ID code: '4U6K' 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 A 1 beta 4 10 7 32 C1' A A 2 beta 27 33 30 54 C1' A A 3 beta 49 55 52 76 C1' G A 4 beta 71 77 74 99 C1' A A 5 beta 94 100 97 121 C1' A A 6 beta 116 122 119 143 C1' G A 7 beta 138 144 141 166 C1' A A 8 beta 161 167 164 188 C1' G A 9 beta 183 189 186 215 C1' NCU B 1 beta 214 201 211 239 C1' NTT B 2 beta 238 226 235 256 C1' DC B 3 beta 252 257 255 275 C1' DT B 4 beta 271 276 274 295 C1' DT B 5 beta 291 296 294 315 C1' DC B 6 beta 311 316 314 334 C1' DT B 7 beta 330 335 333 361 C1' NTT B 8 beta 360 348 357 385 C1' NCU B 9 beta 384 368 381 401 C1' G C 1 beta 396 402 399 424 C1' A C 2 beta 419 425 422 446 C1' A C 3 beta 441 447 444 468 C1' G C 4 beta 463 469 466 491 C1' A C 5 beta 486 492 489 513 C1' A C 6 beta 508 514 511 535 C1' G C 7 beta 530 536 533 558 C1' A C 8 beta 553 559 556 580 C1' G C 9 beta 575 581 578 607 C1' NCU D 1 beta 606 593 603 631 C1' NTT D 2 beta 630 618 627 648 C1' DC D 3 beta 644 649 647 667 C1' DT D 4 beta 663 668 666 687 C1' DT D 5 beta 683 688 686 707 C1' DC D 6 beta 703 708 706 726 C1' DT D 7 beta 722 727 725 753 C1' NTT D 8 beta 752 740 749 777 C1' NCU D 9 beta 776 760 773 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK 9 5 8 30 C2' A A 2 OK 32 28 31 52 C2' A A 3 OK 54 50 53 74 C2' G A 4 OK 76 72 75 97 C2' A A 5 OK 99 95 98 119 C2' A A 6 OK 121 117 120 141 C2' G A 7 OK 143 139 142 164 C2' A A 8 OK 166 162 165 186 C2' G A 9 OK 188 184 187 211 C2' NCU B 1 OK 215 216 218 235 C2' NTT B 2 OK 239 240 242 255 C2' DC B 3 256 253 274 C2' DT B 4 275 272 294 C2' DT B 5 295 292 314 C2' DC B 6 315 312 333 C2' DT B 7 334 331 357 C2' NTT B 8 OK 361 362 364 381 C2' NCU B 9 OK 385 386 388 399 C2' G C 1 OK 401 397 400 422 C2' A C 2 OK 424 420 423 444 C2' A C 3 OK 446 442 445 466 C2' G C 4 OK 468 464 467 489 C2' A C 5 OK 491 487 490 511 C2' A C 6 OK 513 509 512 533 C2' G C 7 OK 535 531 534 556 C2' A C 8 OK 558 554 557 578 C2' G C 9 OK 580 576 579 603 C2' NCU D 1 OK 607 608 610 627 C2' NTT D 2 OK 631 632 634 647 C2' DC D 3 648 645 666 C2' DT D 4 667 664 686 C2' DT D 5 687 684 706 C2' DC D 6 707 704 725 C2' DT D 7 726 723 749 C2' NTT D 8 OK 753 754 756 773 C2' NCU D 9 OK 777 778 780 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 28 C3' A A 2 OK 26 29 30 50 C3' A A 3 OK 48 51 52 72 C3' G A 4 OK 70 73 74 95 C3' A A 5 OK 93 96 97 117 C3' A A 6 OK 115 118 119 139 C3' G A 7 OK 137 140 141 162 C3' A A 8 OK 160 163 164 184 C3' G A 9 OK 182 185 186 216 C3' NCU B 1 OK 213 217 211 240 C3' NTT B 2 OK 237 241 235 253 C3' DC B 3 OK 251 254 255 272 C3' DT B 4 OK 270 273 274 292 C3' DT B 5 OK 290 293 294 312 C3' DC B 6 OK 310 313 314 331 C3' DT B 7 OK 329 332 333 362 C3' NTT B 8 OK 359 363 357 386 C3' NCU B 9 OK 383 387 381 397 C3' G C 1 OK 395 398 399 420 C3' A C 2 OK 418 421 422 442 C3' A C 3 OK 440 443 444 464 C3' G C 4 OK 462 465 466 487 C3' A C 5 OK 485 488 489 509 C3' A C 6 OK 507 510 511 531 C3' G C 7 OK 529 532 533 554 C3' A C 8 OK 552 555 556 576 C3' G C 9 OK 574 577 578 608 C3' NCU D 1 OK 605 609 603 632 C3' NTT D 2 OK 629 633 627 645 C3' DC D 3 OK 643 646 647 664 C3' DT D 4 OK 662 665 666 684 C3' DT D 5 OK 682 685 686 704 C3' DC D 6 OK 702 705 706 723 C3' DT D 7 OK 721 724 725 754 C3' NTT D 8 OK 751 755 749 778 C3' NCU D 9 OK 775 779 773 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 26 C4' A A 2 OK 28 25 27 48 C4' A A 3 OK 50 47 49 70 C4' G A 4 OK 72 69 71 93 C4' A A 5 OK 95 92 94 115 C4' A A 6 OK 117 114 116 137 C4' G A 7 OK 139 136 138 160 C4' A A 8 OK 162 159 161 182 C4' G A 9 OK 184 181 183 213 C4' NCU B 1 OK 216 212 214 237 C4' NTT B 2 OK 240 236 238 251 C4' DC B 3 OK 253 250 252 270 C4' DT B 4 OK 272 269 271 290 C4' DT B 5 OK 292 289 291 310 C4' DC B 6 OK 312 309 311 329 C4' DT B 7 OK 331 328 330 359 C4' NTT B 8 OK 362 358 360 383 C4' NCU B 9 OK 386 382 384 395 C4' G C 1 OK 397 394 396 418 C4' A C 2 OK 420 417 419 440 C4' A C 3 OK 442 439 441 462 C4' G C 4 OK 464 461 463 485 C4' A C 5 OK 487 484 486 507 C4' A C 6 OK 509 506 508 529 C4' G C 7 OK 531 528 530 552 C4' A C 8 OK 554 551 553 574 C4' G C 9 OK 576 573 575 605 C4' NCU D 1 OK 608 604 606 629 C4' NTT D 2 OK 632 628 630 643 C4' DC D 3 OK 645 642 644 662 C4' DT D 4 OK 664 661 663 682 C4' DT D 5 OK 684 681 683 702 C4' DC D 6 OK 704 701 703 721 C4' DT D 7 OK 723 720 722 751 C4' NTT D 8 OK 754 750 752 775 C4' NCU D 9 OK 778 774 776 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 25 C5' A A 2 24 26 47 C5' A A 3 46 48 69 C5' G A 4 68 70 92 C5' A A 5 91 93 114 C5' A A 6 113 115 136 C5' G A 7 135 137 159 C5' A A 8 158 160 181 C5' G A 9 180 182 212 C5' NCU B 1 208 213 236 C5' NTT B 2 225 237 250 C5' DC B 3 249 251 269 C5' DT B 4 268 270 289 C5' DT B 5 288 290 309 C5' DC B 6 308 310 328 C5' DT B 7 327 329 358 C5' NTT B 8 347 359 382 C5' NCU B 9 378 383 394 C5' G C 1 393 395 417 C5' A C 2 416 418 439 C5' A C 3 438 440 461 C5' G C 4 460 462 484 C5' A C 5 483 485 506 C5' A C 6 505 507 528 C5' G C 7 527 529 551 C5' A C 8 550 552 573 C5' G C 9 572 574 604 C5' NCU D 1 600 605 628 C5' NTT D 2 617 629 642 C5' DC D 3 641 643 661 C5' DT D 4 660 662 681 C5' DT D 5 680 682 701 C5' DC D 6 700 702 720 C5' DT D 7 719 721 750 C5' NTT D 8 739 751 774 C5' NCU D 9 770 775 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P A A 2 distorted distorted 6 22 23 24 43 P A A 3 distorted distorted 29 44 45 46 65 P G A 4 distorted distorted 51 66 67 68 88 P A A 5 distorted distorted 73 89 90 91 110 P A A 6 distorted distorted 96 111 112 113 132 P G A 7 distorted distorted 118 133 134 135 155 P A A 8 distorted distorted 140 156 157 158 177 P G A 9 distorted distorted 163 178 179 180 222 P NTT B 2 distorted distorted 217 223 224 225 246 P DC B 3 distorted distorted 241 247 248 249 265 P DT B 4 distorted distorted 254 266 267 268 285 P DT B 5 distorted distorted 273 286 287 288 305 P DC B 6 distorted distorted 293 306 307 308 324 P DT B 7 distorted distorted 313 325 326 327 344 P NTT B 8 distorted distorted 332 345 346 347 375 P NCU B 9 distorted distorted 363 376 377 378 413 P A C 2 distorted distorted 398 414 415 416 435 P A C 3 distorted distorted 421 436 437 438 457 P G C 4 distorted distorted 443 458 459 460 480 P A C 5 distorted distorted 465 481 482 483 502 P A C 6 distorted distorted 488 503 504 505 524 P G C 7 distorted distorted 510 525 526 527 547 P A C 8 distorted distorted 532 548 549 550 569 P G C 9 distorted distorted 555 570 571 572 614 P NTT D 2 distorted distorted 609 615 616 617 638 P DC D 3 distorted distorted 633 639 640 641 657 P DT D 4 distorted distorted 646 658 659 660 677 P DT D 5 distorted distorted 665 678 679 680 697 P DC D 6 distorted distorted 685 698 699 700 716 P DT D 7 distorted distorted 705 717 718 719 736 P NTT D 8 distorted distorted 724 737 738 739 767 P NCU D 9 distorted distorted 755 768 769 770 ---------------------------------------------------------------------------------