ID code: '2GRW' 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 alpha beta 4 27 10 7 44 C1' G A 2 alpha beta 39 62 45 42 78 C1' A A 3 alpha beta 73 95 79 76 111 C1' C A 4 alpha beta 106 126 112 109 142 C1' C A 5 alpha beta 137 157 143 140 173 C1' U A 6 alpha beta 168 188 174 171 203 C1' C A 7 alpha beta 198 218 204 201 234 C1' U A 8 alpha beta 229 249 235 232 264 C1' C A 9 alpha beta 259 279 265 262 295 C1' G A 10 alpha beta 290 313 296 293 329 C1' A A 11 alpha beta 324 346 330 327 362 C1' A A 12 alpha beta 357 379 363 360 395 C1' A A 13 alpha beta 390 412 396 393 428 C1' G A 14 alpha beta 423 446 429 426 462 C1' A A 15 alpha beta 457 479 463 460 495 C1' G A 16 alpha beta 490 513 496 493 529 C1' A A 17 alpha beta 524 546 530 527 562 C1' U A 18 alpha beta 557 577 563 560 592 C1' G A 19 alpha beta 587 610 593 590 626 C1' U A 20 alpha beta 621 641 627 624 656 C1' C A 21 alpha beta 651 671 657 654 687 C1' C A 22 alpha beta 682 703 688 685 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 OK 9 5 25 8 42 C2' G A 2 OK OK 44 40 60 43 76 C2' A A 3 OK OK 78 74 93 77 109 C2' C A 4 OK OK 111 107 124 110 140 C2' C A 5 OK OK 142 138 155 141 171 C2' U A 6 OK OK 173 169 186 172 201 C2' C A 7 OK OK 203 199 216 202 232 C2' U A 8 OK OK 234 230 247 233 262 C2' C A 9 OK OK 264 260 277 263 293 C2' G A 10 OK OK 295 291 311 294 327 C2' A A 11 OK OK 329 325 344 328 360 C2' A A 12 OK OK 362 358 377 361 393 C2' A A 13 OK OK 395 391 410 394 426 C2' G A 14 OK OK 428 424 444 427 460 C2' A A 15 OK OK 462 458 477 461 493 C2' G A 16 OK OK 495 491 511 494 527 C2' A A 17 OK OK 529 525 544 528 560 C2' U A 18 OK OK 562 558 575 561 590 C2' G A 19 OK OK 592 588 608 591 624 C2' U A 20 OK OK 626 622 639 625 654 C2' C A 21 OK OK 656 652 669 655 685 C2' C A 22 OK OK 687 683 701 686 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' A A 3 OK OK 72 92 75 76 107 C3' C A 4 OK OK 105 123 108 109 138 C3' C A 5 OK OK 136 154 139 140 169 C3' U A 6 OK OK 167 185 170 171 199 C3' C A 7 OK OK 197 215 200 201 230 C3' U A 8 OK OK 228 246 231 232 260 C3' C A 9 OK OK 258 276 261 262 291 C3' G A 10 OK OK 289 310 292 293 325 C3' A A 11 OK OK 323 343 326 327 358 C3' A A 12 OK OK 356 376 359 360 391 C3' A A 13 OK OK 389 409 392 393 424 C3' G A 14 OK OK 422 443 425 426 458 C3' A A 15 OK OK 456 476 459 460 491 C3' G A 16 OK OK 489 510 492 493 525 C3' A A 17 OK OK 523 543 526 527 558 C3' U A 18 OK OK 556 574 559 560 588 C3' G A 19 OK OK 586 607 589 590 622 C3' U A 20 OK OK 620 638 623 624 652 C3' C A 21 OK OK 650 668 653 654 683 C3' C A 22 OK OK 681 699 684 685 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' A A 3 OK OK 74 91 71 73 105 C4' C A 4 OK OK 107 122 104 106 136 C4' C A 5 OK OK 138 153 135 137 167 C4' U A 6 OK OK 169 184 166 168 197 C4' C A 7 OK OK 199 214 196 198 228 C4' U A 8 OK OK 230 245 227 229 258 C4' C A 9 OK OK 260 275 257 259 289 C4' G A 10 OK OK 291 309 288 290 323 C4' A A 11 OK OK 325 342 322 324 356 C4' A A 12 OK OK 358 375 355 357 389 C4' A A 13 OK OK 391 408 388 390 422 C4' G A 14 OK OK 424 442 421 423 456 C4' A A 15 OK OK 458 475 455 457 489 C4' G A 16 OK OK 491 509 488 490 523 C4' A A 17 OK OK 525 542 522 524 556 C4' U A 18 OK OK 558 573 555 557 586 C4' G A 19 OK OK 588 606 585 587 620 C4' U A 20 OK OK 622 637 619 621 650 C4' C A 21 OK OK 652 667 649 651 681 C4' C A 22 OK OK 683 698 680 682 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' G A 2 OK OK 36 56 57 38 71 C5' A A 3 OK OK 70 89 90 72 104 C5' C A 4 OK OK 103 120 121 105 135 C5' C A 5 OK OK 134 151 152 136 166 C5' U A 6 OK OK 165 182 183 167 196 C5' C A 7 OK OK 195 212 213 197 227 C5' U A 8 OK OK 226 243 244 228 257 C5' C A 9 OK OK 256 273 274 258 288 C5' G A 10 OK OK 287 307 308 289 322 C5' A A 11 OK OK 321 340 341 323 355 C5' A A 12 OK OK 354 373 374 356 388 C5' A A 13 OK OK 387 406 407 389 421 C5' G A 14 OK OK 420 440 441 422 455 C5' A A 15 OK OK 454 473 474 456 488 C5' G A 16 OK OK 487 507 508 489 522 C5' A A 17 OK OK 521 540 541 523 555 C5' U A 18 OK OK 554 571 572 556 585 C5' G A 19 OK OK 584 604 605 586 619 C5' U A 20 OK OK 618 635 636 620 649 C5' C A 21 OK OK 648 665 666 650 680 C5' C A 22 OK OK 679 696 697 681 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P A A 3 distorted distorted 41 68 69 70 100 P C A 4 distorted distorted 75 101 102 103 131 P C A 5 distorted distorted 108 132 133 134 162 P U A 6 distorted distorted 139 163 164 165 192 P C A 7 distorted distorted 170 193 194 195 223 P U A 8 distorted distorted 200 224 225 226 253 P C A 9 distorted distorted 231 254 255 256 284 P G A 10 distorted distorted 261 285 286 287 318 P A A 11 distorted distorted 292 319 320 321 351 P A A 12 distorted distorted 326 352 353 354 384 P A A 13 distorted distorted 359 385 386 387 417 P G A 14 distorted distorted 392 418 419 420 451 P A A 15 distorted distorted 425 452 453 454 484 P G A 16 distorted distorted 459 485 486 487 518 P A A 17 distorted distorted 492 519 520 521 551 P U A 18 distorted distorted 526 552 553 554 581 P G A 19 distorted distorted 559 582 583 584 615 P U A 20 distorted distorted 589 616 617 618 645 P C A 21 distorted distorted 623 646 647 648 676 P C A 22 distorted distorted 653 677 678 679 ---------------------------------------------------------------------------------