ID code: '1M5L' 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' C A 2 alpha beta 39 59 45 42 75 C1' G A 3 alpha beta 70 93 76 73 109 C1' C A 4 alpha beta 104 124 110 107 140 C1' A A 5 alpha beta 135 157 141 138 173 C1' G A 6 alpha beta 168 191 174 171 207 C1' G A 7 alpha beta 202 225 208 205 241 C1' A A 8 alpha beta 236 258 242 239 274 C1' C A 9 alpha beta 269 289 275 272 305 C1' U A 10 alpha beta 300 320 306 303 335 C1' C A 11 alpha beta 330 350 336 333 366 C1' G A 12 alpha beta 361 384 367 364 400 C1' G A 13 alpha beta 395 418 401 398 434 C1' C A 14 alpha beta 429 449 435 432 465 C1' U A 15 alpha beta 460 480 466 463 495 C1' U A 16 alpha beta 490 510 496 493 525 C1' C A 17 alpha beta 520 540 526 523 556 C1' U A 18 alpha beta 551 571 557 554 586 C1' U A 19 alpha beta 581 601 587 584 616 C1' C A 20 alpha beta 611 631 617 614 647 C1' G A 21 alpha beta 642 665 648 645 681 C1' G A 22 alpha beta 676 699 682 679 715 C1' A A 23 alpha beta 710 732 716 713 748 C1' A A 24 alpha beta 743 765 749 746 781 C1' G A 25 alpha beta 776 799 782 779 815 C1' G A 26 alpha beta 810 833 816 813 849 C1' G A 27 alpha beta 844 867 850 847 883 C1' A A 28 alpha beta 878 900 884 881 916 C1' C A 29 alpha beta 911 931 917 914 947 C1' G A 30 alpha beta 942 965 948 945 981 C1' A A 31 alpha beta 976 998 982 979 1014 C1' G A 32 alpha beta 1009 1032 1015 1012 1048 C1' G A 33 alpha beta 1043 1066 1049 1046 1082 C1' G A 34 alpha beta 1077 1100 1083 1080 1116 C1' G A 35 alpha beta 1111 1134 1117 1114 1150 C1' C A 36 alpha beta 1145 1165 1151 1148 1181 C1' G A 37 alpha beta 1176 1199 1182 1179 1215 C1' C A 38 alpha beta 1210 1231 1216 1213 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 2 OK OK 44 40 57 43 73 C2' G A 3 OK OK 75 71 91 74 107 C2' C A 4 OK OK 109 105 122 108 138 C2' A A 5 OK OK 140 136 155 139 171 C2' G A 6 OK OK 173 169 189 172 205 C2' G A 7 OK OK 207 203 223 206 239 C2' A A 8 OK OK 241 237 256 240 272 C2' C A 9 OK OK 274 270 287 273 303 C2' U A 10 OK OK 305 301 318 304 333 C2' C A 11 OK OK 335 331 348 334 364 C2' G A 12 OK OK 366 362 382 365 398 C2' G A 13 OK OK 400 396 416 399 432 C2' C A 14 OK OK 434 430 447 433 463 C2' U A 15 OK OK 465 461 478 464 493 C2' U A 16 OK OK 495 491 508 494 523 C2' C A 17 OK OK 525 521 538 524 554 C2' U A 18 OK OK 556 552 569 555 584 C2' U A 19 OK OK 586 582 599 585 614 C2' C A 20 OK OK 616 612 629 615 645 C2' G A 21 OK OK 647 643 663 646 679 C2' G A 22 OK OK 681 677 697 680 713 C2' A A 23 OK OK 715 711 730 714 746 C2' A A 24 OK OK 748 744 763 747 779 C2' G A 25 OK OK 781 777 797 780 813 C2' G A 26 OK OK 815 811 831 814 847 C2' G A 27 OK OK 849 845 865 848 881 C2' A A 28 OK OK 883 879 898 882 914 C2' C A 29 OK OK 916 912 929 915 945 C2' G A 30 OK OK 947 943 963 946 979 C2' A A 31 OK OK 981 977 996 980 1012 C2' G A 32 OK OK 1014 1010 1030 1013 1046 C2' G A 33 OK OK 1048 1044 1064 1047 1080 C2' G A 34 OK OK 1082 1078 1098 1081 1114 C2' G A 35 OK OK 1116 1112 1132 1115 1148 C2' C A 36 OK OK 1150 1146 1163 1149 1179 C2' G A 37 OK OK 1181 1177 1197 1180 1213 C2' C A 38 OK OK 1215 1211 1229 1214 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' C A 2 OK OK 38 56 41 42 71 C3' G A 3 OK OK 69 90 72 73 105 C3' C A 4 OK OK 103 121 106 107 136 C3' A A 5 OK OK 134 154 137 138 169 C3' G A 6 OK OK 167 188 170 171 203 C3' G A 7 OK OK 201 222 204 205 237 C3' A A 8 OK OK 235 255 238 239 270 C3' C A 9 OK OK 268 286 271 272 301 C3' U A 10 OK OK 299 317 302 303 331 C3' C A 11 OK OK 329 347 332 333 362 C3' G A 12 OK OK 360 381 363 364 396 C3' G A 13 OK OK 394 415 397 398 430 C3' C A 14 OK OK 428 446 431 432 461 C3' U A 15 OK OK 459 477 462 463 491 C3' U A 16 OK OK 489 507 492 493 521 C3' C A 17 OK OK 519 537 522 523 552 C3' U A 18 OK OK 550 568 553 554 582 C3' U A 19 OK OK 580 598 583 584 612 C3' C A 20 OK OK 610 628 613 614 643 C3' G A 21 OK OK 641 662 644 645 677 C3' G A 22 OK OK 675 696 678 679 711 C3' A A 23 OK OK 709 729 712 713 744 C3' A A 24 OK OK 742 762 745 746 777 C3' G A 25 OK OK 775 796 778 779 811 C3' G A 26 OK OK 809 830 812 813 845 C3' G A 27 OK OK 843 864 846 847 879 C3' A A 28 OK OK 877 897 880 881 912 C3' C A 29 OK OK 910 928 913 914 943 C3' G A 30 OK OK 941 962 944 945 977 C3' A A 31 OK OK 975 995 978 979 1010 C3' G A 32 OK OK 1008 1029 1011 1012 1044 C3' G A 33 OK OK 1042 1063 1045 1046 1078 C3' G A 34 OK OK 1076 1097 1079 1080 1112 C3' G A 35 OK OK 1110 1131 1113 1114 1146 C3' C A 36 OK OK 1144 1162 1147 1148 1177 C3' G A 37 OK OK 1175 1196 1178 1179 1211 C3' C A 38 OK OK 1209 1227 1212 1213 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' C A 2 OK OK 40 55 37 39 69 C4' G A 3 OK OK 71 89 68 70 103 C4' C A 4 OK OK 105 120 102 104 134 C4' A A 5 OK OK 136 153 133 135 167 C4' G A 6 OK OK 169 187 166 168 201 C4' G A 7 OK OK 203 221 200 202 235 C4' A A 8 OK OK 237 254 234 236 268 C4' C A 9 OK OK 270 285 267 269 299 C4' U A 10 OK OK 301 316 298 300 329 C4' C A 11 OK OK 331 346 328 330 360 C4' G A 12 OK OK 362 380 359 361 394 C4' G A 13 OK OK 396 414 393 395 428 C4' C A 14 OK OK 430 445 427 429 459 C4' U A 15 OK OK 461 476 458 460 489 C4' U A 16 OK OK 491 506 488 490 519 C4' C A 17 OK OK 521 536 518 520 550 C4' U A 18 OK OK 552 567 549 551 580 C4' U A 19 OK OK 582 597 579 581 610 C4' C A 20 OK OK 612 627 609 611 641 C4' G A 21 OK OK 643 661 640 642 675 C4' G A 22 OK OK 677 695 674 676 709 C4' A A 23 OK OK 711 728 708 710 742 C4' A A 24 OK OK 744 761 741 743 775 C4' G A 25 OK OK 777 795 774 776 809 C4' G A 26 OK OK 811 829 808 810 843 C4' G A 27 OK OK 845 863 842 844 877 C4' A A 28 OK OK 879 896 876 878 910 C4' C A 29 OK OK 912 927 909 911 941 C4' G A 30 OK OK 943 961 940 942 975 C4' A A 31 OK OK 977 994 974 976 1008 C4' G A 32 OK OK 1010 1028 1007 1009 1042 C4' G A 33 OK OK 1044 1062 1041 1043 1076 C4' G A 34 OK OK 1078 1096 1075 1077 1110 C4' G A 35 OK OK 1112 1130 1109 1111 1144 C4' C A 36 OK OK 1146 1161 1143 1145 1175 C4' G A 37 OK OK 1177 1195 1174 1176 1209 C4' C A 38 OK OK 1211 1226 1208 1210 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 2 OK OK 36 53 54 38 68 C5' G A 3 OK OK 67 87 88 69 102 C5' C A 4 OK OK 101 118 119 103 133 C5' A A 5 OK OK 132 151 152 134 166 C5' G A 6 OK OK 165 185 186 167 200 C5' G A 7 OK OK 199 219 220 201 234 C5' A A 8 OK OK 233 252 253 235 267 C5' C A 9 OK OK 266 283 284 268 298 C5' U A 10 OK OK 297 314 315 299 328 C5' C A 11 OK OK 327 344 345 329 359 C5' G A 12 OK OK 358 378 379 360 393 C5' G A 13 OK OK 392 412 413 394 427 C5' C A 14 OK OK 426 443 444 428 458 C5' U A 15 OK OK 457 474 475 459 488 C5' U A 16 OK OK 487 504 505 489 518 C5' C A 17 OK OK 517 534 535 519 549 C5' U A 18 OK OK 548 565 566 550 579 C5' U A 19 OK OK 578 595 596 580 609 C5' C A 20 OK OK 608 625 626 610 640 C5' G A 21 OK OK 639 659 660 641 674 C5' G A 22 OK OK 673 693 694 675 708 C5' A A 23 OK OK 707 726 727 709 741 C5' A A 24 OK OK 740 759 760 742 774 C5' G A 25 OK OK 773 793 794 775 808 C5' G A 26 OK OK 807 827 828 809 842 C5' G A 27 OK OK 841 861 862 843 876 C5' A A 28 OK OK 875 894 895 877 909 C5' C A 29 OK OK 908 925 926 910 940 C5' G A 30 OK OK 939 959 960 941 974 C5' A A 31 OK OK 973 992 993 975 1007 C5' G A 32 OK OK 1006 1026 1027 1008 1041 C5' G A 33 OK OK 1040 1060 1061 1042 1075 C5' G A 34 OK OK 1074 1094 1095 1076 1109 C5' G A 35 OK OK 1108 1128 1129 1110 1143 C5' C A 36 OK OK 1142 1159 1160 1144 1174 C5' G A 37 OK OK 1173 1193 1194 1175 1208 C5' C A 38 OK OK 1207 1224 1225 1209 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P C A 2 distorted distorted 6 34 35 36 64 P G A 3 distorted distorted 41 65 66 67 98 P C A 4 distorted distorted 72 99 100 101 129 P A A 5 distorted distorted 106 130 131 132 162 P G A 6 distorted distorted 137 163 164 165 196 P G A 7 distorted distorted 170 197 198 199 230 P A A 8 distorted distorted 204 231 232 233 263 P C A 9 distorted distorted 238 264 265 266 294 P U A 10 distorted distorted 271 295 296 297 324 P C A 11 distorted distorted 302 325 326 327 355 P G A 12 distorted distorted 332 356 357 358 389 P G A 13 distorted distorted 363 390 391 392 423 P C A 14 distorted distorted 397 424 425 426 454 P U A 15 distorted distorted 431 455 456 457 484 P U A 16 distorted distorted 462 485 486 487 514 P C A 17 distorted distorted 492 515 516 517 545 P U A 18 distorted distorted 522 546 547 548 575 P U A 19 distorted distorted 553 576 577 578 605 P C A 20 distorted distorted 583 606 607 608 636 P G A 21 distorted distorted 613 637 638 639 670 P G A 22 distorted distorted 644 671 672 673 704 P A A 23 distorted distorted 678 705 706 707 737 P A A 24 distorted distorted 712 738 739 740 770 P G A 25 distorted distorted 745 771 772 773 804 P G A 26 distorted distorted 778 805 806 807 838 P G A 27 distorted distorted 812 839 840 841 872 P A A 28 distorted distorted 846 873 874 875 905 P C A 29 distorted distorted 880 906 907 908 936 P G A 30 distorted distorted 913 937 938 939 970 P A A 31 distorted distorted 944 971 972 973 1003 P G A 32 distorted distorted 978 1004 1005 1006 1037 P G A 33 distorted distorted 1011 1038 1039 1040 1071 P G A 34 distorted distorted 1045 1072 1073 1074 1105 P G A 35 distorted distorted 1079 1106 1107 1108 1139 P C A 36 distorted distorted 1113 1140 1141 1142 1170 P G A 37 distorted distorted 1147 1171 1172 1173 1204 P C A 38 distorted distorted 1178 1205 1206 1207 ---------------------------------------------------------------------------------