ID code: '4E5C' 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' --------------------------------------------------------------------------------- 13 C1' G A 1 beta 8 14 11 36 C1' G A 2 beta 31 37 34 59 C1' C A 3 beta 54 60 57 79 C1' G A 4 beta 74 80 77 102 C1' G A 5 beta 97 103 100 125 C1' C A 6 beta 120 126 123 145 C1' G A 7 beta 140 146 143 168 C1' G A 8 beta 163 169 166 191 C1' C A 9 beta 186 192 189 211 C1' G A 10 beta 206 212 209 234 C1' G A 11 beta 229 235 232 257 C1' C A 12 beta 252 258 255 277 C1' U A 13 beta 272 278 275 297 C1' G A 14 beta 292 298 295 320 C1' C A 15 beta 315 321 318 340 C1' U A 16 beta 335 341 338 360 C1' G A 17 beta 355 361 358 383 C1' C A 18 beta 378 384 381 403 C1' C A 19 beta 398 404 401 425 C1' G B 1 beta 420 426 423 448 C1' G B 2 beta 443 449 446 471 C1' C B 3 beta 466 472 469 491 C1' G B 4 beta 486 492 489 514 C1' G B 5 beta 509 515 512 537 C1' C B 6 beta 532 538 535 557 C1' G B 7 beta 552 558 555 580 C1' G B 8 beta 575 581 578 603 C1' C B 9 beta 598 604 601 623 C1' G B 10 beta 618 624 621 646 C1' G B 11 beta 641 647 644 669 C1' C B 12 beta 664 670 667 689 C1' U B 13 beta 684 690 687 709 C1' G B 14 beta 704 710 707 732 C1' C B 15 beta 727 733 730 752 C1' U B 16 beta 747 753 750 772 C1' G B 17 beta 767 773 770 795 C1' C B 18 beta 790 796 793 815 C1' C B 19 beta 810 816 813 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G A 1 OK 13 9 12 34 C2' G A 2 OK 36 32 35 57 C2' C A 3 OK 59 55 58 77 C2' G A 4 OK 79 75 78 100 C2' G A 5 OK 102 98 101 123 C2' C A 6 OK 125 121 124 143 C2' G A 7 OK 145 141 144 166 C2' G A 8 OK 168 164 167 189 C2' C A 9 OK 191 187 190 209 C2' G A 10 OK 211 207 210 232 C2' G A 11 OK 234 230 233 255 C2' C A 12 OK 257 253 256 275 C2' U A 13 OK 277 273 276 295 C2' G A 14 OK 297 293 296 318 C2' C A 15 OK 320 316 319 338 C2' U A 16 OK 340 336 339 358 C2' G A 17 OK 360 356 359 381 C2' C A 18 OK 383 379 382 401 C2' C A 19 OK 403 399 402 423 C2' G B 1 OK 425 421 424 446 C2' G B 2 OK 448 444 447 469 C2' C B 3 OK 471 467 470 489 C2' G B 4 OK 491 487 490 512 C2' G B 5 OK 514 510 513 535 C2' C B 6 OK 537 533 536 555 C2' G B 7 OK 557 553 556 578 C2' G B 8 OK 580 576 579 601 C2' C B 9 OK 603 599 602 621 C2' G B 10 OK 623 619 622 644 C2' G B 11 OK 646 642 645 667 C2' C B 12 OK 669 665 668 687 C2' U B 13 OK 689 685 688 707 C2' G B 14 OK 709 705 708 730 C2' C B 15 OK 732 728 731 750 C2' U B 16 OK 752 748 751 770 C2' G B 17 OK 772 768 771 793 C2' C B 18 OK 795 791 794 813 C2' C B 19 OK 815 811 814 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G A 1 OK 7 10 11 32 C3' G A 2 OK 30 33 34 55 C3' C A 3 OK 53 56 57 75 C3' G A 4 OK 73 76 77 98 C3' G A 5 OK 96 99 100 121 C3' C A 6 OK 119 122 123 141 C3' G A 7 OK 139 142 143 164 C3' G A 8 OK 162 165 166 187 C3' C A 9 OK 185 188 189 207 C3' G A 10 OK 205 208 209 230 C3' G A 11 OK 228 231 232 253 C3' C A 12 OK 251 254 255 273 C3' U A 13 OK 271 274 275 293 C3' G A 14 OK 291 294 295 316 C3' C A 15 OK 314 317 318 336 C3' U A 16 OK 334 337 338 356 C3' G A 17 OK 354 357 358 379 C3' C A 18 OK 377 380 381 399 C3' C A 19 OK 397 400 401 421 C3' G B 1 OK 419 422 423 444 C3' G B 2 OK 442 445 446 467 C3' C B 3 OK 465 468 469 487 C3' G B 4 OK 485 488 489 510 C3' G B 5 OK 508 511 512 533 C3' C B 6 OK 531 534 535 553 C3' G B 7 OK 551 554 555 576 C3' G B 8 OK 574 577 578 599 C3' C B 9 OK 597 600 601 619 C3' G B 10 OK 617 620 621 642 C3' G B 11 OK 640 643 644 665 C3' C B 12 OK 663 666 667 685 C3' U B 13 OK 683 686 687 705 C3' G B 14 OK 703 706 707 728 C3' C B 15 OK 726 729 730 748 C3' U B 16 OK 746 749 750 768 C3' G B 17 OK 766 769 770 791 C3' C B 18 OK 789 792 793 811 C3' C B 19 OK 809 812 813 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G A 1 OK 9 6 8 30 C4' G A 2 OK 32 29 31 53 C4' C A 3 OK 55 52 54 73 C4' G A 4 OK 75 72 74 96 C4' G A 5 OK 98 95 97 119 C4' C A 6 OK 121 118 120 139 C4' G A 7 OK 141 138 140 162 C4' G A 8 OK 164 161 163 185 C4' C A 9 OK 187 184 186 205 C4' G A 10 OK 207 204 206 228 C4' G A 11 OK 230 227 229 251 C4' C A 12 OK 253 250 252 271 C4' U A 13 OK 273 270 272 291 C4' G A 14 OK 293 290 292 314 C4' C A 15 OK 316 313 315 334 C4' U A 16 OK 336 333 335 354 C4' G A 17 OK 356 353 355 377 C4' C A 18 OK 379 376 378 397 C4' C A 19 OK 399 396 398 419 C4' G B 1 OK 421 418 420 442 C4' G B 2 OK 444 441 443 465 C4' C B 3 OK 467 464 466 485 C4' G B 4 OK 487 484 486 508 C4' G B 5 OK 510 507 509 531 C4' C B 6 OK 533 530 532 551 C4' G B 7 OK 553 550 552 574 C4' G B 8 OK 576 573 575 597 C4' C B 9 OK 599 596 598 617 C4' G B 10 OK 619 616 618 640 C4' G B 11 OK 642 639 641 663 C4' C B 12 OK 665 662 664 683 C4' U B 13 OK 685 682 684 703 C4' G B 14 OK 705 702 704 726 C4' C B 15 OK 728 725 727 746 C4' U B 16 OK 748 745 747 766 C4' G B 17 OK 768 765 767 789 C4' C B 18 OK 791 788 790 809 C4' C B 19 OK 811 808 810 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G A 1 5 7 29 C5' G A 2 28 30 52 C5' C A 3 51 53 72 C5' G A 4 71 73 95 C5' G A 5 94 96 118 C5' C A 6 117 119 138 C5' G A 7 137 139 161 C5' G A 8 160 162 184 C5' C A 9 183 185 204 C5' G A 10 203 205 227 C5' G A 11 226 228 250 C5' C A 12 249 251 270 C5' U A 13 269 271 290 C5' G A 14 289 291 313 C5' C A 15 312 314 333 C5' U A 16 332 334 353 C5' G A 17 352 354 376 C5' C A 18 375 377 396 C5' C A 19 395 397 418 C5' G B 1 417 419 441 C5' G B 2 440 442 464 C5' C B 3 463 465 484 C5' G B 4 483 485 507 C5' G B 5 506 508 530 C5' C B 6 529 531 550 C5' G B 7 549 551 573 C5' G B 8 572 574 596 C5' C B 9 595 597 616 C5' G B 10 615 617 639 C5' G B 11 638 640 662 C5' C B 12 661 663 682 C5' U B 13 681 683 702 C5' G B 14 701 703 725 C5' C B 15 724 726 745 C5' U B 16 744 746 765 C5' G B 17 764 766 788 C5' C B 18 787 789 808 C5' C B 19 807 809 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G A 1 distorted distorted 3 4 5 25 P G A 2 distorted distorted 10 26 27 28 48 P C A 3 distorted distorted 33 49 50 51 68 P G A 4 distorted distorted 56 69 70 71 91 P G A 5 distorted distorted 76 92 93 94 114 P C A 6 distorted distorted 99 115 116 117 134 P G A 7 distorted distorted 122 135 136 137 157 P G A 8 distorted distorted 142 158 159 160 180 P C A 9 distorted distorted 165 181 182 183 200 P G A 10 distorted distorted 188 201 202 203 223 P G A 11 distorted distorted 208 224 225 226 246 P C A 12 distorted distorted 231 247 248 249 266 P U A 13 distorted distorted 254 267 268 269 286 P G A 14 distorted distorted 274 287 288 289 309 P C A 15 distorted distorted 294 310 311 312 329 P U A 16 distorted distorted 317 330 331 332 349 P G A 17 distorted distorted 337 350 351 352 372 P C A 18 distorted distorted 357 373 374 375 392 P C A 19 distorted distorted 380 393 394 395 414 P G B 1 distorted distorted 415 416 417 437 P G B 2 distorted distorted 422 438 439 440 460 P C B 3 distorted distorted 445 461 462 463 480 P G B 4 distorted distorted 468 481 482 483 503 P G B 5 distorted distorted 488 504 505 506 526 P C B 6 distorted distorted 511 527 528 529 546 P G B 7 distorted distorted 534 547 548 549 569 P G B 8 distorted distorted 554 570 571 572 592 P C B 9 distorted distorted 577 593 594 595 612 P G B 10 distorted distorted 600 613 614 615 635 P G B 11 distorted distorted 620 636 637 638 658 P C B 12 distorted distorted 643 659 660 661 678 P U B 13 distorted distorted 666 679 680 681 698 P G B 14 distorted distorted 686 699 700 701 721 P C B 15 distorted distorted 706 722 723 724 741 P U B 16 distorted distorted 729 742 743 744 761 P G B 17 distorted distorted 749 762 763 764 784 P C B 18 distorted distorted 769 785 786 787 804 P C B 19 distorted distorted 792 805 806 807 ---------------------------------------------------------------------------------