ID code: '2GIP' 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' C A 3 alpha beta 73 93 79 76 109 C1' C A 4 alpha beta 104 124 110 107 140 C1' A A 5 alpha beta 135 157 141 138 173 C1' U A 6 alpha beta 168 188 174 171 203 C1' C A 7 alpha beta 198 218 204 201 234 C1' U A 8 alpha beta 229 249 235 232 264 C1' U A 9 alpha beta 259 279 265 262 294 C1' C A 10 alpha beta 289 309 295 292 325 C1' U A 11 alpha beta 320 340 326 323 355 C1' C A 12 alpha beta 350 370 356 353 386 C1' U A 13 alpha beta 381 401 387 384 416 C1' U A 14 alpha beta 411 431 417 414 446 C1' C A 15 alpha beta 441 461 447 444 477 C1' G A 16 alpha beta 472 495 478 475 511 C1' G A 17 alpha beta 506 529 512 509 545 C1' A A 18 alpha beta 540 562 546 543 578 C1' G A 19 alpha beta 573 596 579 576 612 C1' G A 20 alpha beta 607 630 613 610 646 C1' A A 21 alpha beta 641 663 647 644 679 C1' U A 22 alpha beta 674 694 680 677 709 C1' U A 23 alpha beta 704 724 710 707 739 C1' U A 24 alpha beta 734 754 740 737 769 C1' G A 25 alpha beta 764 787 770 767 803 C1' G A 26 alpha beta 798 821 804 801 837 C1' C A 27 alpha beta 832 852 838 835 868 C1' C A 28 alpha beta 863 884 869 866 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 3 OK OK 78 74 91 77 107 C2' C A 4 OK OK 109 105 122 108 138 C2' A A 5 OK OK 140 136 155 139 171 C2' U A 6 OK OK 173 169 186 172 201 C2' C A 7 OK OK 203 199 216 202 232 C2' U A 8 OK OK 234 230 247 233 262 C2' U A 9 OK OK 264 260 277 263 292 C2' C A 10 OK OK 294 290 307 293 323 C2' U A 11 OK OK 325 321 338 324 353 C2' C A 12 OK OK 355 351 368 354 384 C2' U A 13 OK OK 386 382 399 385 414 C2' U A 14 OK OK 416 412 429 415 444 C2' C A 15 OK OK 446 442 459 445 475 C2' G A 16 OK OK 477 473 493 476 509 C2' G A 17 OK OK 511 507 527 510 543 C2' A A 18 OK OK 545 541 560 544 576 C2' G A 19 OK OK 578 574 594 577 610 C2' G A 20 OK OK 612 608 628 611 644 C2' A A 21 OK OK 646 642 661 645 677 C2' U A 22 OK OK 679 675 692 678 707 C2' U A 23 OK OK 709 705 722 708 737 C2' U A 24 OK OK 739 735 752 738 767 C2' G A 25 OK OK 769 765 785 768 801 C2' G A 26 OK OK 803 799 819 802 835 C2' C A 27 OK OK 837 833 850 836 866 C2' C A 28 OK OK 868 864 882 867 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 72 90 75 76 105 C3' C A 4 OK OK 103 121 106 107 136 C3' A A 5 OK OK 134 154 137 138 169 C3' U A 6 OK OK 167 185 170 171 199 C3' C A 7 OK OK 197 215 200 201 230 C3' U A 8 OK OK 228 246 231 232 260 C3' U A 9 OK OK 258 276 261 262 290 C3' C A 10 OK OK 288 306 291 292 321 C3' U A 11 OK OK 319 337 322 323 351 C3' C A 12 OK OK 349 367 352 353 382 C3' U A 13 OK OK 380 398 383 384 412 C3' U A 14 OK OK 410 428 413 414 442 C3' C A 15 OK OK 440 458 443 444 473 C3' G A 16 OK OK 471 492 474 475 507 C3' G A 17 OK OK 505 526 508 509 541 C3' A A 18 OK OK 539 559 542 543 574 C3' G A 19 OK OK 572 593 575 576 608 C3' G A 20 OK OK 606 627 609 610 642 C3' A A 21 OK OK 640 660 643 644 675 C3' U A 22 OK OK 673 691 676 677 705 C3' U A 23 OK OK 703 721 706 707 735 C3' U A 24 OK OK 733 751 736 737 765 C3' G A 25 OK OK 763 784 766 767 799 C3' G A 26 OK OK 797 818 800 801 833 C3' C A 27 OK OK 831 849 834 835 864 C3' C A 28 OK OK 862 880 865 866 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 74 89 71 73 103 C4' C A 4 OK OK 105 120 102 104 134 C4' A A 5 OK OK 136 153 133 135 167 C4' U A 6 OK OK 169 184 166 168 197 C4' C A 7 OK OK 199 214 196 198 228 C4' U A 8 OK OK 230 245 227 229 258 C4' U A 9 OK OK 260 275 257 259 288 C4' C A 10 OK OK 290 305 287 289 319 C4' U A 11 OK OK 321 336 318 320 349 C4' C A 12 OK OK 351 366 348 350 380 C4' U A 13 OK OK 382 397 379 381 410 C4' U A 14 OK OK 412 427 409 411 440 C4' C A 15 OK OK 442 457 439 441 471 C4' G A 16 OK OK 473 491 470 472 505 C4' G A 17 OK OK 507 525 504 506 539 C4' A A 18 OK OK 541 558 538 540 572 C4' G A 19 OK OK 574 592 571 573 606 C4' G A 20 OK OK 608 626 605 607 640 C4' A A 21 OK OK 642 659 639 641 673 C4' U A 22 OK OK 675 690 672 674 703 C4' U A 23 OK OK 705 720 702 704 733 C4' U A 24 OK OK 735 750 732 734 763 C4' G A 25 OK OK 765 783 762 764 797 C4' G A 26 OK OK 799 817 796 798 831 C4' C A 27 OK OK 833 848 830 832 862 C4' C A 28 OK OK 864 879 861 863 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 70 87 88 72 102 C5' C A 4 OK OK 101 118 119 103 133 C5' A A 5 OK OK 132 151 152 134 166 C5' U A 6 OK OK 165 182 183 167 196 C5' C A 7 OK OK 195 212 213 197 227 C5' U A 8 OK OK 226 243 244 228 257 C5' U A 9 OK OK 256 273 274 258 287 C5' C A 10 OK OK 286 303 304 288 318 C5' U A 11 OK OK 317 334 335 319 348 C5' C A 12 OK OK 347 364 365 349 379 C5' U A 13 OK OK 378 395 396 380 409 C5' U A 14 OK OK 408 425 426 410 439 C5' C A 15 OK OK 438 455 456 440 470 C5' G A 16 OK OK 469 489 490 471 504 C5' G A 17 OK OK 503 523 524 505 538 C5' A A 18 OK OK 537 556 557 539 571 C5' G A 19 OK OK 570 590 591 572 605 C5' G A 20 OK OK 604 624 625 606 639 C5' A A 21 OK OK 638 657 658 640 672 C5' U A 22 OK OK 671 688 689 673 702 C5' U A 23 OK OK 701 718 719 703 732 C5' U A 24 OK OK 731 748 749 733 762 C5' G A 25 OK OK 761 781 782 763 796 C5' G A 26 OK OK 795 815 816 797 830 C5' C A 27 OK OK 829 846 847 831 861 C5' C A 28 OK OK 860 877 878 862 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P C A 4 distorted distorted 75 99 100 101 129 P A A 5 distorted distorted 106 130 131 132 162 P U A 6 distorted distorted 137 163 164 165 192 P C A 7 distorted distorted 170 193 194 195 223 P U A 8 distorted distorted 200 224 225 226 253 P U A 9 distorted distorted 231 254 255 256 283 P C A 10 distorted distorted 261 284 285 286 314 P U A 11 distorted distorted 291 315 316 317 344 P C A 12 distorted distorted 322 345 346 347 375 P U A 13 distorted distorted 352 376 377 378 405 P U A 14 distorted distorted 383 406 407 408 435 P C A 15 distorted distorted 413 436 437 438 466 P G A 16 distorted distorted 443 467 468 469 500 P G A 17 distorted distorted 474 501 502 503 534 P A A 18 distorted distorted 508 535 536 537 567 P G A 19 distorted distorted 542 568 569 570 601 P G A 20 distorted distorted 575 602 603 604 635 P A A 21 distorted distorted 609 636 637 638 668 P U A 22 distorted distorted 643 669 670 671 698 P U A 23 distorted distorted 676 699 700 701 728 P U A 24 distorted distorted 706 729 730 731 758 P G A 25 distorted distorted 736 759 760 761 792 P G A 26 distorted distorted 766 793 794 795 826 P C A 27 distorted distorted 800 827 828 829 857 P C A 28 distorted distorted 834 858 859 860 ---------------------------------------------------------------------------------