ID code: '4MCE' 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 beta 4 10 7 29 C1' A A 2 beta 24 30 27 51 C1' G A 3 beta 46 52 49 74 C1' U A 4 beta 69 75 72 94 C1' G A 5 beta 89 95 92 117 C1' G A 6 beta 112 118 115 140 C1' U A 7 beta 135 141 138 160 C1' C A 8 beta 155 161 158 180 C1' U A 9 beta 175 181 178 200 C1' U A 10 beta 195 201 198 218 C1' A B 1 beta 213 219 216 240 C1' A B 2 beta 235 241 238 262 C1' G B 3 beta 257 263 260 285 C1' A B 4 beta 280 286 283 307 C1' C B 5 beta 302 308 305 327 C1' U B 6 beta 322 328 325 347 C1' G B 7 beta 342 348 345 370 C1' C B 8 beta 365 371 368 390 C1' C B 9 beta 385 391 388 410 C1' U B 10 beta 405 411 408 428 C1' C C 1 beta 423 429 426 448 C1' A C 2 beta 443 449 446 470 C1' G C 3 beta 465 471 468 493 C1' U C 4 beta 488 494 491 513 C1' G C 5 beta 508 514 511 536 C1' G C 6 beta 531 537 534 559 C1' U C 7 beta 554 560 557 579 C1' C C 8 beta 574 580 577 599 C1' U C 9 beta 594 600 597 619 C1' U C 10 beta 614 620 617 637 C1' A D 1 beta 632 638 635 659 C1' A D 2 beta 654 660 657 681 C1' G D 3 beta 676 682 679 704 C1' A D 4 beta 699 705 702 726 C1' C D 5 beta 721 727 724 746 C1' U D 6 beta 741 747 744 766 C1' G D 7 beta 761 767 764 789 C1' C D 8 beta 784 790 787 809 C1' C D 9 beta 804 810 807 829 C1' U D 10 beta 824 830 827 849 C1' G D 11 beta 844 850 847 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 9 5 8 27 C2' A A 2 OK 29 25 28 49 C2' G A 3 OK 51 47 50 72 C2' U A 4 OK 74 70 73 92 C2' G A 5 OK 94 90 93 115 C2' G A 6 OK 117 113 116 138 C2' U A 7 OK 140 136 139 158 C2' C A 8 OK 160 156 159 178 C2' U A 9 OK 180 176 179 198 C2' U A 10 OK 200 196 199 216 C2' A B 1 OK 218 214 217 238 C2' A B 2 OK 240 236 239 260 C2' G B 3 OK 262 258 261 283 C2' A B 4 OK 285 281 284 305 C2' C B 5 OK 307 303 306 325 C2' U B 6 OK 327 323 326 345 C2' G B 7 OK 347 343 346 368 C2' C B 8 OK 370 366 369 388 C2' C B 9 OK 390 386 389 408 C2' U B 10 OK 410 406 409 426 C2' C C 1 OK 428 424 427 446 C2' A C 2 OK 448 444 447 468 C2' G C 3 OK 470 466 469 491 C2' U C 4 OK 493 489 492 511 C2' G C 5 OK 513 509 512 534 C2' G C 6 OK 536 532 535 557 C2' U C 7 OK 559 555 558 577 C2' C C 8 OK 579 575 578 597 C2' U C 9 OK 599 595 598 617 C2' U C 10 OK 619 615 618 635 C2' A D 1 OK 637 633 636 657 C2' A D 2 OK 659 655 658 679 C2' G D 3 OK 681 677 680 702 C2' A D 4 OK 704 700 703 724 C2' C D 5 OK 726 722 725 744 C2' U D 6 OK 746 742 745 764 C2' G D 7 OK 766 762 765 787 C2' C D 8 OK 789 785 788 807 C2' C D 9 OK 809 805 808 827 C2' U D 10 OK 829 825 828 847 C2' G D 11 OK 849 845 848 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK 3 6 7 25 C3' A A 2 OK 23 26 27 47 C3' G A 3 OK 45 48 49 70 C3' U A 4 OK 68 71 72 90 C3' G A 5 OK 88 91 92 113 C3' G A 6 OK 111 114 115 136 C3' U A 7 OK 134 137 138 156 C3' C A 8 OK 154 157 158 176 C3' U A 9 OK 174 177 178 196 C3' U A 10 OK 194 197 198 214 C3' A B 1 OK 212 215 216 236 C3' A B 2 OK 234 237 238 258 C3' G B 3 OK 256 259 260 281 C3' A B 4 OK 279 282 283 303 C3' C B 5 OK 301 304 305 323 C3' U B 6 OK 321 324 325 343 C3' G B 7 OK 341 344 345 366 C3' C B 8 OK 364 367 368 386 C3' C B 9 OK 384 387 388 406 C3' U B 10 OK 404 407 408 424 C3' C C 1 OK 422 425 426 444 C3' A C 2 OK 442 445 446 466 C3' G C 3 OK 464 467 468 489 C3' U C 4 OK 487 490 491 509 C3' G C 5 OK 507 510 511 532 C3' G C 6 OK 530 533 534 555 C3' U C 7 OK 553 556 557 575 C3' C C 8 OK 573 576 577 595 C3' U C 9 OK 593 596 597 615 C3' U C 10 OK 613 616 617 633 C3' A D 1 OK 631 634 635 655 C3' A D 2 OK 653 656 657 677 C3' G D 3 OK 675 678 679 700 C3' A D 4 OK 698 701 702 722 C3' C D 5 OK 720 723 724 742 C3' U D 6 OK 740 743 744 762 C3' G D 7 OK 760 763 764 785 C3' C D 8 OK 783 786 787 805 C3' C D 9 OK 803 806 807 825 C3' U D 10 OK 823 826 827 845 C3' G D 11 OK 843 846 847 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK 5 2 4 23 C4' A A 2 OK 25 22 24 45 C4' G A 3 OK 47 44 46 68 C4' U A 4 OK 70 67 69 88 C4' G A 5 OK 90 87 89 111 C4' G A 6 OK 113 110 112 134 C4' U A 7 OK 136 133 135 154 C4' C A 8 OK 156 153 155 174 C4' U A 9 OK 176 173 175 194 C4' U A 10 OK 196 193 195 212 C4' A B 1 OK 214 211 213 234 C4' A B 2 OK 236 233 235 256 C4' G B 3 OK 258 255 257 279 C4' A B 4 OK 281 278 280 301 C4' C B 5 OK 303 300 302 321 C4' U B 6 OK 323 320 322 341 C4' G B 7 OK 343 340 342 364 C4' C B 8 OK 366 363 365 384 C4' C B 9 OK 386 383 385 404 C4' U B 10 OK 406 403 405 422 C4' C C 1 OK 424 421 423 442 C4' A C 2 OK 444 441 443 464 C4' G C 3 OK 466 463 465 487 C4' U C 4 OK 489 486 488 507 C4' G C 5 OK 509 506 508 530 C4' G C 6 OK 532 529 531 553 C4' U C 7 OK 555 552 554 573 C4' C C 8 OK 575 572 574 593 C4' U C 9 OK 595 592 594 613 C4' U C 10 OK 615 612 614 631 C4' A D 1 OK 633 630 632 653 C4' A D 2 OK 655 652 654 675 C4' G D 3 OK 677 674 676 698 C4' A D 4 OK 700 697 699 720 C4' C D 5 OK 722 719 721 740 C4' U D 6 OK 742 739 741 760 C4' G D 7 OK 762 759 761 783 C4' C D 8 OK 785 782 784 803 C4' C D 9 OK 805 802 804 823 C4' U D 10 OK 825 822 824 843 C4' G D 11 OK 845 842 844 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 1 3 22 C5' A A 2 21 23 44 C5' G A 3 43 45 67 C5' U A 4 66 68 87 C5' G A 5 86 88 110 C5' G A 6 109 111 133 C5' U A 7 132 134 153 C5' C A 8 152 154 173 C5' U A 9 172 174 193 C5' U A 10 192 194 211 C5' A B 1 210 212 233 C5' A B 2 232 234 255 C5' G B 3 254 256 278 C5' A B 4 277 279 300 C5' C B 5 299 301 320 C5' U B 6 319 321 340 C5' G B 7 339 341 363 C5' C B 8 362 364 383 C5' C B 9 382 384 403 C5' U B 10 402 404 421 C5' C C 1 420 422 441 C5' A C 2 440 442 463 C5' G C 3 462 464 486 C5' U C 4 485 487 506 C5' G C 5 505 507 529 C5' G C 6 528 530 552 C5' U C 7 551 553 572 C5' C C 8 571 573 592 C5' U C 9 591 593 612 C5' U C 10 611 613 630 C5' A D 1 629 631 652 C5' A D 2 651 653 674 C5' G D 3 673 675 697 C5' A D 4 696 698 719 C5' C D 5 718 720 739 C5' U D 6 738 740 759 C5' G D 7 758 760 782 C5' C D 8 781 783 802 C5' C D 9 801 803 822 C5' U D 10 821 823 842 C5' G D 11 841 843 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P A A 2 distorted distorted 6 19 20 21 40 P G A 3 distorted distorted 26 41 42 43 63 P U A 4 distorted distorted 48 64 65 66 83 P G A 5 distorted distorted 71 84 85 86 106 P G A 6 distorted distorted 91 107 108 109 129 P U A 7 distorted distorted 114 130 131 132 149 P C A 8 distorted distorted 137 150 151 152 169 P U A 9 distorted distorted 157 170 171 172 189 P U A 10 distorted distorted 177 190 191 192 229 P A B 2 distorted distorted 215 230 231 232 251 P G B 3 distorted distorted 237 252 253 254 274 P A B 4 distorted distorted 259 275 276 277 296 P C B 5 distorted distorted 282 297 298 299 316 P U B 6 distorted distorted 304 317 318 319 336 P G B 7 distorted distorted 324 337 338 339 359 P C B 8 distorted distorted 344 360 361 362 379 P C B 9 distorted distorted 367 380 381 382 399 P U B 10 distorted distorted 387 400 401 402 437 P A C 2 distorted distorted 425 438 439 440 459 P G C 3 distorted distorted 445 460 461 462 482 P U C 4 distorted distorted 467 483 484 485 502 P G C 5 distorted distorted 490 503 504 505 525 P G C 6 distorted distorted 510 526 527 528 548 P U C 7 distorted distorted 533 549 550 551 568 P C C 8 distorted distorted 556 569 570 571 588 P U C 9 distorted distorted 576 589 590 591 608 P U C 10 distorted distorted 596 609 610 611 648 P A D 2 distorted distorted 634 649 650 651 670 P G D 3 distorted distorted 656 671 672 673 693 P A D 4 distorted distorted 678 694 695 696 715 P C D 5 distorted distorted 701 716 717 718 735 P U D 6 distorted distorted 723 736 737 738 755 P G D 7 distorted distorted 743 756 757 758 778 P C D 8 distorted distorted 763 779 780 781 798 P C D 9 distorted distorted 786 799 800 801 818 P U D 10 distorted distorted 806 819 820 821 838 P G D 11 distorted distorted 826 839 840 841 ---------------------------------------------------------------------------------