ID code: '4O41' 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' --------------------------------------------------------------------------------- 12 C1' G A 102 beta 7 13 10 35 C1' A A 103 beta 30 36 33 57 C1' G A 104 beta 52 58 55 80 C1' C A 105 beta 75 81 78 98 C1' URU A 106 beta 99 100 96 139 C1' C A 108 beta 134 140 137 159 C1' G A 109 beta 154 160 157 182 C1' G A 110 beta 177 183 180 205 C1' C A 111 beta 200 206 203 225 C1' U A 112 beta 220 226 223 245 C1' C A 113 beta 240 246 243 263 C1' U B 201 beta 258 264 261 283 C1' G B 202 beta 278 284 281 306 C1' A B 203 beta 301 307 304 414 C1' URU B 206 beta 415 416 412 460 C1' C B 208 beta 455 461 458 480 C1' G B 209 beta 475 481 478 503 C1' G B 210 beta 498 504 501 526 C1' C B 211 beta 521 527 524 546 C1' U B 212 beta 541 547 544 566 C1' C B 213 beta 561 567 564 587 C1' G C 302 beta 582 588 585 610 C1' A C 303 beta 605 611 608 632 C1' G C 304 beta 627 633 630 655 C1' C C 305 beta 650 656 653 673 C1' URU C 306 beta 674 675 671 714 C1' C C 308 beta 709 715 712 734 C1' G C 309 beta 729 735 732 757 C1' G C 310 beta 752 758 755 780 C1' C C 311 beta 775 781 778 800 C1' U C 312 beta 795 801 798 820 C1' C C 313 beta 815 821 818 841 C1' G D 402 beta 836 842 839 864 C1' A D 403 beta 859 865 862 886 C1' G D 404 beta 881 887 884 909 C1' C D 405 beta 904 910 907 927 C1' URU D 406 beta 928 929 925 968 C1' C D 408 beta 963 969 966 988 C1' G D 409 beta 983 989 986 1011 C1' G D 410 beta 1006 1012 1009 1034 C1' C D 411 beta 1029 1035 1032 1054 C1' U D 412 beta 1049 1055 1052 1074 C1' C D 413 beta 1069 1075 1072 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 102 OK 12 8 11 33 C2' A A 103 OK 35 31 34 55 C2' G A 104 OK 57 53 56 78 C2' C A 105 OK 80 76 79 96 C2' URU A 106 OK 98 94 97 137 C2' C A 108 OK 139 135 138 157 C2' G A 109 OK 159 155 158 180 C2' G A 110 OK 182 178 181 203 C2' C A 111 OK 205 201 204 223 C2' U A 112 OK 225 221 224 243 C2' C A 113 OK 245 241 244 261 C2' U B 201 OK 263 259 262 281 C2' G B 202 OK 283 279 282 304 C2' A B 203 OK 306 302 305 412 C2' URU B 206 OK 414 410 413 458 C2' C B 208 OK 460 456 459 478 C2' G B 209 OK 480 476 479 501 C2' G B 210 OK 503 499 502 524 C2' C B 211 OK 526 522 525 544 C2' U B 212 OK 546 542 545 564 C2' C B 213 OK 566 562 565 585 C2' G C 302 OK 587 583 586 608 C2' A C 303 OK 610 606 609 630 C2' G C 304 OK 632 628 631 653 C2' C C 305 OK 655 651 654 671 C2' URU C 306 OK 673 669 672 712 C2' C C 308 OK 714 710 713 732 C2' G C 309 OK 734 730 733 755 C2' G C 310 OK 757 753 756 778 C2' C C 311 OK 780 776 779 798 C2' U C 312 OK 800 796 799 818 C2' C C 313 OK 820 816 819 839 C2' G D 402 OK 841 837 840 862 C2' A D 403 OK 864 860 863 884 C2' G D 404 OK 886 882 885 907 C2' C D 405 OK 909 905 908 925 C2' URU D 406 OK 927 923 926 966 C2' C D 408 OK 968 964 967 986 C2' G D 409 OK 988 984 987 1009 C2' G D 410 OK 1011 1007 1010 1032 C2' C D 411 OK 1034 1030 1033 1052 C2' U D 412 OK 1054 1050 1053 1072 C2' C D 413 OK 1074 1070 1073 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 102 OK 6 9 10 31 C3' A A 103 OK 29 32 33 53 C3' G A 104 OK 51 54 55 76 C3' C A 105 OK 74 77 78 94 C3' URU A 106 93 96 135 C3' C A 108 OK 133 136 137 155 C3' G A 109 OK 153 156 157 178 C3' G A 110 OK 176 179 180 201 C3' C A 111 OK 199 202 203 221 C3' U A 112 OK 219 222 223 241 C3' C A 113 OK 239 242 243 259 C3' U B 201 OK 257 260 261 279 C3' G B 202 OK 277 280 281 302 C3' A B 203 OK 300 303 304 410 C3' URU B 206 409 412 456 C3' C B 208 OK 454 457 458 476 C3' G B 209 OK 474 477 478 499 C3' G B 210 OK 497 500 501 522 C3' C B 211 OK 520 523 524 542 C3' U B 212 OK 540 543 544 562 C3' C B 213 OK 560 563 564 583 C3' G C 302 OK 581 584 585 606 C3' A C 303 OK 604 607 608 628 C3' G C 304 OK 626 629 630 651 C3' C C 305 OK 649 652 653 669 C3' URU C 306 668 671 710 C3' C C 308 OK 708 711 712 730 C3' G C 309 OK 728 731 732 753 C3' G C 310 OK 751 754 755 776 C3' C C 311 OK 774 777 778 796 C3' U C 312 OK 794 797 798 816 C3' C C 313 OK 814 817 818 837 C3' G D 402 OK 835 838 839 860 C3' A D 403 OK 858 861 862 882 C3' G D 404 OK 880 883 884 905 C3' C D 405 OK 903 906 907 923 C3' URU D 406 922 925 964 C3' C D 408 OK 962 965 966 984 C3' G D 409 OK 982 985 986 1007 C3' G D 410 OK 1005 1008 1009 1030 C3' C D 411 OK 1028 1031 1032 1050 C3' U D 412 OK 1048 1051 1052 1070 C3' C D 413 OK 1068 1071 1072 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 102 OK 8 5 7 29 C4' A A 103 OK 31 28 30 51 C4' G A 104 OK 53 50 52 74 C4' C A 105 OK 76 73 75 93 C4' URU A 106 OK 94 92 99 133 C4' C A 108 OK 135 132 134 153 C4' G A 109 OK 155 152 154 176 C4' G A 110 OK 178 175 177 199 C4' C A 111 OK 201 198 200 219 C4' U A 112 OK 221 218 220 239 C4' C A 113 OK 241 238 240 257 C4' U B 201 OK 259 256 258 277 C4' G B 202 OK 279 276 278 300 C4' A B 203 OK 302 299 301 409 C4' URU B 206 OK 410 408 415 454 C4' C B 208 OK 456 453 455 474 C4' G B 209 OK 476 473 475 497 C4' G B 210 OK 499 496 498 520 C4' C B 211 OK 522 519 521 540 C4' U B 212 OK 542 539 541 560 C4' C B 213 OK 562 559 561 581 C4' G C 302 OK 583 580 582 604 C4' A C 303 OK 606 603 605 626 C4' G C 304 OK 628 625 627 649 C4' C C 305 OK 651 648 650 668 C4' URU C 306 OK 669 667 674 708 C4' C C 308 OK 710 707 709 728 C4' G C 309 OK 730 727 729 751 C4' G C 310 OK 753 750 752 774 C4' C C 311 OK 776 773 775 794 C4' U C 312 OK 796 793 795 814 C4' C C 313 OK 816 813 815 835 C4' G D 402 OK 837 834 836 858 C4' A D 403 OK 860 857 859 880 C4' G D 404 OK 882 879 881 903 C4' C D 405 OK 905 902 904 922 C4' URU D 406 OK 923 921 928 962 C4' C D 408 OK 964 961 963 982 C4' G D 409 OK 984 981 983 1005 C4' G D 410 OK 1007 1004 1006 1028 C4' C D 411 OK 1030 1027 1029 1048 C4' U D 412 OK 1050 1047 1049 1068 C4' C D 413 OK 1070 1067 1069 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 102 4 6 28 C5' A A 103 27 29 50 C5' G A 104 49 51 73 C5' C A 105 72 74 92 C5' URU A 106 91 93 132 C5' C A 108 131 133 152 C5' G A 109 151 153 175 C5' G A 110 174 176 198 C5' C A 111 197 199 218 C5' U A 112 217 219 238 C5' C A 113 237 239 256 C5' U B 201 255 257 276 C5' G B 202 275 277 299 C5' A B 203 298 300 408 C5' URU B 206 407 409 453 C5' C B 208 452 454 473 C5' G B 209 472 474 496 C5' G B 210 495 497 519 C5' C B 211 518 520 539 C5' U B 212 538 540 559 C5' C B 213 558 560 580 C5' G C 302 579 581 603 C5' A C 303 602 604 625 C5' G C 304 624 626 648 C5' C C 305 647 649 667 C5' URU C 306 666 668 707 C5' C C 308 706 708 727 C5' G C 309 726 728 750 C5' G C 310 749 751 773 C5' C C 311 772 774 793 C5' U C 312 792 794 813 C5' C C 313 812 814 834 C5' G D 402 833 835 857 C5' A D 403 856 858 879 C5' G D 404 878 880 902 C5' C D 405 901 903 921 C5' URU D 406 920 922 961 C5' C D 408 960 962 981 C5' G D 409 980 982 1004 C5' G D 410 1003 1005 1027 C5' C D 411 1026 1028 1047 C5' U D 412 1046 1048 1067 C5' C D 413 1066 1068 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 102 distorted distorted 2 3 4 24 P A A 103 distorted distorted 9 25 26 27 46 P G A 104 distorted distorted 32 47 48 49 69 P C A 105 distorted distorted 54 70 71 72 89 P URU A 106 distorted distorted 77 90 108 91 128 P C A 108 distorted distorted 129 130 131 148 P G A 109 distorted distorted 136 149 150 151 171 P G A 110 distorted distorted 156 172 173 174 194 P C A 111 distorted distorted 179 195 196 197 214 P U A 112 distorted distorted 202 215 216 217 234 P C A 113 distorted distorted 222 235 236 237 272 P G B 202 distorted distorted 260 273 274 275 295 P A B 203 distorted distorted 280 296 297 298 317 P G B 204 303 318 P G B 204 303 363 P C B 205 364 P C B 205 403 P URU B 206 407 404 P URU B 206 407 449 P C B 208 distorted distorted 450 451 452 469 P G B 209 distorted distorted 457 470 471 472 492 P G B 210 distorted distorted 477 493 494 495 515 P C B 211 distorted distorted 500 516 517 518 535 P U B 212 distorted distorted 523 536 537 538 555 P C B 213 distorted distorted 543 556 557 558 576 P G C 302 distorted distorted 577 578 579 599 P A C 303 distorted distorted 584 600 601 602 621 P G C 304 distorted distorted 607 622 623 624 644 P C C 305 distorted distorted 629 645 646 647 664 P URU C 306 distorted distorted 652 665 683 666 703 P C C 308 distorted distorted 704 705 706 723 P G C 309 distorted distorted 711 724 725 726 746 P G C 310 distorted distorted 731 747 748 749 769 P C C 311 distorted distorted 754 770 771 772 789 P U C 312 distorted distorted 777 790 791 792 809 P C C 313 distorted distorted 797 810 811 812 830 P G D 402 distorted distorted 831 832 833 853 P A D 403 distorted distorted 838 854 855 856 875 P G D 404 distorted distorted 861 876 877 878 898 P C D 405 distorted distorted 883 899 900 901 918 P URU D 406 distorted distorted 906 919 937 920 957 P C D 408 distorted distorted 958 959 960 977 P G D 409 distorted distorted 965 978 979 980 1000 P G D 410 distorted distorted 985 1001 1002 1003 1023 P C D 411 distorted distorted 1008 1024 1025 1026 1043 P U D 412 distorted distorted 1031 1044 1045 1046 1063 P C D 413 distorted distorted 1051 1064 1065 1066 ---------------------------------------------------------------------------------