ID code: '1DSZ' 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' --------------------------------------------------------------------------------- 8 C1' C C1495 beta 4 9 7 27 C1' A C1496 beta 23 28 26 48 C1' G C1497 beta 44 49 47 70 C1' G C1498 beta 66 71 69 92 C1' T C1499 beta 88 93 91 112 C1' C C1500 beta 108 113 111 131 C1' A C1501 beta 127 132 130 152 C1' A C1502 beta 148 153 151 173 C1' A C1503 beta 169 174 172 194 C1' G C1504 beta 190 195 193 216 C1' G C1505 beta 212 217 215 238 C1' T C1506 beta 234 239 237 258 C1' C C1507 beta 254 259 257 277 C1' A C1508 beta 273 278 276 298 C1' G C1509 beta 294 299 297 318 C1' C D1531 beta 314 319 317 337 C1' T D1532 beta 333 338 336 357 C1' G D1533 beta 353 358 356 379 C1' A D1534 beta 375 380 378 400 C1' C D1535 beta 396 401 399 419 C1' C D1536 beta 415 420 418 438 C1' T D1537 beta 434 439 437 458 C1' T D1538 beta 454 459 457 478 C1' T D1539 beta 474 479 477 498 C1' G D1540 beta 494 499 497 520 C1' A D1541 beta 516 521 519 541 C1' C D1542 beta 537 542 540 560 C1' C D1543 beta 556 561 559 579 C1' T D1544 beta 575 580 578 599 C1' G D1545 beta 595 600 598 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C C1495 8 5 26 C2' A C1496 27 24 47 C2' G C1497 48 45 69 C2' G C1498 70 67 91 C2' T C1499 92 89 111 C2' C C1500 112 109 130 C2' A C1501 131 128 151 C2' A C1502 152 149 172 C2' A C1503 173 170 193 C2' G C1504 194 191 215 C2' G C1505 216 213 237 C2' T C1506 238 235 257 C2' C C1507 258 255 276 C2' A C1508 277 274 297 C2' G C1509 298 295 317 C2' C D1531 318 315 336 C2' T D1532 337 334 356 C2' G D1533 357 354 378 C2' A D1534 379 376 399 C2' C D1535 400 397 418 C2' C D1536 419 416 437 C2' T D1537 438 435 457 C2' T D1538 458 455 477 C2' T D1539 478 475 497 C2' G D1540 498 495 519 C2' A D1541 520 517 540 C2' C D1542 541 538 559 C2' C D1543 560 557 578 C2' T D1544 579 576 598 C2' G D1545 599 596 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C C1495 OK 3 6 7 24 C3' A C1496 OK 22 25 26 45 C3' G C1497 OK 43 46 47 67 C3' G C1498 OK 65 68 69 89 C3' T C1499 OK 87 90 91 109 C3' C C1500 OK 107 110 111 128 C3' A C1501 OK 126 129 130 149 C3' A C1502 OK 147 150 151 170 C3' A C1503 OK 168 171 172 191 C3' G C1504 OK 189 192 193 213 C3' G C1505 OK 211 214 215 235 C3' T C1506 OK 233 236 237 255 C3' C C1507 OK 253 256 257 274 C3' A C1508 OK 272 275 276 295 C3' G C1509 OK 293 296 297 315 C3' C D1531 OK 313 316 317 334 C3' T D1532 OK 332 335 336 354 C3' G D1533 OK 352 355 356 376 C3' A D1534 OK 374 377 378 397 C3' C D1535 OK 395 398 399 416 C3' C D1536 OK 414 417 418 435 C3' T D1537 OK 433 436 437 455 C3' T D1538 OK 453 456 457 475 C3' T D1539 OK 473 476 477 495 C3' G D1540 OK 493 496 497 517 C3' A D1541 OK 515 518 519 538 C3' C D1542 OK 536 539 540 557 C3' C D1543 OK 555 558 559 576 C3' T D1544 OK 574 577 578 596 C3' G D1545 OK 594 597 598 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C C1495 OK 5 2 4 22 C4' A C1496 OK 24 21 23 43 C4' G C1497 OK 45 42 44 65 C4' G C1498 OK 67 64 66 87 C4' T C1499 OK 89 86 88 107 C4' C C1500 OK 109 106 108 126 C4' A C1501 OK 128 125 127 147 C4' A C1502 OK 149 146 148 168 C4' A C1503 OK 170 167 169 189 C4' G C1504 OK 191 188 190 211 C4' G C1505 OK 213 210 212 233 C4' T C1506 OK 235 232 234 253 C4' C C1507 OK 255 252 254 272 C4' A C1508 OK 274 271 273 293 C4' G C1509 OK 295 292 294 313 C4' C D1531 OK 315 312 314 332 C4' T D1532 OK 334 331 333 352 C4' G D1533 OK 354 351 353 374 C4' A D1534 OK 376 373 375 395 C4' C D1535 OK 397 394 396 414 C4' C D1536 OK 416 413 415 433 C4' T D1537 OK 435 432 434 453 C4' T D1538 OK 455 452 454 473 C4' T D1539 OK 475 472 474 493 C4' G D1540 OK 495 492 494 515 C4' A D1541 OK 517 514 516 536 C4' C D1542 OK 538 535 537 555 C4' C D1543 OK 557 554 556 574 C4' T D1544 OK 576 573 575 594 C4' G D1545 OK 596 593 595 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C C1495 1 3 21 C5' A C1496 20 22 42 C5' G C1497 41 43 64 C5' G C1498 63 65 86 C5' T C1499 85 87 106 C5' C C1500 105 107 125 C5' A C1501 124 126 146 C5' A C1502 145 147 167 C5' A C1503 166 168 188 C5' G C1504 187 189 210 C5' G C1505 209 211 232 C5' T C1506 231 233 252 C5' C C1507 251 253 271 C5' A C1508 270 272 292 C5' G C1509 291 293 312 C5' C D1531 311 313 331 C5' T D1532 330 332 351 C5' G D1533 350 352 373 C5' A D1534 372 374 394 C5' C D1535 393 395 413 C5' C D1536 412 414 432 C5' T D1537 431 433 452 C5' T D1538 451 453 472 C5' T D1539 471 473 492 C5' G D1540 491 493 514 C5' A D1541 513 515 535 C5' C D1542 534 536 554 C5' C D1543 553 555 573 C5' T D1544 572 574 593 C5' G D1545 592 594 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 17 P A C1496 distorted distorted 6 18 19 20 38 P G C1497 distorted distorted 25 39 40 41 60 P G C1498 distorted distorted 46 61 62 63 82 P T C1499 distorted distorted 68 83 84 85 102 P C C1500 distorted distorted 90 103 104 105 121 P A C1501 distorted distorted 110 122 123 124 142 P A C1502 distorted distorted 129 143 144 145 163 P A C1503 distorted distorted 150 164 165 166 184 P G C1504 distorted distorted 171 185 186 187 206 P G C1505 distorted distorted 192 207 208 209 228 P T C1506 distorted distorted 214 229 230 231 248 P C C1507 distorted distorted 236 249 250 251 267 P A C1508 distorted distorted 256 268 269 270 288 P G C1509 distorted distorted 275 289 290 291 327 P T D1532 distorted distorted 316 328 329 330 347 P G D1533 distorted distorted 335 348 349 350 369 P A D1534 distorted distorted 355 370 371 372 390 P C D1535 distorted distorted 377 391 392 393 409 P C D1536 distorted distorted 398 410 411 412 428 P T D1537 distorted distorted 417 429 430 431 448 P T D1538 distorted distorted 436 449 450 451 468 P T D1539 distorted distorted 456 469 470 471 488 P G D1540 distorted distorted 476 489 490 491 510 P A D1541 distorted distorted 496 511 512 513 531 P C D1542 distorted distorted 518 532 533 534 550 P C D1543 distorted distorted 539 551 552 553 569 P T D1544 distorted distorted 558 570 571 572 589 P G D1545 distorted distorted 577 590 591 592 ---------------------------------------------------------------------------------