK 168 187 188 170 202 C5' C A 7 OK OK 201 218 219 203 233 C5' U A 8 OK OK 232 249 250 234 263 C5' C A 9 OK OK 262 279 280 264 294 C5' C A 10 OK OK 293 310 311 295 325 C5' A A 11 OK OK 324 343 344 326 358 C5' G A 12 OK OK 357 377 378 359 392 C5' A A 13 OK OK 391 410 411 393 425 C5' G A 14 OK OK 424 444 445 426 459 C5' G A 15 OK OK 458 478 479 460 493 C5' U A 16 OK OK 492 509 510 494 523 C5' C A 17 OK OK 522 539 540 524 554 C5' G A 18 OK OK 553 573 574 555 588 C5' A A 19 OK OK 587 606 607 589 621 C5' G A 20 OK OK 620 640 641 622 655 C5' A A 21 OK OK 654 673 674 656 688 C5' G A 22 OK OK 687 707 708 689 722 C5' A A 23 OK OK 721 740 741 723 755 C5' C A 24 OK OK 754 771 772 756 786 C5' C A 25 OK OK 785 802 803 787 817 C5' G A 26 OK OK 816 836 837 818 851 C5' G A 27 OK OK 850 870 871 852 885 C5' A A 28 OK OK 884 903 904 886 918 C5' G A 29 OK OK 917 937 938 919 952 C5' A A 30 OK OK 951 970 971 953 985 C5' U A 31 OK OK 984 1001 1002 986 1015 C5' A A 32 OK OK 1014 1033 1034 1016 1048 C5' U A 33 OK OK 1047 1064 1065 1049 1078 C5' C A 34 OK OK 1077 1094 1095 1079 1109 C5' A A 35 OK OK 1108 1127 1128 1110 1142 C5' C A 36 OK OK 1141 1158 1159 1143 1173 C5' C A 37 OK OK 1172 1189 1190 1174 1204 C5' C A 38 OK OK 1203 1220 1221 1205 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 U A 4 distorted distorted 75 102 103 104 131 P G A 5 distorted distorted 109 132 133 134 165 P A A 6 distorted distorted 139 166 167 168 198 P C A 7 distorted distorted 173 199 200 201 229 P U A 8 distorted distorted 206 230 231 232 259 P C A 9 distorted distorted 237 260 261 262 290 P C A 10 distorted distorted 267 291 292 293 321 P A A 11 distorted distorted 298 322 323 324 354 P G A 12 distorted distorted 329 355 356 357 388 P A A 13 distorted distorted 362 389 390 391 421 P G A 14 distorted distorted 396 422 423 424 455 P G A 15 distorted distorted 429 456 457 458 489 P U A 16 distorted distorted 463 490 491 492 519 P C A 17 distorted distorted 497 520 521 522 550 P G A 18 distorted distorted 527 551 552 553 584 P A A 19 distorted distorted 558 585 586 587 617 P G A 20 distorted distorted 592 618 619 620 651 P A A 21 distorted distorted 625 652 653 654 684 P G A 22 distorted distorted 659 685 686 687 718 P A A 23 distorted distorted 692 719 720 721 751 P C A 24 distorted distorted 726 752 753 754 782 P C A 25 distorted distorted 759 783 784 785 813 P G A 26 distorted distorted 790 814 815 816 847 P G A 27 distorted distorted 821 848 849 850 881 P A A 28 distorted distorted 855 882 883 884 914 P G A 29 distorted distorted 889 915 916 917 948 P A A 30 distorted distorted 922 949 950 951 981 P U A 31 distorted distorted 956 982 983 984 1011 P A A 32 distorted distorted 989 1012 1013 1014 1044 P U A 33 distorted distorted 1019 1045 1046 1047 1074 P C A 34 distorted distorted 1052 1075 1076 1077 1105 P A A 35 distorted distorted 1082 1106 1107 1108 1138 P C A 36 distorted distorted 1113 1139 1140 1141 1169 P C A 37 distorted distorted 1146 1170 1171 1172 1200 P C A 38 distorted distorted 1177 1201 1202 1203 ---------------------------------------------------------------------------------