ID code: '1FG1' 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 A2025 beta 4 10 7 32 C1' U A2024 beta 27 33 30 52 C1' G A2023 beta 47 53 50 75 C1' G A2022 beta 70 76 73 98 C1' U A2021 beta 93 99 96 118 C1' C A2030 beta 113 119 116 138 C1' U A2040 beta 133 139 136 158 C1' G A2050 beta 153 159 156 181 C1' A A2060 beta 176 182 179 203 C1' U A2070 beta 198 204 201 223 C1' G A2080 beta 218 224 221 246 C1' A A2090 beta 241 247 244 268 C1' G A2101 beta 263 269 266 291 C1' G A2102 beta 286 292 289 314 C1' C A2103 beta 309 315 312 334 C1' C A2104 beta 329 335 332 352 C1' G B2114 beta 347 353 350 375 C1' G B2113 beta 370 376 373 398 C1' C B2112 beta 393 399 396 418 C1' C B2111 beta 413 419 416 438 C1' G B2120 beta 433 439 436 461 C1' A B2130 beta 456 462 459 483 C1' A B2140 beta 478 484 481 505 C1' A B2151 beta 500 506 503 527 C1' C B2152 beta 522 528 525 547 C1' U B2153 beta 542 548 545 567 C1' C B2154 beta 562 568 565 587 C1' G B2931 beta 582 588 585 610 C1' U B2932 beta 605 611 608 630 C1' A B2933 beta 625 631 628 652 C1' A B2934 beta 647 653 650 674 C1' G B2164 beta 669 675 672 697 C1' A B2163 beta 692 698 695 719 C1' G B2162 beta 714 720 717 742 C1' U B2161 beta 737 743 740 762 C1' C B2170 beta 757 763 760 782 C1' A B2011 beta 777 783 780 804 C1' C B2012 beta 799 805 802 824 C1' C B2013 beta 819 825 822 844 C1' A B2014 beta 839 845 842 866 C1' C B2015 beta 861 867 864 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A2025 OK 9 5 8 30 C2' U A2024 OK 32 28 31 50 C2' G A2023 OK 52 48 51 73 C2' G A2022 OK 75 71 74 96 C2' U A2021 OK 98 94 97 116 C2' C A2030 OK 118 114 117 136 C2' U A2040 OK 138 134 137 156 C2' G A2050 OK 158 154 157 179 C2' A A2060 OK 181 177 180 201 C2' U A2070 OK 203 199 202 221 C2' G A2080 OK 223 219 222 244 C2' A A2090 OK 246 242 245 266 C2' G A2101 OK 268 264 267 289 C2' G A2102 OK 291 287 290 312 C2' C A2103 OK 314 310 313 332 C2' C A2104 OK 334 330 333 350 C2' G B2114 OK 352 348 351 373 C2' G B2113 OK 375 371 374 396 C2' C B2112 OK 398 394 397 416 C2' C B2111 OK 418 414 417 436 C2' G B2120 OK 438 434 437 459 C2' A B2130 OK 461 457 460 481 C2' A B2140 OK 483 479 482 503 C2' A B2151 OK 505 501 504 525 C2' C B2152 OK 527 523 526 545 C2' U B2153 OK 547 543 546 565 C2' C B2154 OK 567 563 566 585 C2' G B2931 OK 587 583 586 608 C2' U B2932 OK 610 606 609 628 C2' A B2933 OK 630 626 629 650 C2' A B2934 OK 652 648 651 672 C2' G B2164 OK 674 670 673 695 C2' A B2163 OK 697 693 696 717 C2' G B2162 OK 719 715 718 740 C2' U B2161 OK 742 738 741 760 C2' C B2170 OK 762 758 761 780 C2' A B2011 OK 782 778 781 802 C2' C B2012 OK 804 800 803 822 C2' C B2013 OK 824 820 823 842 C2' A B2014 OK 844 840 843 864 C2' C B2015 OK 866 862 865 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A2025 OK 3 6 7 28 C3' U A2024 OK 26 29 30 48 C3' G A2023 OK 46 49 50 71 C3' G A2022 OK 69 72 73 94 C3' U A2021 OK 92 95 96 114 C3' C A2030 OK 112 115 116 134 C3' U A2040 OK 132 135 136 154 C3' G A2050 OK 152 155 156 177 C3' A A2060 OK 175 178 179 199 C3' U A2070 OK 197 200 201 219 C3' G A2080 OK 217 220 221 242 C3' A A2090 OK 240 243 244 264 C3' G A2101 OK 262 265 266 287 C3' G A2102 OK 285 288 289 310 C3' C A2103 OK 308 311 312 330 C3' C A2104 OK 328 331 332 348 C3' G B2114 OK 346 349 350 371 C3' G B2113 OK 369 372 373 394 C3' C B2112 OK 392 395 396 414 C3' C B2111 OK 412 415 416 434 C3' G B2120 OK 432 435 436 457 C3' A B2130 OK 455 458 459 479 C3' A B2140 OK 477 480 481 501 C3' A B2151 OK 499 502 503 523 C3' C B2152 OK 521 524 525 543 C3' U B2153 OK 541 544 545 563 C3' C B2154 OK 561 564 565 583 C3' G B2931 OK 581 584 585 606 C3' U B2932 OK 604 607 608 626 C3' A B2933 OK 624 627 628 648 C3' A B2934 OK 646 649 650 670 C3' G B2164 OK 668 671 672 693 C3' A B2163 OK 691 694 695 715 C3' G B2162 OK 713 716 717 738 C3' U B2161 OK 736 739 740 758 C3' C B2170 OK 756 759 760 778 C3' A B2011 OK 776 779 780 800 C3' C B2012 OK 798 801 802 820 C3' C B2013 OK 818 821 822 840 C3' A B2014 OK 838 841 842 862 C3' C B2015 OK 860 863 864 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A2025 OK 5 2 4 26 C4' U A2024 OK 28 25 27 46 C4' G A2023 OK 48 45 47 69 C4' G A2022 OK 71 68 70 92 C4' U A2021 OK 94 91 93 112 C4' C A2030 OK 114 111 113 132 C4' U A2040 OK 134 131 133 152 C4' G A2050 OK 154 151 153 175 C4' A A2060 OK 177 174 176 197 C4' U A2070 OK 199 196 198 217 C4' G A2080 OK 219 216 218 240 C4' A A2090 OK 242 239 241 262 C4' G A2101 OK 264 261 263 285 C4' G A2102 OK 287 284 286 308 C4' C A2103 OK 310 307 309 328 C4' C A2104 OK 330 327 329 346 C4' G B2114 OK 348 345 347 369 C4' G B2113 OK 371 368 370 392 C4' C B2112 OK 394 391 393 412 C4' C B2111 OK 414 411 413 432 C4' G B2120 OK 434 431 433 455 C4' A B2130 OK 457 454 456 477 C4' A B2140 OK 479 476 478 499 C4' A B2151 OK 501 498 500 521 C4' C B2152 OK 523 520 522 541 C4' U B2153 OK 543 540 542 561 C4' C B2154 OK 563 560 562 581 C4' G B2931 OK 583 580 582 604 C4' U B2932 OK 606 603 605 624 C4' A B2933 OK 626 623 625 646 C4' A B2934 OK 648 645 647 668 C4' G B2164 OK 670 667 669 691 C4' A B2163 OK 693 690 692 713 C4' G B2162 OK 715 712 714 736 C4' U B2161 OK 738 735 737 756 C4' C B2170 OK 758 755 757 776 C4' A B2011 OK 778 775 777 798 C4' C B2012 OK 800 797 799 818 C4' C B2013 OK 820 817 819 838 C4' A B2014 OK 840 837 839 860 C4' C B2015 OK 862 859 861 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A2025 1 3 25 C5' U A2024 24 26 45 C5' G A2023 44 46 68 C5' G A2022 67 69 91 C5' U A2021 90 92 111 C5' C A2030 110 112 131 C5' U A2040 130 132 151 C5' G A2050 150 152 174 C5' A A2060 173 175 196 C5' U A2070 195 197 216 C5' G A2080 215 217 239 C5' A A2090 238 240 261 C5' G A2101 260 262 284 C5' G A2102 283 285 307 C5' C A2103 306 308 327 C5' C A2104 326 328 345 C5' G B2114 344 346 368 C5' G B2113 367 369 391 C5' C B2112 390 392 411 C5' C B2111 410 412 431 C5' G B2120 430 432 454 C5' A B2130 453 455 476 C5' A B2140 475 477 498 C5' A B2151 497 499 520 C5' C B2152 519 521 540 C5' U B2153 539 541 560 C5' C B2154 559 561 580 C5' G B2931 579 581 603 C5' U B2932 602 604 623 C5' A B2933 622 624 645 C5' A B2934 644 646 667 C5' G B2164 666 668 690 C5' A B2163 689 691 712 C5' G B2162 711 713 735 C5' U B2161 734 736 755 C5' C B2170 754 756 775 C5' A B2011 774 776 797 C5' C B2012 796 798 817 C5' C B2013 816 818 837 C5' A B2014 836 838 859 C5' C B2015 858 860 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P U A2024 distorted distorted 6 22 23 24 41 P G A2023 distorted distorted 29 42 43 44 64 P G A2022 distorted distorted 49 65 66 67 87 P U A2021 distorted distorted 72 88 89 90 107 P C A2030 distorted distorted 95 108 109 110 127 P U A2040 distorted distorted 115 128 129 130 147 P G A2050 distorted distorted 135 148 149 150 170 P A A2060 distorted distorted 155 171 172 173 192 P U A2070 distorted distorted 178 193 194 195 212 P G A2080 distorted distorted 200 213 214 215 235 P A A2090 distorted distorted 220 236 237 238 257 P G A2101 distorted distorted 243 258 259 260 280 P G A2102 distorted distorted 265 281 282 283 303 P C A2103 distorted distorted 288 304 305 306 323 P C A2104 distorted distorted 311 324 325 326 364 P G B2113 distorted distorted 349 365 366 367 387 P C B2112 distorted distorted 372 388 389 390 407 P C B2111 distorted distorted 395 408 409 410 427 P G B2120 distorted distorted 415 428 429 430 450 P A B2130 distorted distorted 435 451 452 453 472 P A B2140 distorted distorted 458 473 474 475 494 P A B2151 distorted distorted 480 495 496 497 516 P C B2152 distorted distorted 502 517 518 519 536 P U B2153 distorted distorted 524 537 538 539 556 P C B2154 distorted distorted 544 557 558 559 576 P G B2931 distorted distorted 564 577 578 579 599 P U B2932 distorted distorted 584 600 601 602 619 P A B2933 distorted distorted 607 620 621 622 641 P A B2934 distorted distorted 627 642 643 644 663 P G B2164 distorted distorted 649 664 665 666 686 P A B2163 distorted distorted 671 687 688 689 708 P G B2162 distorted distorted 694 709 710 711 731 P U B2161 distorted distorted 716 732 733 734 751 P C B2170 distorted distorted 739 752 753 754 771 P A B2011 distorted distorted 759 772 773 774 793 P C B2012 distorted distorted 779 794 795 796 813 P C B2013 distorted distorted 801 814 815 816 833 P A B2014 distorted distorted 821 834 835 836 855 P C B2015 distorted distorted 841 856 857 858 ---------------------------------------------------------------------------------