ID code: '17RA' 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' G A 4 alpha beta 104 127 110 107 143 C1' U A 5 alpha beta 138 158 144 141 173 C1' A A 6 alpha beta 168 190 174 171 206 C1' A A 7 alpha beta 201 223 207 204 239 C1' G A 8 alpha beta 234 257 240 237 273 C1' G A 9 alpha beta 268 291 274 271 307 C1' A A 10 alpha beta 302 324 308 305 340 C1' U A 11 alpha beta 335 355 341 338 370 C1' U A 12 alpha beta 365 385 371 368 400 C1' A A 13 alpha beta 395 417 401 398 433 C1' C A 14 alpha beta 428 448 434 431 464 C1' C A 15 alpha beta 459 479 465 462 495 C1' U A 16 alpha beta 490 510 496 493 525 C1' A A 17 alpha beta 520 542 526 523 558 C1' U A 18 alpha beta 553 573 559 556 588 C1' G A 19 alpha beta 583 606 589 586 622 C1' C A 20 alpha beta 617 637 623 620 653 C1' C A 21 alpha beta 648 669 654 651 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 4 OK OK 109 105 125 108 141 C2' U A 5 OK OK 143 139 156 142 171 C2' A A 6 OK OK 173 169 188 172 204 C2' A A 7 OK OK 206 202 221 205 237 C2' G A 8 OK OK 239 235 255 238 271 C2' G A 9 OK OK 273 269 289 272 305 C2' A A 10 OK OK 307 303 322 306 338 C2' U A 11 OK OK 340 336 353 339 368 C2' U A 12 OK OK 370 366 383 369 398 C2' A A 13 OK OK 400 396 415 399 431 C2' C A 14 OK OK 433 429 446 432 462 C2' C A 15 OK OK 464 460 477 463 493 C2' U A 16 OK OK 495 491 508 494 523 C2' A A 17 OK OK 525 521 540 524 556 C2' U A 18 OK OK 558 554 571 557 586 C2' G A 19 OK OK 588 584 604 587 620 C2' C A 20 OK OK 622 618 635 621 651 C2' C A 21 OK OK 653 649 667 652 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 4 OK OK 103 124 106 107 139 C3' U A 5 OK OK 137 155 140 141 169 C3' A A 6 OK OK 167 187 170 171 202 C3' A A 7 OK OK 200 220 203 204 235 C3' G A 8 OK OK 233 254 236 237 269 C3' G A 9 OK OK 267 288 270 271 303 C3' A A 10 OK OK 301 321 304 305 336 C3' U A 11 OK OK 334 352 337 338 366 C3' U A 12 OK OK 364 382 367 368 396 C3' A A 13 OK OK 394 414 397 398 429 C3' C A 14 OK OK 427 445 430 431 460 C3' C A 15 OK OK 458 476 461 462 491 C3' U A 16 OK OK 489 507 492 493 521 C3' A A 17 OK OK 519 539 522 523 554 C3' U A 18 OK OK 552 570 555 556 584 C3' G A 19 OK OK 582 603 585 586 618 C3' C A 20 OK OK 616 634 619 620 649 C3' C A 21 OK OK 647 665 650 651 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 4 OK OK 105 123 102 104 137 C4' U A 5 OK OK 139 154 136 138 167 C4' A A 6 OK OK 169 186 166 168 200 C4' A A 7 OK OK 202 219 199 201 233 C4' G A 8 OK OK 235 253 232 234 267 C4' G A 9 OK OK 269 287 266 268 301 C4' A A 10 OK OK 303 320 300 302 334 C4' U A 11 OK OK 336 351 333 335 364 C4' U A 12 OK OK 366 381 363 365 394 C4' A A 13 OK OK 396 413 393 395 427 C4' C A 14 OK OK 429 444 426 428 458 C4' C A 15 OK OK 460 475 457 459 489 C4' U A 16 OK OK 491 506 488 490 519 C4' A A 17 OK OK 521 538 518 520 552 C4' U A 18 OK OK 554 569 551 553 582 C4' G A 19 OK OK 584 602 581 583 616 C4' C A 20 OK OK 618 633 615 617 647 C4' C A 21 OK OK 649 664 646 648 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 4 OK OK 101 121 122 103 136 C5' U A 5 OK OK 135 152 153 137 166 C5' A A 6 OK OK 165 184 185 167 199 C5' A A 7 OK OK 198 217 218 200 232 C5' G A 8 OK OK 231 251 252 233 266 C5' G A 9 OK OK 265 285 286 267 300 C5' A A 10 OK OK 299 318 319 301 333 C5' U A 11 OK OK 332 349 350 334 363 C5' U A 12 OK OK 362 379 380 364 393 C5' A A 13 OK OK 392 411 412 394 426 C5' C A 14 OK OK 425 442 443 427 457 C5' C A 15 OK OK 456 473 474 458 488 C5' U A 16 OK OK 487 504 505 489 518 C5' A A 17 OK OK 517 536 537 519 551 C5' U A 18 OK OK 550 567 568 552 581 C5' G A 19 OK OK 580 600 601 582 615 C5' C A 20 OK OK 614 631 632 616 646 C5' C A 21 OK OK 645 662 663 647 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 G A 4 distorted distorted 75 99 100 101 132 P U A 5 distorted distorted 106 133 134 135 162 P A A 6 distorted distorted 140 163 164 165 195 P A A 7 distorted distorted 170 196 197 198 228 P G A 8 distorted distorted 203 229 230 231 262 P G A 9 distorted distorted 236 263 264 265 296 P A A 10 distorted distorted 270 297 298 299 329 P U A 11 distorted distorted 304 330 331 332 359 P U A 12 distorted distorted 337 360 361 362 389 P A A 13 distorted distorted 367 390 391 392 422 P C A 14 distorted distorted 397 423 424 425 453 P C A 15 distorted distorted 430 454 455 456 484 P U A 16 distorted distorted 461 485 486 487 514 P A A 17 distorted distorted 492 515 516 517 547 P U A 18 distorted distorted 522 548 549 550 577 P G A 19 distorted distorted 555 578 579 580 611 P C A 20 distorted distorted 585 612 613 614 642 P C A 21 distorted distorted 619 643 644 645 ---------------------------------------------------------------------------------