ID code: '2GV3' 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' C A 3 alpha beta 73 93 79 76 109 C1' C A 4 alpha beta 104 124 110 107 140 C1' A A 5 alpha beta 135 157 141 138 173 C1' G A 6 alpha beta 168 191 174 171 207 C1' A A 7 alpha beta 202 224 208 205 240 C1' C A 8 alpha beta 235 255 241 238 271 C1' U A 9 alpha beta 266 286 272 269 301 C1' C A 10 alpha beta 296 316 302 299 332 C1' C A 11 alpha beta 327 347 333 330 363 C1' C A 12 alpha beta 358 378 364 361 394 C1' G A 13 alpha beta 389 412 395 392 428 C1' A A 14 alpha beta 423 445 429 426 461 C1' A A 15 alpha beta 456 478 462 459 494 C1' U A 16 alpha beta 489 509 495 492 524 C1' C A 17 alpha beta 519 539 525 522 555 C1' U A 18 alpha beta 550 570 556 553 585 C1' G A 19 alpha beta 580 603 586 583 619 C1' G A 20 alpha beta 614 637 620 617 653 C1' C A 21 alpha beta 648 668 654 651 684 C1' C A 22 alpha beta 679 700 685 682 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 3 OK OK 78 74 91 77 107 C2' C A 4 OK OK 109 105 122 108 138 C2' A A 5 OK OK 140 136 155 139 171 C2' G A 6 OK OK 173 169 189 172 205 C2' A A 7 OK OK 207 203 222 206 238 C2' C A 8 OK OK 240 236 253 239 269 C2' U A 9 OK OK 271 267 284 270 299 C2' C A 10 OK OK 301 297 314 300 330 C2' C A 11 OK OK 332 328 345 331 361 C2' C A 12 OK OK 363 359 376 362 392 C2' G A 13 OK OK 394 390 410 393 426 C2' A A 14 OK OK 428 424 443 427 459 C2' A A 15 OK OK 461 457 476 460 492 C2' U A 16 OK OK 494 490 507 493 522 C2' C A 17 OK OK 524 520 537 523 553 C2' U A 18 OK OK 555 551 568 554 583 C2' G A 19 OK OK 585 581 601 584 617 C2' G A 20 OK OK 619 615 635 618 651 C2' C A 21 OK OK 653 649 666 652 682 C2' C A 22 OK OK 684 680 698 683 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 72 90 75 76 105 C3' C A 4 OK OK 103 121 106 107 136 C3' A A 5 OK OK 134 154 137 138 169 C3' G A 6 OK OK 167 188 170 171 203 C3' A A 7 OK OK 201 221 204 205 236 C3' C A 8 OK OK 234 252 237 238 267 C3' U A 9 OK OK 265 283 268 269 297 C3' C A 10 OK OK 295 313 298 299 328 C3' C A 11 OK OK 326 344 329 330 359 C3' C A 12 OK OK 357 375 360 361 390 C3' G A 13 OK OK 388 409 391 392 424 C3' A A 14 OK OK 422 442 425 426 457 C3' A A 15 OK OK 455 475 458 459 490 C3' U A 16 OK OK 488 506 491 492 520 C3' C A 17 OK OK 518 536 521 522 551 C3' U A 18 OK OK 549 567 552 553 581 C3' G A 19 OK OK 579 600 582 583 615 C3' G A 20 OK OK 613 634 616 617 649 C3' C A 21 OK OK 647 665 650 651 680 C3' C A 22 OK OK 678 696 681 682 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 74 89 71 73 103 C4' C A 4 OK OK 105 120 102 104 134 C4' A A 5 OK OK 136 153 133 135 167 C4' G A 6 OK OK 169 187 166 168 201 C4' A A 7 OK OK 203 220 200 202 234 C4' C A 8 OK OK 236 251 233 235 265 C4' U A 9 OK OK 267 282 264 266 295 C4' C A 10 OK OK 297 312 294 296 326 C4' C A 11 OK OK 328 343 325 327 357 C4' C A 12 OK OK 359 374 356 358 388 C4' G A 13 OK OK 390 408 387 389 422 C4' A A 14 OK OK 424 441 421 423 455 C4' A A 15 OK OK 457 474 454 456 488 C4' U A 16 OK OK 490 505 487 489 518 C4' C A 17 OK OK 520 535 517 519 549 C4' U A 18 OK OK 551 566 548 550 579 C4' G A 19 OK OK 581 599 578 580 613 C4' G A 20 OK OK 615 633 612 614 647 C4' C A 21 OK OK 649 664 646 648 678 C4' C A 22 OK OK 680 695 677 679 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 3 OK OK 70 87 88 72 102 C5' C A 4 OK OK 101 118 119 103 133 C5' A A 5 OK OK 132 151 152 134 166 C5' G A 6 OK OK 165 185 186 167 200 C5' A A 7 OK OK 199 218 219 201 233 C5' C A 8 OK OK 232 249 250 234 264 C5' U A 9 OK OK 263 280 281 265 294 C5' C A 10 OK OK 293 310 311 295 325 C5' C A 11 OK OK 324 341 342 326 356 C5' C A 12 OK OK 355 372 373 357 387 C5' G A 13 OK OK 386 406 407 388 421 C5' A A 14 OK OK 420 439 440 422 454 C5' A A 15 OK OK 453 472 473 455 487 C5' U A 16 OK OK 486 503 504 488 517 C5' C A 17 OK OK 516 533 534 518 548 C5' U A 18 OK OK 547 564 565 549 578 C5' G A 19 OK OK 577 597 598 579 612 C5' G A 20 OK OK 611 631 632 613 646 C5' C A 21 OK OK 645 662 663 647 677 C5' C A 22 OK OK 676 693 694 678 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P C A 3 distorted distorted 41 68 69 70 98 P C A 4 distorted distorted 75 99 100 101 129 P A A 5 distorted distorted 106 130 131 132 162 P G A 6 distorted distorted 137 163 164 165 196 P A A 7 distorted distorted 170 197 198 199 229 P C A 8 distorted distorted 204 230 231 232 260 P U A 9 distorted distorted 237 261 262 263 290 P C A 10 distorted distorted 268 291 292 293 321 P C A 11 distorted distorted 298 322 323 324 352 P C A 12 distorted distorted 329 353 354 355 383 P G A 13 distorted distorted 360 384 385 386 417 P A A 14 distorted distorted 391 418 419 420 450 P A A 15 distorted distorted 425 451 452 453 483 P U A 16 distorted distorted 458 484 485 486 513 P C A 17 distorted distorted 491 514 515 516 544 P U A 18 distorted distorted 521 545 546 547 574 P G A 19 distorted distorted 552 575 576 577 608 P G A 20 distorted distorted 582 609 610 611 642 P C A 21 distorted distorted 616 643 644 645 673 P C A 22 distorted distorted 650 674 675 676 ---------------------------------------------------------------------------------