ID code: '1YVP' 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 C 1 beta 4 10 7 32 C1' C C 2 beta 27 33 30 52 C1' IU C 3 beta 47 53 50 73 C1' G C 4 beta 68 74 71 96 C1' G C 5 beta 91 97 94 119 C1' U C 6 beta 114 120 117 139 C1' C C 7 beta 134 140 137 159 C1' C C 8 beta 154 160 157 179 C1' G C 9 beta 174 180 177 202 C1' A C 10 beta 197 203 200 222 C1' IU D 1 beta 217 223 220 243 C1' IU D 2 beta 238 244 241 264 C1' G D 3 beta 259 265 262 287 C1' A D 4 beta 282 288 285 309 C1' C D 5 beta 304 310 307 329 C1' IU D 6 beta 324 330 327 350 C1' A D 7 beta 345 351 348 372 C1' G D 8 beta 367 373 370 395 C1' C D 9 beta 390 396 393 415 C1' C D 10 beta 410 416 413 433 C1' G E 1 beta 428 434 431 456 C1' C E 2 beta 451 457 454 476 C1' IU E 3 beta 471 477 474 497 C1' G E 4 beta 492 498 495 520 C1' G E 5 beta 515 521 518 543 C1' U E 6 beta 538 544 541 563 C1' C E 7 beta 558 564 561 583 C1' C E 8 beta 578 584 581 603 C1' G E 9 beta 598 604 601 626 C1' A E 10 beta 621 627 624 646 C1' IU F 1 beta 641 647 644 667 C1' IU F 2 beta 662 668 665 688 C1' G F 3 beta 683 689 686 711 C1' A F 4 beta 706 712 709 733 C1' C F 5 beta 728 734 731 753 C1' IU F 6 beta 748 754 751 774 C1' A F 7 beta 769 775 772 796 C1' G F 8 beta 791 797 794 819 C1' C F 9 beta 814 820 817 839 C1' C F 10 beta 834 840 837 857 C1' U G 6 alpha 852 858 855 877 C1' C G 7 beta 872 878 875 897 C1' C G 8 beta 892 898 895 917 C1' G G 9 beta 912 918 915 940 C1' A G 10 beta 935 941 938 960 C1' G H 4 beta 955 961 958 983 C1' G H 5 beta 978 984 981 1006 C1' U H 6 beta 1001 1007 1004 1026 C1' C H 7 beta 1021 1027 1024 1046 C1' C H 8 beta 1041 1047 1044 1066 C1' G H 9 beta 1061 1067 1064 1089 C1' A H 10 beta 1084 1090 1087 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G C 1 OK 9 5 8 30 C2' C C 2 OK 32 28 31 50 C2' IU C 3 OK 52 48 51 71 C2' G C 4 OK 73 69 72 94 C2' G C 5 OK 96 92 95 117 C2' U C 6 OK 119 115 118 137 C2' C C 7 OK 139 135 138 157 C2' C C 8 OK 159 155 158 177 C2' G C 9 OK 179 175 178 200 C2' A C 10 OK 202 198 201 220 C2' IU D 1 OK 222 218 221 241 C2' IU D 2 OK 243 239 242 262 C2' G D 3 OK 264 260 263 285 C2' A D 4 OK 287 283 286 307 C2' C D 5 OK 309 305 308 327 C2' IU D 6 OK 329 325 328 348 C2' A D 7 OK 350 346 349 370 C2' G D 8 OK 372 368 371 393 C2' C D 9 OK 395 391 394 413 C2' C D 10 OK 415 411 414 431 C2' G E 1 OK 433 429 432 454 C2' C E 2 OK 456 452 455 474 C2' IU E 3 OK 476 472 475 495 C2' G E 4 OK 497 493 496 518 C2' G E 5 OK 520 516 519 541 C2' U E 6 OK 543 539 542 561 C2' C E 7 OK 563 559 562 581 C2' C E 8 OK 583 579 582 601 C2' G E 9 OK 603 599 602 624 C2' A E 10 OK 626 622 625 644 C2' IU F 1 OK 646 642 645 665 C2' IU F 2 OK 667 663 666 686 C2' G F 3 OK 688 684 687 709 C2' A F 4 OK 711 707 710 731 C2' C F 5 OK 733 729 732 751 C2' IU F 6 OK 753 749 752 772 C2' A F 7 OK 774 770 773 794 C2' G F 8 OK 796 792 795 817 C2' C F 9 OK 819 815 818 837 C2' C F 10 OK 839 835 838 855 C2' U G 6 OK 857 853 856 875 C2' C G 7 OK 877 873 876 895 C2' C G 8 OK 897 893 896 915 C2' G G 9 OK 917 913 916 938 C2' A G 10 OK 940 936 939 958 C2' G H 4 OK 960 956 959 981 C2' G H 5 OK 983 979 982 1004 C2' U H 6 OK 1006 1002 1005 1024 C2' C H 7 OK 1026 1022 1025 1044 C2' C H 8 OK 1046 1042 1045 1064 C2' G H 9 OK 1066 1062 1065 1087 C2' A H 10 OK 1089 1085 1088 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G C 1 OK 3 6 7 28 C3' C C 2 OK 26 29 30 48 C3' IU C 3 OK 46 49 50 69 C3' G C 4 OK 67 70 71 92 C3' G C 5 OK 90 93 94 115 C3' U C 6 OK 113 116 117 135 C3' C C 7 OK 133 136 137 155 C3' C C 8 OK 153 156 157 175 C3' G C 9 OK 173 176 177 198 C3' A C 10 OK 196 199 200 218 C3' IU D 1 OK 216 219 220 239 C3' IU D 2 OK 237 240 241 260 C3' G D 3 OK 258 261 262 283 C3' A D 4 OK 281 284 285 305 C3' C D 5 OK 303 306 307 325 C3' IU D 6 OK 323 326 327 346 C3' A D 7 OK 344 347 348 368 C3' G D 8 OK 366 369 370 391 C3' C D 9 OK 389 392 393 411 C3' C D 10 OK 409 412 413 429 C3' G E 1 OK 427 430 431 452 C3' C E 2 OK 450 453 454 472 C3' IU E 3 OK 470 473 474 493 C3' G E 4 OK 491 494 495 516 C3' G E 5 OK 514 517 518 539 C3' U E 6 OK 537 540 541 559 C3' C E 7 OK 557 560 561 579 C3' C E 8 OK 577 580 581 599 C3' G E 9 OK 597 600 601 622 C3' A E 10 OK 620 623 624 642 C3' IU F 1 OK 640 643 644 663 C3' IU F 2 OK 661 664 665 684 C3' G F 3 OK 682 685 686 707 C3' A F 4 OK 705 708 709 729 C3' C F 5 OK 727 730 731 749 C3' IU F 6 OK 747 750 751 770 C3' A F 7 OK 768 771 772 792 C3' G F 8 OK 790 793 794 815 C3' C F 9 OK 813 816 817 835 C3' C F 10 OK 833 836 837 853 C3' U G 6 OK 851 854 855 873 C3' C G 7 OK 871 874 875 893 C3' C G 8 OK 891 894 895 913 C3' G G 9 OK 911 914 915 936 C3' A G 10 OK 934 937 938 956 C3' G H 4 OK 954 957 958 979 C3' G H 5 OK 977 980 981 1002 C3' U H 6 OK 1000 1003 1004 1022 C3' C H 7 OK 1020 1023 1024 1042 C3' C H 8 OK 1040 1043 1044 1062 C3' G H 9 OK 1060 1063 1064 1085 C3' A H 10 OK 1083 1086 1087 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G C 1 OK 5 2 4 26 C4' C C 2 OK 28 25 27 46 C4' IU C 3 OK 48 45 47 67 C4' G C 4 OK 69 66 68 90 C4' G C 5 OK 92 89 91 113 C4' U C 6 OK 115 112 114 133 C4' C C 7 OK 135 132 134 153 C4' C C 8 OK 155 152 154 173 C4' G C 9 OK 175 172 174 196 C4' A C 10 OK 198 195 197 216 C4' IU D 1 OK 218 215 217 237 C4' IU D 2 OK 239 236 238 258 C4' G D 3 OK 260 257 259 281 C4' A D 4 OK 283 280 282 303 C4' C D 5 OK 305 302 304 323 C4' IU D 6 OK 325 322 324 344 C4' A D 7 OK 346 343 345 366 C4' G D 8 OK 368 365 367 389 C4' C D 9 OK 391 388 390 409 C4' C D 10 OK 411 408 410 427 C4' G E 1 OK 429 426 428 450 C4' C E 2 OK 452 449 451 470 C4' IU E 3 OK 472 469 471 491 C4' G E 4 OK 493 490 492 514 C4' G E 5 OK 516 513 515 537 C4' U E 6 OK 539 536 538 557 C4' C E 7 OK 559 556 558 577 C4' C E 8 OK 579 576 578 597 C4' G E 9 OK 599 596 598 620 C4' A E 10 OK 622 619 621 640 C4' IU F 1 OK 642 639 641 661 C4' IU F 2 OK 663 660 662 682 C4' G F 3 OK 684 681 683 705 C4' A F 4 OK 707 704 706 727 C4' C F 5 OK 729 726 728 747 C4' IU F 6 OK 749 746 748 768 C4' A F 7 OK 770 767 769 790 C4' G F 8 OK 792 789 791 813 C4' C F 9 OK 815 812 814 833 C4' C F 10 OK 835 832 834 851 C4' U G 6 OK 853 850 852 871 C4' C G 7 OK 873 870 872 891 C4' C G 8 OK 893 890 892 911 C4' G G 9 OK 913 910 912 934 C4' A G 10 OK 936 933 935 954 C4' G H 4 OK 956 953 955 977 C4' G H 5 OK 979 976 978 1000 C4' U H 6 OK 1002 999 1001 1020 C4' C H 7 OK 1022 1019 1021 1040 C4' C H 8 OK 1042 1039 1041 1060 C4' G H 9 OK 1062 1059 1061 1083 C4' A H 10 OK 1085 1082 1084 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G C 1 1 3 25 C5' C C 2 24 26 45 C5' IU C 3 44 46 66 C5' G C 4 65 67 89 C5' G C 5 88 90 112 C5' U C 6 111 113 132 C5' C C 7 131 133 152 C5' C C 8 151 153 172 C5' G C 9 171 173 195 C5' A C 10 194 196 215 C5' IU D 1 214 216 236 C5' IU D 2 235 237 257 C5' G D 3 256 258 280 C5' A D 4 279 281 302 C5' C D 5 301 303 322 C5' IU D 6 321 323 343 C5' A D 7 342 344 365 C5' G D 8 364 366 388 C5' C D 9 387 389 408 C5' C D 10 407 409 426 C5' G E 1 425 427 449 C5' C E 2 448 450 469 C5' IU E 3 468 470 490 C5' G E 4 489 491 513 C5' G E 5 512 514 536 C5' U E 6 535 537 556 C5' C E 7 555 557 576 C5' C E 8 575 577 596 C5' G E 9 595 597 619 C5' A E 10 618 620 639 C5' IU F 1 638 640 660 C5' IU F 2 659 661 681 C5' G F 3 680 682 704 C5' A F 4 703 705 726 C5' C F 5 725 727 746 C5' IU F 6 745 747 767 C5' A F 7 766 768 789 C5' G F 8 788 790 812 C5' C F 9 811 813 832 C5' C F 10 831 833 850 C5' U G 6 849 851 870 C5' C G 7 869 871 890 C5' C G 8 889 891 910 C5' G G 9 909 911 933 C5' A G 10 932 934 953 C5' G H 4 952 954 976 C5' G H 5 975 977 999 C5' U H 6 998 1000 1019 C5' C H 7 1018 1020 1039 C5' C H 8 1038 1040 1059 C5' G H 9 1058 1060 1082 C5' A H 10 1081 1083 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P C C 2 distorted distorted 6 22 23 24 41 P IU C 3 distorted distorted 29 42 43 44 62 P G C 4 distorted distorted 49 63 64 65 85 P G C 5 distorted distorted 70 86 87 88 108 P U C 6 distorted distorted 93 109 110 111 128 P C C 7 distorted distorted 116 129 130 131 148 P C C 8 distorted distorted 136 149 150 151 168 P G C 9 distorted distorted 156 169 170 171 191 P A C 10 distorted distorted 176 192 193 194 232 P IU D 2 distorted distorted 219 233 234 235 253 P G D 3 distorted distorted 240 254 255 256 276 P A D 4 distorted distorted 261 277 278 279 298 P C D 5 distorted distorted 284 299 300 301 318 P IU D 6 distorted distorted 306 319 320 321 339 P A D 7 distorted distorted 326 340 341 342 361 P G D 8 distorted distorted 347 362 363 364 384 P C D 9 distorted distorted 369 385 386 387 404 P C D 10 distorted distorted 392 405 406 407 445 P C E 2 distorted distorted 430 446 447 448 465 P IU E 3 distorted distorted 453 466 467 468 486 P G E 4 distorted distorted 473 487 488 489 509 P G E 5 distorted distorted 494 510 511 512 532 P U E 6 distorted distorted 517 533 534 535 552 P C E 7 distorted distorted 540 553 554 555 572 P C E 8 distorted distorted 560 573 574 575 592 P G E 9 distorted distorted 580 593 594 595 615 P A E 10 distorted distorted 600 616 617 618 656 P IU F 2 distorted distorted 643 657 658 659 677 P G F 3 distorted distorted 664 678 679 680 700 P A F 4 distorted distorted 685 701 702 703 722 P C F 5 distorted distorted 708 723 724 725 742 P IU F 6 distorted distorted 730 743 744 745 763 P A F 7 distorted distorted 750 764 765 766 785 P G F 8 distorted distorted 771 786 787 788 808 P C F 9 distorted distorted 793 809 810 811 828 P C F 10 distorted distorted 816 829 830 831 866 P C G 7 distorted distorted 854 867 868 869 886 P C G 8 distorted distorted 874 887 888 889 906 P G G 9 distorted distorted 894 907 908 909 929 P A G 10 distorted distorted 914 930 931 932 972 P G H 5 distorted distorted 957 973 974 975 995 P U H 6 distorted distorted 980 996 997 998 1015 P C H 7 distorted distorted 1003 1016 1017 1018 1035 P C H 8 distorted distorted 1023 1036 1037 1038 1055 P G H 9 distorted distorted 1043 1056 1057 1058 1078 P A H 10 distorted distorted 1063 1079 1080 1081 ---------------------------------------------------------------------------------