ID code: '4MSB' 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' C A 1 beta 4 10 7 29 C1' C A 2 beta 24 30 27 49 C1' G A 3 beta 44 50 47 72 C1' G A 4 beta 67 73 70 95 C1' C A 5 beta 90 96 93 115 C1' G A 6 beta 110 116 113 138 C1' C A 7 beta 133 139 136 158 C1' C A 8 beta 153 159 156 178 C1' G A 9 beta 173 179 176 201 C1' G A 10 beta 196 202 199 222 C1' C B 1 beta 217 223 220 242 C1' C B 2 beta 237 243 240 262 C1' G B 3 beta 257 263 260 285 C1' G B 4 beta 280 286 283 308 C1' C B 5 beta 303 309 306 328 C1' G B 6 beta 323 329 326 351 C1' C B 7 beta 346 352 349 371 C1' C B 8 beta 366 372 369 391 C1' G B 9 beta 386 392 389 414 C1' G B 10 beta 409 415 412 435 C1' C C 1 beta 430 436 433 455 C1' C C 2 beta 450 456 453 475 C1' G C 3 beta 470 476 473 498 C1' G C 4 beta 493 499 496 521 C1' C C 5 beta 516 522 519 541 C1' G C 6 beta 536 542 539 564 C1' C C 7 beta 559 565 562 584 C1' C C 8 beta 579 585 582 604 C1' G C 9 beta 599 605 602 627 C1' G C 10 beta 622 628 625 648 C1' C D 1 beta 643 649 646 668 C1' C D 2 beta 663 669 666 688 C1' G D 3 beta 683 689 686 711 C1' G D 4 beta 706 712 709 734 C1' C D 5 beta 729 735 732 754 C1' G D 6 beta 749 755 752 777 C1' C D 7 beta 772 778 775 797 C1' C D 8 beta 792 798 795 817 C1' G D 9 beta 812 818 815 840 C1' G D 10 beta 835 841 838 861 C1' C E 1 beta 856 862 859 881 C1' C E 2 beta 876 882 879 901 C1' G E 3 beta 896 902 899 924 C1' G E 4 beta 919 925 922 947 C1' C E 5 beta 942 948 945 967 C1' G E 6 beta 962 968 965 990 C1' C E 7 beta 985 991 988 1010 C1' C E 8 beta 1005 1011 1008 1030 C1' G E 9 beta 1025 1031 1028 1053 C1' G E 10 beta 1048 1054 1051 1074 C1' C F 1 beta 1069 1075 1072 1094 C1' C F 2 beta 1089 1095 1092 1114 C1' G F 3 beta 1109 1115 1112 1137 C1' G F 4 beta 1132 1138 1135 1160 C1' C F 5 beta 1155 1161 1158 1180 C1' G F 6 beta 1175 1181 1178 1203 C1' C F 7 beta 1198 1204 1201 1223 C1' C F 8 beta 1218 1224 1221 1243 C1' G F 9 beta 1238 1244 1241 1266 C1' G F 10 beta 1261 1267 1264 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 1 OK 9 5 8 27 C2' C A 2 OK 29 25 28 47 C2' G A 3 OK 49 45 48 70 C2' G A 4 OK 72 68 71 93 C2' C A 5 OK 95 91 94 113 C2' G A 6 OK 115 111 114 136 C2' C A 7 OK 138 134 137 156 C2' C A 8 OK 158 154 157 176 C2' G A 9 OK 178 174 177 199 C2' G A 10 OK 201 197 200 220 C2' C B 1 OK 222 218 221 240 C2' C B 2 OK 242 238 241 260 C2' G B 3 OK 262 258 261 283 C2' G B 4 OK 285 281 284 306 C2' C B 5 OK 308 304 307 326 C2' G B 6 OK 328 324 327 349 C2' C B 7 OK 351 347 350 369 C2' C B 8 OK 371 367 370 389 C2' G B 9 OK 391 387 390 412 C2' G B 10 OK 414 410 413 433 C2' C C 1 OK 435 431 434 453 C2' C C 2 OK 455 451 454 473 C2' G C 3 OK 475 471 474 496 C2' G C 4 OK 498 494 497 519 C2' C C 5 OK 521 517 520 539 C2' G C 6 OK 541 537 540 562 C2' C C 7 OK 564 560 563 582 C2' C C 8 OK 584 580 583 602 C2' G C 9 OK 604 600 603 625 C2' G C 10 OK 627 623 626 646 C2' C D 1 OK 648 644 647 666 C2' C D 2 OK 668 664 667 686 C2' G D 3 OK 688 684 687 709 C2' G D 4 OK 711 707 710 732 C2' C D 5 OK 734 730 733 752 C2' G D 6 OK 754 750 753 775 C2' C D 7 OK 777 773 776 795 C2' C D 8 OK 797 793 796 815 C2' G D 9 OK 817 813 816 838 C2' G D 10 OK 840 836 839 859 C2' C E 1 OK 861 857 860 879 C2' C E 2 OK 881 877 880 899 C2' G E 3 OK 901 897 900 922 C2' G E 4 OK 924 920 923 945 C2' C E 5 OK 947 943 946 965 C2' G E 6 OK 967 963 966 988 C2' C E 7 OK 990 986 989 1008 C2' C E 8 OK 1010 1006 1009 1028 C2' G E 9 OK 1030 1026 1029 1051 C2' G E 10 OK 1053 1049 1052 1072 C2' C F 1 OK 1074 1070 1073 1092 C2' C F 2 OK 1094 1090 1093 1112 C2' G F 3 OK 1114 1110 1113 1135 C2' G F 4 OK 1137 1133 1136 1158 C2' C F 5 OK 1160 1156 1159 1178 C2' G F 6 OK 1180 1176 1179 1201 C2' C F 7 OK 1203 1199 1202 1221 C2' C F 8 OK 1223 1219 1222 1241 C2' G F 9 OK 1243 1239 1242 1264 C2' G F 10 OK 1266 1262 1265 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK 3 6 7 25 C3' C A 2 OK 23 26 27 45 C3' G A 3 OK 43 46 47 68 C3' G A 4 OK 66 69 70 91 C3' C A 5 OK 89 92 93 111 C3' G A 6 OK 109 112 113 134 C3' C A 7 OK 132 135 136 154 C3' C A 8 OK 152 155 156 174 C3' G A 9 OK 172 175 176 197 C3' G A 10 OK 195 198 199 218 C3' C B 1 OK 216 219 220 238 C3' C B 2 OK 236 239 240 258 C3' G B 3 OK 256 259 260 281 C3' G B 4 OK 279 282 283 304 C3' C B 5 OK 302 305 306 324 C3' G B 6 OK 322 325 326 347 C3' C B 7 OK 345 348 349 367 C3' C B 8 OK 365 368 369 387 C3' G B 9 OK 385 388 389 410 C3' G B 10 OK 408 411 412 431 C3' C C 1 OK 429 432 433 451 C3' C C 2 OK 449 452 453 471 C3' G C 3 OK 469 472 473 494 C3' G C 4 OK 492 495 496 517 C3' C C 5 OK 515 518 519 537 C3' G C 6 OK 535 538 539 560 C3' C C 7 OK 558 561 562 580 C3' C C 8 OK 578 581 582 600 C3' G C 9 OK 598 601 602 623 C3' G C 10 OK 621 624 625 644 C3' C D 1 OK 642 645 646 664 C3' C D 2 OK 662 665 666 684 C3' G D 3 OK 682 685 686 707 C3' G D 4 OK 705 708 709 730 C3' C D 5 OK 728 731 732 750 C3' G D 6 OK 748 751 752 773 C3' C D 7 OK 771 774 775 793 C3' C D 8 OK 791 794 795 813 C3' G D 9 OK 811 814 815 836 C3' G D 10 OK 834 837 838 857 C3' C E 1 OK 855 858 859 877 C3' C E 2 OK 875 878 879 897 C3' G E 3 OK 895 898 899 920 C3' G E 4 OK 918 921 922 943 C3' C E 5 OK 941 944 945 963 C3' G E 6 OK 961 964 965 986 C3' C E 7 OK 984 987 988 1006 C3' C E 8 OK 1004 1007 1008 1026 C3' G E 9 OK 1024 1027 1028 1049 C3' G E 10 OK 1047 1050 1051 1070 C3' C F 1 OK 1068 1071 1072 1090 C3' C F 2 OK 1088 1091 1092 1110 C3' G F 3 OK 1108 1111 1112 1133 C3' G F 4 OK 1131 1134 1135 1156 C3' C F 5 OK 1154 1157 1158 1176 C3' G F 6 OK 1174 1177 1178 1199 C3' C F 7 OK 1197 1200 1201 1219 C3' C F 8 OK 1217 1220 1221 1239 C3' G F 9 OK 1237 1240 1241 1262 C3' G F 10 OK 1260 1263 1264 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK 5 2 4 23 C4' C A 2 OK 25 22 24 43 C4' G A 3 OK 45 42 44 66 C4' G A 4 OK 68 65 67 89 C4' C A 5 OK 91 88 90 109 C4' G A 6 OK 111 108 110 132 C4' C A 7 OK 134 131 133 152 C4' C A 8 OK 154 151 153 172 C4' G A 9 OK 174 171 173 195 C4' G A 10 OK 197 194 196 216 C4' C B 1 OK 218 215 217 236 C4' C B 2 OK 238 235 237 256 C4' G B 3 OK 258 255 257 279 C4' G B 4 OK 281 278 280 302 C4' C B 5 OK 304 301 303 322 C4' G B 6 OK 324 321 323 345 C4' C B 7 OK 347 344 346 365 C4' C B 8 OK 367 364 366 385 C4' G B 9 OK 387 384 386 408 C4' G B 10 OK 410 407 409 429 C4' C C 1 OK 431 428 430 449 C4' C C 2 OK 451 448 450 469 C4' G C 3 OK 471 468 470 492 C4' G C 4 OK 494 491 493 515 C4' C C 5 OK 517 514 516 535 C4' G C 6 OK 537 534 536 558 C4' C C 7 OK 560 557 559 578 C4' C C 8 OK 580 577 579 598 C4' G C 9 OK 600 597 599 621 C4' G C 10 OK 623 620 622 642 C4' C D 1 OK 644 641 643 662 C4' C D 2 OK 664 661 663 682 C4' G D 3 OK 684 681 683 705 C4' G D 4 OK 707 704 706 728 C4' C D 5 OK 730 727 729 748 C4' G D 6 OK 750 747 749 771 C4' C D 7 OK 773 770 772 791 C4' C D 8 OK 793 790 792 811 C4' G D 9 OK 813 810 812 834 C4' G D 10 OK 836 833 835 855 C4' C E 1 OK 857 854 856 875 C4' C E 2 OK 877 874 876 895 C4' G E 3 OK 897 894 896 918 C4' G E 4 OK 920 917 919 941 C4' C E 5 OK 943 940 942 961 C4' G E 6 OK 963 960 962 984 C4' C E 7 OK 986 983 985 1004 C4' C E 8 OK 1006 1003 1005 1024 C4' G E 9 OK 1026 1023 1025 1047 C4' G E 10 OK 1049 1046 1048 1068 C4' C F 1 OK 1070 1067 1069 1088 C4' C F 2 OK 1090 1087 1089 1108 C4' G F 3 OK 1110 1107 1109 1131 C4' G F 4 OK 1133 1130 1132 1154 C4' C F 5 OK 1156 1153 1155 1174 C4' G F 6 OK 1176 1173 1175 1197 C4' C F 7 OK 1199 1196 1198 1217 C4' C F 8 OK 1219 1216 1218 1237 C4' G F 9 OK 1239 1236 1238 1260 C4' G F 10 OK 1262 1259 1261 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 1 3 22 C5' C A 2 21 23 42 C5' G A 3 41 43 65 C5' G A 4 64 66 88 C5' C A 5 87 89 108 C5' G A 6 107 109 131 C5' C A 7 130 132 151 C5' C A 8 150 152 171 C5' G A 9 170 172 194 C5' G A 10 193 195 215 C5' C B 1 214 216 235 C5' C B 2 234 236 255 C5' G B 3 254 256 278 C5' G B 4 277 279 301 C5' C B 5 300 302 321 C5' G B 6 320 322 344 C5' C B 7 343 345 364 C5' C B 8 363 365 384 C5' G B 9 383 385 407 C5' G B 10 406 408 428 C5' C C 1 427 429 448 C5' C C 2 447 449 468 C5' G C 3 467 469 491 C5' G C 4 490 492 514 C5' C C 5 513 515 534 C5' G C 6 533 535 557 C5' C C 7 556 558 577 C5' C C 8 576 578 597 C5' G C 9 596 598 620 C5' G C 10 619 621 641 C5' C D 1 640 642 661 C5' C D 2 660 662 681 C5' G D 3 680 682 704 C5' G D 4 703 705 727 C5' C D 5 726 728 747 C5' G D 6 746 748 770 C5' C D 7 769 771 790 C5' C D 8 789 791 810 C5' G D 9 809 811 833 C5' G D 10 832 834 854 C5' C E 1 853 855 874 C5' C E 2 873 875 894 C5' G E 3 893 895 917 C5' G E 4 916 918 940 C5' C E 5 939 941 960 C5' G E 6 959 961 983 C5' C E 7 982 984 1003 C5' C E 8 1002 1004 1023 C5' G E 9 1022 1024 1046 C5' G E 10 1045 1047 1067 C5' C F 1 1066 1068 1087 C5' C F 2 1086 1088 1107 C5' G F 3 1106 1108 1130 C5' G F 4 1129 1131 1153 C5' C F 5 1152 1154 1173 C5' G F 6 1172 1174 1196 C5' C F 7 1195 1197 1216 C5' C F 8 1215 1217 1236 C5' G F 9 1235 1237 1259 C5' G F 10 1258 1260 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P C A 2 distorted distorted 6 19 20 21 38 P G A 3 distorted distorted 26 39 40 41 61 P G A 4 distorted distorted 46 62 63 64 84 P C A 5 distorted distorted 69 85 86 87 104 P G A 6 OK OK 105 106 107 127 P C A 7 distorted distorted 112 128 129 130 147 P C A 8 distorted distorted 135 148 149 150 167 P G A 9 distorted distorted 155 168 169 170 190 P G A 10 distorted distorted 175 191 192 193 231 P C B 2 distorted distorted 219 232 233 234 251 P G B 3 distorted distorted 239 252 253 254 274 P G B 4 distorted distorted 259 275 276 277 297 P C B 5 distorted distorted 282 298 299 300 317 P G B 6 distorted distorted 318 319 320 340 P C B 7 distorted distorted 325 341 342 343 360 P C B 8 distorted distorted 348 361 362 363 380 P G B 9 distorted distorted 368 381 382 383 403 P G B 10 distorted distorted 388 404 405 406 444 P C C 2 distorted distorted 432 445 446 447 464 P G C 3 distorted distorted 452 465 466 467 487 P G C 4 distorted distorted 472 488 489 490 510 P C C 5 distorted distorted 495 511 512 513 530 P G C 6 OK OK 531 532 533 553 P C C 7 distorted distorted 538 554 555 556 573 P C C 8 distorted distorted 561 574 575 576 593 P G C 9 distorted distorted 581 594 595 596 616 P G C 10 distorted distorted 601 617 618 619 657 P C D 2 distorted distorted 645 658 659 660 677 P G D 3 distorted distorted 665 678 679 680 700 P G D 4 distorted distorted 685 701 702 703 723 P C D 5 distorted distorted 708 724 725 726 743 P G D 6 distorted distorted 744 745 746 766 P C D 7 distorted distorted 751 767 768 769 786 P C D 8 distorted distorted 774 787 788 789 806 P G D 9 distorted distorted 794 807 808 809 829 P G D 10 distorted distorted 814 830 831 832 870 P C E 2 distorted distorted 858 871 872 873 890 P G E 3 distorted distorted 878 891 892 893 913 P G E 4 distorted distorted 898 914 915 916 936 P C E 5 distorted distorted 921 937 938 939 956 P G E 6 OK OK 957 958 959 979 P C E 7 distorted distorted 964 980 981 982 999 P C E 8 distorted distorted 987 1000 1001 1002 1019 P G E 9 distorted distorted 1007 1020 1021 1022 1042 P G E 10 distorted distorted 1027 1043 1044 1045 1083 P C F 2 distorted distorted 1071 1084 1085 1086 1103 P G F 3 distorted distorted 1091 1104 1105 1106 1126 P G F 4 distorted distorted 1111 1127 1128 1129 1149 P C F 5 distorted distorted 1134 1150 1151 1152 1169 P G F 6 distorted distorted 1170 1171 1172 1192 P C F 7 distorted distorted 1177 1193 1194 1195 1212 P C F 8 distorted distorted 1200 1213 1214 1215 1232 P G F 9 distorted distorted 1220 1233 1234 1235 1255 P G F 10 distorted distorted 1240 1256 1257 1258 ---------------------------------------------------------------------------------