ID code: '2KYD' 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 alpha beta 4 24 10 7 41 C1' U A 2 alpha beta 36 56 42 39 71 C1' A A 3 alpha beta 66 88 72 69 104 C1' G A 4 alpha beta 99 122 105 102 138 C1' U A 5 alpha beta 133 153 139 136 168 C1' U A 6 alpha beta 163 183 169 166 198 C1' A A 7 alpha beta 193 215 199 196 231 C1' G A 8 alpha beta 226 249 232 229 265 C1' C A 9 alpha beta 260 280 266 263 296 C1' U A 10 alpha beta 291 311 297 294 326 C1' A A 11 alpha beta 321 343 327 324 359 C1' A A 12 alpha beta 354 376 360 357 392 C1' C A 13 alpha beta 387 407 393 390 423 C1' U A 14 alpha beta 418 438 424 421 453 C1' A A 15 alpha beta 448 470 454 451 486 C1' G A 16 alpha beta 481 505 487 484 519 C1' C B 17 alpha beta 514 534 520 517 551 C1' U B 18 alpha beta 546 566 552 549 581 C1' A B 19 alpha beta 576 598 582 579 614 C1' G B 20 alpha beta 609 632 615 612 648 C1' U B 21 alpha beta 643 663 649 646 678 C1' U B 22 alpha beta 673 693 679 676 708 C1' A B 23 alpha beta 703 725 709 706 741 C1' G B 24 alpha beta 736 759 742 739 775 C1' C B 25 alpha beta 770 790 776 773 806 C1' U B 26 alpha beta 801 821 807 804 836 C1' A B 27 alpha beta 831 853 837 834 869 C1' A B 28 alpha beta 864 886 870 867 902 C1' C B 29 alpha beta 897 917 903 900 933 C1' U B 30 alpha beta 928 948 934 931 963 C1' A B 31 alpha beta 958 980 964 961 996 C1' G B 32 alpha beta 991 1015 997 994 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 OK 9 5 22 8 39 C2' U A 2 OK OK 41 37 54 40 69 C2' A A 3 OK OK 71 67 86 70 102 C2' G A 4 OK OK 104 100 120 103 136 C2' U A 5 OK OK 138 134 151 137 166 C2' U A 6 OK OK 168 164 181 167 196 C2' A A 7 OK OK 198 194 213 197 229 C2' G A 8 OK OK 231 227 247 230 263 C2' C A 9 OK OK 265 261 278 264 294 C2' U A 10 OK OK 296 292 309 295 324 C2' A A 11 OK OK 326 322 341 325 357 C2' A A 12 OK OK 359 355 374 358 390 C2' C A 13 OK OK 392 388 405 391 421 C2' U A 14 OK OK 423 419 436 422 451 C2' A A 15 OK OK 453 449 468 452 484 C2' G A 16 OK OK 486 482 503 485 517 C2' C B 17 OK OK 519 515 532 518 549 C2' U B 18 OK OK 551 547 564 550 579 C2' A B 19 OK OK 581 577 596 580 612 C2' G B 20 OK OK 614 610 630 613 646 C2' U B 21 OK OK 648 644 661 647 676 C2' U B 22 OK OK 678 674 691 677 706 C2' A B 23 OK OK 708 704 723 707 739 C2' G B 24 OK OK 741 737 757 740 773 C2' C B 25 OK OK 775 771 788 774 804 C2' U B 26 OK OK 806 802 819 805 834 C2' A B 27 OK OK 836 832 851 835 867 C2' A B 28 OK OK 869 865 884 868 900 C2' C B 29 OK OK 902 898 915 901 931 C2' U B 30 OK OK 933 929 946 932 961 C2' A B 31 OK OK 963 959 978 962 994 C2' G B 32 OK OK 996 992 1013 995 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK OK 3 21 6 7 37 C3' U A 2 OK OK 35 53 38 39 67 C3' A A 3 OK OK 65 85 68 69 100 C3' G A 4 OK OK 98 119 101 102 134 C3' U A 5 OK OK 132 150 135 136 164 C3' U A 6 OK OK 162 180 165 166 194 C3' A A 7 OK OK 192 212 195 196 227 C3' G A 8 OK OK 225 246 228 229 261 C3' C A 9 OK OK 259 277 262 263 292 C3' U A 10 OK OK 290 308 293 294 322 C3' A A 11 OK OK 320 340 323 324 355 C3' A A 12 OK OK 353 373 356 357 388 C3' C A 13 OK OK 386 404 389 390 419 C3' U A 14 OK OK 417 435 420 421 449 C3' A A 15 OK OK 447 467 450 451 482 C3' G A 16 OK OK 480 501 483 484 515 C3' C B 17 OK OK 513 531 516 517 547 C3' U B 18 OK OK 545 563 548 549 577 C3' A B 19 OK OK 575 595 578 579 610 C3' G B 20 OK OK 608 629 611 612 644 C3' U B 21 OK OK 642 660 645 646 674 C3' U B 22 OK OK 672 690 675 676 704 C3' A B 23 OK OK 702 722 705 706 737 C3' G B 24 OK OK 735 756 738 739 771 C3' C B 25 OK OK 769 787 772 773 802 C3' U B 26 OK OK 800 818 803 804 832 C3' A B 27 OK OK 830 850 833 834 865 C3' A B 28 OK OK 863 883 866 867 898 C3' C B 29 OK OK 896 914 899 900 929 C3' U B 30 OK OK 927 945 930 931 959 C3' A B 31 OK OK 957 977 960 961 992 C3' G B 32 OK OK 990 1011 993 994 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK OK 5 20 2 4 35 C4' U A 2 OK OK 37 52 34 36 65 C4' A A 3 OK OK 67 84 64 66 98 C4' G A 4 OK OK 100 118 97 99 132 C4' U A 5 OK OK 134 149 131 133 162 C4' U A 6 OK OK 164 179 161 163 192 C4' A A 7 OK OK 194 211 191 193 225 C4' G A 8 OK OK 227 245 224 226 259 C4' C A 9 OK OK 261 276 258 260 290 C4' U A 10 OK OK 292 307 289 291 320 C4' A A 11 OK OK 322 339 319 321 353 C4' A A 12 OK OK 355 372 352 354 386 C4' C A 13 OK OK 388 403 385 387 417 C4' U A 14 OK OK 419 434 416 418 447 C4' A A 15 OK OK 449 466 446 448 480 C4' G A 16 OK OK 482 500 479 481 513 C4' C B 17 OK OK 515 530 512 514 545 C4' U B 18 OK OK 547 562 544 546 575 C4' A B 19 OK OK 577 594 574 576 608 C4' G B 20 OK OK 610 628 607 609 642 C4' U B 21 OK OK 644 659 641 643 672 C4' U B 22 OK OK 674 689 671 673 702 C4' A B 23 OK OK 704 721 701 703 735 C4' G B 24 OK OK 737 755 734 736 769 C4' C B 25 OK OK 771 786 768 770 800 C4' U B 26 OK OK 802 817 799 801 830 C4' A B 27 OK OK 832 849 829 831 863 C4' A B 28 OK OK 865 882 862 864 896 C4' C B 29 OK OK 898 913 895 897 927 C4' U B 30 OK OK 929 944 926 928 957 C4' A B 31 OK OK 959 976 956 958 990 C4' G B 32 OK OK 992 1010 989 991 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 OK OK 1 18 19 3 34 C5' U A 2 OK OK 33 50 51 35 64 C5' A A 3 OK OK 63 82 83 65 97 C5' G A 4 OK OK 96 116 117 98 131 C5' U A 5 OK OK 130 147 148 132 161 C5' U A 6 OK OK 160 177 178 162 191 C5' A A 7 OK OK 190 209 210 192 224 C5' G A 8 OK OK 223 243 244 225 258 C5' C A 9 OK OK 257 274 275 259 289 C5' U A 10 OK OK 288 305 306 290 319 C5' A A 11 OK OK 318 337 338 320 352 C5' A A 12 OK OK 351 370 371 353 385 C5' C A 13 OK OK 384 401 402 386 416 C5' U A 14 OK OK 415 432 433 417 446 C5' A A 15 OK OK 445 464 465 447 479 C5' G A 16 OK OK 478 498 499 480 512 C5' C B 17 OK OK 511 528 529 513 544 C5' U B 18 OK OK 543 560 561 545 574 C5' A B 19 OK OK 573 592 593 575 607 C5' G B 20 OK OK 606 626 627 608 641 C5' U B 21 OK OK 640 657 658 642 671 C5' U B 22 OK OK 670 687 688 672 701 C5' A B 23 OK OK 700 719 720 702 734 C5' G B 24 OK OK 733 753 754 735 768 C5' C B 25 OK OK 767 784 785 769 799 C5' U B 26 OK OK 798 815 816 800 829 C5' A B 27 OK OK 828 847 848 830 862 C5' A B 28 OK OK 861 880 881 863 895 C5' C B 29 OK OK 894 911 912 896 926 C5' U B 30 OK OK 925 942 943 927 956 C5' A B 31 OK OK 955 974 975 957 989 C5' G B 32 OK OK 988 1008 1009 990 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 30 P U A 2 distorted distorted 6 31 32 33 60 P A A 3 distorted distorted 38 61 62 63 93 P G A 4 distorted distorted 68 94 95 96 127 P U A 5 distorted distorted 101 128 129 130 157 P U A 6 distorted distorted 135 158 159 160 187 P A A 7 distorted distorted 165 188 189 190 220 P G A 8 distorted distorted 195 221 222 223 254 P C A 9 distorted distorted 228 255 256 257 285 P U A 10 distorted distorted 262 286 287 288 315 P A A 11 distorted distorted 293 316 317 318 348 P A A 12 distorted distorted 323 349 350 351 381 P C A 13 distorted distorted 356 382 383 384 412 P U A 14 distorted distorted 389 413 414 415 442 P A A 15 distorted distorted 420 443 444 445 475 P G A 16 distorted distorted 450 476 477 478 540 P U B 18 distorted distorted 516 541 542 543 570 P A B 19 distorted distorted 548 571 572 573 603 P G B 20 distorted distorted 578 604 605 606 637 P U B 21 distorted distorted 611 638 639 640 667 P U B 22 distorted distorted 645 668 669 670 697 P A B 23 distorted distorted 675 698 699 700 730 P G B 24 distorted distorted 705 731 732 733 764 P C B 25 distorted distorted 738 765 766 767 795 P U B 26 distorted distorted 772 796 797 798 825 P A B 27 distorted distorted 803 826 827 828 858 P A B 28 distorted distorted 833 859 860 861 891 P C B 29 distorted distorted 866 892 893 894 922 P U B 30 distorted distorted 899 923 924 925 952 P A B 31 distorted distorted 930 953 954 955 985 P G B 32 distorted distorted 960 986 987 988 ---------------------------------------------------------------------------------