ID code: '2L1V' 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' A A 3 alpha beta 73 95 79 76 111 C1' G A 4 alpha beta 106 129 112 109 145 C1' A A 5 alpha beta 140 162 146 143 178 C1' G A 6 alpha beta 173 196 179 176 212 C1' G A 7 alpha beta 207 230 213 210 246 C1' U A 8 alpha beta 241 261 247 244 276 C1' U A 9 alpha beta 271 291 277 274 306 C1' C A 10 alpha beta 301 321 307 304 337 C1' U A 11 alpha beta 332 352 338 335 367 C1' A A 12 alpha beta 362 384 368 365 400 C1' G A 13 alpha beta 395 418 401 398 434 C1' U A 14 alpha beta 429 449 435 432 464 C1' U A 15 alpha beta 459 479 465 462 494 C1' A A 16 alpha beta 489 511 495 492 527 C1' U A 17 alpha beta 522 542 528 525 557 C1' A A 18 alpha beta 552 574 558 555 590 C1' C A 19 alpha beta 585 605 591 588 621 C1' C A 20 alpha beta 616 636 622 619 652 C1' C A 21 alpha beta 647 667 653 650 683 C1' U A 22 alpha beta 678 698 684 681 713 C1' C A 23 alpha beta 708 728 714 711 744 C1' U A 24 alpha beta 739 759 745 742 774 C1' A A 25 alpha beta 769 791 775 772 807 C1' U A 26 alpha beta 802 822 808 805 837 C1' A A 27 alpha beta 832 854 838 835 870 C1' A A 28 alpha beta 865 887 871 868 903 C1' A A 29 alpha beta 898 920 904 901 936 C1' A A 30 alpha beta 931 953 937 934 969 C1' A A 31 alpha beta 964 986 970 967 1002 C1' A A 32 alpha beta 997 1019 1003 1000 1035 C1' C A 33 alpha beta 1030 1050 1036 1033 1066 C1' U A 34 alpha beta 1061 1081 1067 1064 1096 C1' A A 35 alpha beta 1091 1113 1097 1094 1129 C1' A A 36 alpha beta 1124 1147 1130 1127 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 3 OK OK 78 74 93 77 109 C2' G A 4 OK OK 111 107 127 110 143 C2' A A 5 OK OK 145 141 160 144 176 C2' G A 6 OK OK 178 174 194 177 210 C2' G A 7 OK OK 212 208 228 211 244 C2' U A 8 OK OK 246 242 259 245 274 C2' U A 9 OK OK 276 272 289 275 304 C2' C A 10 OK OK 306 302 319 305 335 C2' U A 11 OK OK 337 333 350 336 365 C2' A A 12 OK OK 367 363 382 366 398 C2' G A 13 OK OK 400 396 416 399 432 C2' U A 14 OK OK 434 430 447 433 462 C2' U A 15 OK OK 464 460 477 463 492 C2' A A 16 OK OK 494 490 509 493 525 C2' U A 17 OK OK 527 523 540 526 555 C2' A A 18 OK OK 557 553 572 556 588 C2' C A 19 OK OK 590 586 603 589 619 C2' C A 20 OK OK 621 617 634 620 650 C2' C A 21 OK OK 652 648 665 651 681 C2' U A 22 OK OK 683 679 696 682 711 C2' C A 23 OK OK 713 709 726 712 742 C2' U A 24 OK OK 744 740 757 743 772 C2' A A 25 OK OK 774 770 789 773 805 C2' U A 26 OK OK 807 803 820 806 835 C2' A A 27 OK OK 837 833 852 836 868 C2' A A 28 OK OK 870 866 885 869 901 C2' A A 29 OK OK 903 899 918 902 934 C2' A A 30 OK OK 936 932 951 935 967 C2' A A 31 OK OK 969 965 984 968 1000 C2' A A 32 OK OK 1002 998 1017 1001 1033 C2' C A 33 OK OK 1035 1031 1048 1034 1064 C2' U A 34 OK OK 1066 1062 1079 1065 1094 C2' A A 35 OK OK 1096 1092 1111 1095 1127 C2' A A 36 OK OK 1129 1125 1145 1128 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 72 92 75 76 107 C3' G A 4 OK OK 105 126 108 109 141 C3' A A 5 OK OK 139 159 142 143 174 C3' G A 6 OK OK 172 193 175 176 208 C3' G A 7 OK OK 206 227 209 210 242 C3' U A 8 OK OK 240 258 243 244 272 C3' U A 9 OK OK 270 288 273 274 302 C3' C A 10 OK OK 300 318 303 304 333 C3' U A 11 OK OK 331 349 334 335 363 C3' A A 12 OK OK 361 381 364 365 396 C3' G A 13 OK OK 394 415 397 398 430 C3' U A 14 OK OK 428 446 431 432 460 C3' U A 15 OK OK 458 476 461 462 490 C3' A A 16 OK OK 488 508 491 492 523 C3' U A 17 OK OK 521 539 524 525 553 C3' A A 18 OK OK 551 571 554 555 586 C3' C A 19 OK OK 584 602 587 588 617 C3' C A 20 OK OK 615 633 618 619 648 C3' C A 21 OK OK 646 664 649 650 679 C3' U A 22 OK OK 677 695 680 681 709 C3' C A 23 OK OK 707 725 710 711 740 C3' U A 24 OK OK 738 756 741 742 770 C3' A A 25 OK OK 768 788 771 772 803 C3' U A 26 OK OK 801 819 804 805 833 C3' A A 27 OK OK 831 851 834 835 866 C3' A A 28 OK OK 864 884 867 868 899 C3' A A 29 OK OK 897 917 900 901 932 C3' A A 30 OK OK 930 950 933 934 965 C3' A A 31 OK OK 963 983 966 967 998 C3' A A 32 OK OK 996 1016 999 1000 1031 C3' C A 33 OK OK 1029 1047 1032 1033 1062 C3' U A 34 OK OK 1060 1078 1063 1064 1092 C3' A A 35 OK OK 1090 1110 1093 1094 1125 C3' A A 36 OK OK 1123 1143 1126 1127 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 74 91 71 73 105 C4' G A 4 OK OK 107 125 104 106 139 C4' A A 5 OK OK 141 158 138 140 172 C4' G A 6 OK OK 174 192 171 173 206 C4' G A 7 OK OK 208 226 205 207 240 C4' U A 8 OK OK 242 257 239 241 270 C4' U A 9 OK OK 272 287 269 271 300 C4' C A 10 OK OK 302 317 299 301 331 C4' U A 11 OK OK 333 348 330 332 361 C4' A A 12 OK OK 363 380 360 362 394 C4' G A 13 OK OK 396 414 393 395 428 C4' U A 14 OK OK 430 445 427 429 458 C4' U A 15 OK OK 460 475 457 459 488 C4' A A 16 OK OK 490 507 487 489 521 C4' U A 17 OK OK 523 538 520 522 551 C4' A A 18 OK OK 553 570 550 552 584 C4' C A 19 OK OK 586 601 583 585 615 C4' C A 20 OK OK 617 632 614 616 646 C4' C A 21 OK OK 648 663 645 647 677 C4' U A 22 OK OK 679 694 676 678 707 C4' C A 23 OK OK 709 724 706 708 738 C4' U A 24 OK OK 740 755 737 739 768 C4' A A 25 OK OK 770 787 767 769 801 C4' U A 26 OK OK 803 818 800 802 831 C4' A A 27 OK OK 833 850 830 832 864 C4' A A 28 OK OK 866 883 863 865 897 C4' A A 29 OK OK 899 916 896 898 930 C4' A A 30 OK OK 932 949 929 931 963 C4' A A 31 OK OK 965 982 962 964 996 C4' A A 32 OK OK 998 1015 995 997 1029 C4' C A 33 OK OK 1031 1046 1028 1030 1060 C4' U A 34 OK OK 1062 1077 1059 1061 1090 C4' A A 35 OK OK 1092 1109 1089 1091 1123 C4' A A 36 OK OK 1125 1142 1122 1124 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 3 OK OK 70 89 90 72 104 C5' G A 4 OK OK 103 123 124 105 138 C5' A A 5 OK OK 137 156 157 139 171 C5' G A 6 OK OK 170 190 191 172 205 C5' G A 7 OK OK 204 224 225 206 239 C5' U A 8 OK OK 238 255 256 240 269 C5' U A 9 OK OK 268 285 286 270 299 C5' C A 10 OK OK 298 315 316 300 330 C5' U A 11 OK OK 329 346 347 331 360 C5' A A 12 OK OK 359 378 379 361 393 C5' G A 13 OK OK 392 412 413 394 427 C5' U A 14 OK OK 426 443 444 428 457 C5' U A 15 OK OK 456 473 474 458 487 C5' A A 16 OK OK 486 505 506 488 520 C5' U A 17 OK OK 519 536 537 521 550 C5' A A 18 OK OK 549 568 569 551 583 C5' C A 19 OK OK 582 599 600 584 614 C5' C A 20 OK OK 613 630 631 615 645 C5' C A 21 OK OK 644 661 662 646 676 C5' U A 22 OK OK 675 692 693 677 706 C5' C A 23 OK OK 705 722 723 707 737 C5' U A 24 OK OK 736 753 754 738 767 C5' A A 25 OK OK 766 785 786 768 800 C5' U A 26 OK OK 799 816 817 801 830 C5' A A 27 OK OK 829 848 849 831 863 C5' A A 28 OK OK 862 881 882 864 896 C5' A A 29 OK OK 895 914 915 897 929 C5' A A 30 OK OK 928 947 948 930 962 C5' A A 31 OK OK 961 980 981 963 995 C5' A A 32 OK OK 994 1013 1014 996 1028 C5' C A 33 OK OK 1027 1044 1045 1029 1059 C5' U A 34 OK OK 1058 1075 1076 1060 1089 C5' A A 35 OK OK 1088 1107 1108 1090 1122 C5' A A 36 OK OK 1121 1140 1141 1123 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P A A 3 distorted distorted 41 68 69 70 100 P G A 4 distorted distorted 75 101 102 103 134 P A A 5 distorted distorted 108 135 136 137 167 P G A 6 distorted distorted 142 168 169 170 201 P G A 7 distorted distorted 175 202 203 204 235 P U A 8 distorted distorted 209 236 237 238 265 P U A 9 distorted distorted 243 266 267 268 295 P C A 10 distorted distorted 273 296 297 298 326 P U A 11 distorted distorted 303 327 328 329 356 P A A 12 distorted distorted 334 357 358 359 389 P G A 13 distorted distorted 364 390 391 392 423 P U A 14 distorted distorted 397 424 425 426 453 P U A 15 distorted distorted 431 454 455 456 483 P A A 16 distorted distorted 461 484 485 486 516 P U A 17 distorted distorted 491 517 518 519 546 P A A 18 distorted distorted 524 547 548 549 579 P C A 19 distorted distorted 554 580 581 582 610 P C A 20 distorted distorted 587 611 612 613 641 P C A 21 distorted distorted 618 642 643 644 672 P U A 22 distorted distorted 649 673 674 675 702 P C A 23 distorted distorted 680 703 704 705 733 P U A 24 distorted distorted 710 734 735 736 763 P A A 25 distorted distorted 741 764 765 766 796 P U A 26 distorted distorted 771 797 798 799 826 P A A 27 distorted distorted 804 827 828 829 859 P A A 28 distorted distorted 834 860 861 862 892 P A A 29 distorted distorted 867 893 894 895 925 P A A 30 distorted distorted 900 926 927 928 958 P A A 31 distorted distorted 933 959 960 961 991 P A A 32 distorted distorted 966 992 993 994 1024 P C A 33 distorted distorted 999 1025 1026 1027 1055 P U A 34 distorted distorted 1032 1056 1057 1058 1085 P A A 35 distorted distorted 1063 1086 1087 1088 1118 P A A 36 distorted distorted 1093 1119 1120 1121 ---------------------------------------------------------------------------------