ID code: '1AL5' 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 alpha beta 4 24 10 7 41 C1' G A 2 alpha beta 36 59 42 39 75 C1' C A 3 alpha beta 70 90 76 73 106 C1' A A 4 alpha beta 101 123 107 104 139 C1' A A 5 alpha beta 134 156 140 137 172 C1' A A 6 alpha beta 167 189 173 170 205 C1' U A 7 alpha beta 200 220 206 203 235 C1' U A 8 alpha beta 230 250 236 233 265 C1' U A 9 alpha beta 260 280 266 263 295 C1' G A 10 alpha beta 290 313 296 293 329 C1' C A 11 alpha beta 324 344 330 327 360 C1' G A 12 alpha beta 355 379 361 358 393 C1' C B 1 alpha beta 388 408 394 391 425 C1' G B 2 alpha beta 420 443 426 423 459 C1' C B 3 alpha beta 454 474 460 457 490 C1' A B 4 alpha beta 485 507 491 488 523 C1' A B 5 alpha beta 518 540 524 521 556 C1' A B 6 alpha beta 551 573 557 554 589 C1' U B 7 alpha beta 584 604 590 587 619 C1' U B 8 alpha beta 614 634 620 617 649 C1' U B 9 alpha beta 644 664 650 647 679 C1' G B 10 alpha beta 674 697 680 677 713 C1' C B 11 alpha beta 708 728 714 711 744 C1' G B 12 alpha beta 739 763 745 742 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 OK 9 5 22 8 39 C2' G A 2 OK OK 41 37 57 40 73 C2' C A 3 OK OK 75 71 88 74 104 C2' A A 4 OK OK 106 102 121 105 137 C2' A A 5 OK OK 139 135 154 138 170 C2' A A 6 OK OK 172 168 187 171 203 C2' U A 7 OK OK 205 201 218 204 233 C2' U A 8 OK OK 235 231 248 234 263 C2' U A 9 OK OK 265 261 278 264 293 C2' G A 10 OK OK 295 291 311 294 327 C2' C A 11 OK OK 329 325 342 328 358 C2' G A 12 OK OK 360 356 377 359 391 C2' C B 1 OK OK 393 389 406 392 423 C2' G B 2 OK OK 425 421 441 424 457 C2' C B 3 OK OK 459 455 472 458 488 C2' A B 4 OK OK 490 486 505 489 521 C2' A B 5 OK OK 523 519 538 522 554 C2' A B 6 OK OK 556 552 571 555 587 C2' U B 7 OK OK 589 585 602 588 617 C2' U B 8 OK OK 619 615 632 618 647 C2' U B 9 OK OK 649 645 662 648 677 C2' G B 10 OK OK 679 675 695 678 711 C2' C B 11 OK OK 713 709 726 712 742 C2' G B 12 OK OK 744 740 761 743 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK OK 3 21 6 7 37 C3' G A 2 OK OK 35 56 38 39 71 C3' C A 3 OK OK 69 87 72 73 102 C3' A A 4 OK OK 100 120 103 104 135 C3' A A 5 OK OK 133 153 136 137 168 C3' A A 6 OK OK 166 186 169 170 201 C3' U A 7 OK OK 199 217 202 203 231 C3' U A 8 OK OK 229 247 232 233 261 C3' U A 9 OK OK 259 277 262 263 291 C3' G A 10 OK OK 289 310 292 293 325 C3' C A 11 OK OK 323 341 326 327 356 C3' G A 12 OK OK 354 375 357 358 389 C3' C B 1 OK OK 387 405 390 391 421 C3' G B 2 OK OK 419 440 422 423 455 C3' C B 3 OK OK 453 471 456 457 486 C3' A B 4 OK OK 484 504 487 488 519 C3' A B 5 OK OK 517 537 520 521 552 C3' A B 6 OK OK 550 570 553 554 585 C3' U B 7 OK OK 583 601 586 587 615 C3' U B 8 OK OK 613 631 616 617 645 C3' U B 9 OK OK 643 661 646 647 675 C3' G B 10 OK OK 673 694 676 677 709 C3' C B 11 OK OK 707 725 710 711 740 C3' G B 12 OK OK 738 759 741 742 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK OK 5 20 2 4 35 C4' G A 2 OK OK 37 55 34 36 69 C4' C A 3 OK OK 71 86 68 70 100 C4' A A 4 OK OK 102 119 99 101 133 C4' A A 5 OK OK 135 152 132 134 166 C4' A A 6 OK OK 168 185 165 167 199 C4' U A 7 OK OK 201 216 198 200 229 C4' U A 8 OK OK 231 246 228 230 259 C4' U A 9 OK OK 261 276 258 260 289 C4' G A 10 OK OK 291 309 288 290 323 C4' C A 11 OK OK 325 340 322 324 354 C4' G A 12 OK OK 356 374 353 355 387 C4' C B 1 OK OK 389 404 386 388 419 C4' G B 2 OK OK 421 439 418 420 453 C4' C B 3 OK OK 455 470 452 454 484 C4' A B 4 OK OK 486 503 483 485 517 C4' A B 5 OK OK 519 536 516 518 550 C4' A B 6 OK OK 552 569 549 551 583 C4' U B 7 OK OK 585 600 582 584 613 C4' U B 8 OK OK 615 630 612 614 643 C4' U B 9 OK OK 645 660 642 644 673 C4' G B 10 OK OK 675 693 672 674 707 C4' C B 11 OK OK 709 724 706 708 738 C4' G B 12 OK OK 740 758 737 739 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 OK OK 1 18 19 3 34 C5' G A 2 OK OK 33 53 54 35 68 C5' C A 3 OK OK 67 84 85 69 99 C5' A A 4 OK OK 98 117 118 100 132 C5' A A 5 OK OK 131 150 151 133 165 C5' A A 6 OK OK 164 183 184 166 198 C5' U A 7 OK OK 197 214 215 199 228 C5' U A 8 OK OK 227 244 245 229 258 C5' U A 9 OK OK 257 274 275 259 288 C5' G A 10 OK OK 287 307 308 289 322 C5' C A 11 OK OK 321 338 339 323 353 C5' G A 12 OK OK 352 372 373 354 386 C5' C B 1 OK OK 385 402 403 387 418 C5' G B 2 OK OK 417 437 438 419 452 C5' C B 3 OK OK 451 468 469 453 483 C5' A B 4 OK OK 482 501 502 484 516 C5' A B 5 OK OK 515 534 535 517 549 C5' A B 6 OK OK 548 567 568 550 582 C5' U B 7 OK OK 581 598 599 583 612 C5' U B 8 OK OK 611 628 629 613 642 C5' U B 9 OK OK 641 658 659 643 672 C5' G B 10 OK OK 671 691 692 673 706 C5' C B 11 OK OK 705 722 723 707 737 C5' G B 12 OK OK 736 756 757 738 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 30 P G A 2 distorted distorted 6 31 32 33 64 P C A 3 distorted distorted 38 65 66 67 95 P A A 4 distorted distorted 72 96 97 98 128 P A A 5 distorted distorted 103 129 130 131 161 P A A 6 distorted distorted 136 162 163 164 194 P U A 7 distorted distorted 169 195 196 197 224 P U A 8 distorted distorted 202 225 226 227 254 P U A 9 distorted distorted 232 255 256 257 284 P G A 10 distorted distorted 262 285 286 287 318 P C A 11 distorted distorted 292 319 320 321 349 P G A 12 distorted distorted 326 350 351 352 414 P G B 2 distorted distorted 390 415 416 417 448 P C B 3 distorted distorted 422 449 450 451 479 P A B 4 distorted distorted 456 480 481 482 512 P A B 5 distorted distorted 487 513 514 515 545 P A B 6 distorted distorted 520 546 547 548 578 P U B 7 distorted distorted 553 579 580 581 608 P U B 8 distorted distorted 586 609 610 611 638 P U B 9 distorted distorted 616 639 640 641 668 P G B 10 distorted distorted 646 669 670 671 702 P C B 11 distorted distorted 676 703 704 705 733 P G B 12 distorted distorted 710 734 735 736 ---------------------------------------------------------------------------------