ID code: '3GM7' 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 G 1 beta 4 10 7 29 C1' U G 2 beta 24 30 27 49 C1' G G 3 beta 44 50 47 72 C1' C G 4 beta 67 73 70 92 C1' U G 5 beta 87 93 90 112 C1' G G 6 beta 107 113 110 135 C1' C G 7 beta 130 136 133 155 C1' U G 8 beta 150 156 153 175 C1' G G 9 beta 170 176 173 198 C1' C G 10 beta 193 199 196 218 C1' U G 11 beta 213 219 216 238 C1' G G 12 beta 233 239 236 261 C1' C G 13 beta 256 262 259 281 C1' U G 14 beta 276 282 279 301 C1' G G 15 beta 296 302 299 324 C1' C G 16 beta 319 325 322 344 C1' U G 17 beta 339 345 342 364 C1' G G 18 beta 359 365 362 385 C1' C H 1 beta 380 386 383 405 C1' U H 2 beta 400 406 403 425 C1' G H 3 beta 420 426 423 448 C1' C H 4 beta 443 449 446 468 C1' U H 5 beta 463 469 466 488 C1' G H 6 beta 483 489 486 511 C1' C H 7 beta 506 512 509 531 C1' U H 8 beta 526 532 529 551 C1' G H 9 beta 546 552 549 574 C1' C H 10 beta 569 575 572 594 C1' U H 11 beta 589 595 592 614 C1' G H 12 beta 609 615 612 637 C1' C H 13 beta 632 638 635 657 C1' U H 14 beta 652 658 655 677 C1' G H 15 beta 672 678 675 700 C1' C H 16 beta 695 701 698 720 C1' U H 17 beta 715 721 718 740 C1' G H 18 beta 735 741 738 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C G 1 OK 9 5 8 27 C2' U G 2 OK 29 25 28 47 C2' G G 3 OK 49 45 48 70 C2' C G 4 OK 72 68 71 90 C2' U G 5 OK 92 88 91 110 C2' G G 6 OK 112 108 111 133 C2' C G 7 OK 135 131 134 153 C2' U G 8 OK 155 151 154 173 C2' G G 9 OK 175 171 174 196 C2' C G 10 OK 198 194 197 216 C2' U G 11 OK 218 214 217 236 C2' G G 12 OK 238 234 237 259 C2' C G 13 OK 261 257 260 279 C2' U G 14 OK 281 277 280 299 C2' G G 15 OK 301 297 300 322 C2' C G 16 OK 324 320 323 342 C2' U G 17 OK 344 340 343 362 C2' G G 18 OK 364 360 363 383 C2' C H 1 OK 385 381 384 403 C2' U H 2 OK 405 401 404 423 C2' G H 3 OK 425 421 424 446 C2' C H 4 OK 448 444 447 466 C2' U H 5 OK 468 464 467 486 C2' G H 6 OK 488 484 487 509 C2' C H 7 OK 511 507 510 529 C2' U H 8 OK 531 527 530 549 C2' G H 9 OK 551 547 550 572 C2' C H 10 OK 574 570 573 592 C2' U H 11 OK 594 590 593 612 C2' G H 12 OK 614 610 613 635 C2' C H 13 OK 637 633 636 655 C2' U H 14 OK 657 653 656 675 C2' G H 15 OK 677 673 676 698 C2' C H 16 OK 700 696 699 718 C2' U H 17 OK 720 716 719 738 C2' G H 18 OK 740 736 739 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C G 1 OK 3 6 7 25 C3' U G 2 OK 23 26 27 45 C3' G G 3 OK 43 46 47 68 C3' C G 4 OK 66 69 70 88 C3' U G 5 OK 86 89 90 108 C3' G G 6 OK 106 109 110 131 C3' C G 7 OK 129 132 133 151 C3' U G 8 OK 149 152 153 171 C3' G G 9 OK 169 172 173 194 C3' C G 10 OK 192 195 196 214 C3' U G 11 OK 212 215 216 234 C3' G G 12 OK 232 235 236 257 C3' C G 13 OK 255 258 259 277 C3' U G 14 OK 275 278 279 297 C3' G G 15 OK 295 298 299 320 C3' C G 16 OK 318 321 322 340 C3' U G 17 OK 338 341 342 360 C3' G G 18 OK 358 361 362 381 C3' C H 1 OK 379 382 383 401 C3' U H 2 OK 399 402 403 421 C3' G H 3 OK 419 422 423 444 C3' C H 4 OK 442 445 446 464 C3' U H 5 OK 462 465 466 484 C3' G H 6 OK 482 485 486 507 C3' C H 7 OK 505 508 509 527 C3' U H 8 OK 525 528 529 547 C3' G H 9 OK 545 548 549 570 C3' C H 10 OK 568 571 572 590 C3' U H 11 OK 588 591 592 610 C3' G H 12 OK 608 611 612 633 C3' C H 13 OK 631 634 635 653 C3' U H 14 OK 651 654 655 673 C3' G H 15 OK 671 674 675 696 C3' C H 16 OK 694 697 698 716 C3' U H 17 OK 714 717 718 736 C3' G H 18 OK 734 737 738 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C G 1 OK 5 2 4 23 C4' U G 2 OK 25 22 24 43 C4' G G 3 OK 45 42 44 66 C4' C G 4 OK 68 65 67 86 C4' U G 5 OK 88 85 87 106 C4' G G 6 OK 108 105 107 129 C4' C G 7 OK 131 128 130 149 C4' U G 8 OK 151 148 150 169 C4' G G 9 OK 171 168 170 192 C4' C G 10 OK 194 191 193 212 C4' U G 11 OK 214 211 213 232 C4' G G 12 OK 234 231 233 255 C4' C G 13 OK 257 254 256 275 C4' U G 14 OK 277 274 276 295 C4' G G 15 OK 297 294 296 318 C4' C G 16 OK 320 317 319 338 C4' U G 17 OK 340 337 339 358 C4' G G 18 OK 360 357 359 379 C4' C H 1 OK 381 378 380 399 C4' U H 2 OK 401 398 400 419 C4' G H 3 OK 421 418 420 442 C4' C H 4 OK 444 441 443 462 C4' U H 5 OK 464 461 463 482 C4' G H 6 OK 484 481 483 505 C4' C H 7 OK 507 504 506 525 C4' U H 8 OK 527 524 526 545 C4' G H 9 OK 547 544 546 568 C4' C H 10 OK 570 567 569 588 C4' U H 11 OK 590 587 589 608 C4' G H 12 OK 610 607 609 631 C4' C H 13 OK 633 630 632 651 C4' U H 14 OK 653 650 652 671 C4' G H 15 OK 673 670 672 694 C4' C H 16 OK 696 693 695 714 C4' U H 17 OK 716 713 715 734 C4' G H 18 OK 736 733 735 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C G 1 1 3 22 C5' U G 2 21 23 42 C5' G G 3 41 43 65 C5' C G 4 64 66 85 C5' U G 5 84 86 105 C5' G G 6 104 106 128 C5' C G 7 127 129 148 C5' U G 8 147 149 168 C5' G G 9 167 169 191 C5' C G 10 190 192 211 C5' U G 11 210 212 231 C5' G G 12 230 232 254 C5' C G 13 253 255 274 C5' U G 14 273 275 294 C5' G G 15 293 295 317 C5' C G 16 316 318 337 C5' U G 17 336 338 357 C5' G G 18 356 358 378 C5' C H 1 377 379 398 C5' U H 2 397 399 418 C5' G H 3 417 419 441 C5' C H 4 440 442 461 C5' U H 5 460 462 481 C5' G H 6 480 482 504 C5' C H 7 503 505 524 C5' U H 8 523 525 544 C5' G H 9 543 545 567 C5' C H 10 566 568 587 C5' U H 11 586 588 607 C5' G H 12 606 608 630 C5' C H 13 629 631 650 C5' U H 14 649 651 670 C5' G H 15 669 671 693 C5' C H 16 692 694 713 C5' U H 17 712 714 733 C5' G H 18 732 734 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P U G 2 distorted distorted 6 19 20 21 38 P G G 3 distorted distorted 26 39 40 41 61 P C G 4 distorted distorted 46 62 63 64 81 P U G 5 distorted distorted 69 82 83 84 101 P G G 6 distorted distorted 89 102 103 104 124 P C G 7 distorted distorted 109 125 126 127 144 P U G 8 distorted distorted 132 145 146 147 164 P G G 9 distorted distorted 152 165 166 167 187 P C G 10 distorted distorted 172 188 189 190 207 P U G 11 distorted distorted 195 208 209 210 227 P G G 12 distorted distorted 215 228 229 230 250 P C G 13 distorted distorted 235 251 252 253 270 P U G 14 distorted distorted 258 271 272 273 290 P G G 15 distorted distorted 278 291 292 293 313 P C G 16 distorted distorted 298 314 315 316 333 P U G 17 distorted distorted 321 334 335 336 353 P G G 18 distorted distorted 341 354 355 356 394 P U H 2 distorted distorted 382 395 396 397 414 P G H 3 distorted distorted 402 415 416 417 437 P C H 4 distorted distorted 422 438 439 440 457 P U H 5 distorted distorted 445 458 459 460 477 P G H 6 distorted distorted 465 478 479 480 500 P C H 7 distorted distorted 485 501 502 503 520 P U H 8 distorted distorted 508 521 522 523 540 P G H 9 distorted distorted 528 541 542 543 563 P C H 10 distorted distorted 548 564 565 566 583 P U H 11 distorted distorted 571 584 585 586 603 P G H 12 distorted distorted 591 604 605 606 626 P C H 13 distorted distorted 611 627 628 629 646 P U H 14 distorted distorted 634 647 648 649 666 P G H 15 distorted distorted 654 667 668 669 689 P C H 16 distorted distorted 674 690 691 692 709 P U H 17 distorted distorted 697 710 711 712 729 P G H 18 distorted distorted 717 730 731 732 ---------------------------------------------------------------------------------