ID code: '1BY4' 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' T E1495 beta 4 9 7 28 C1' A E1496 beta 24 29 27 49 C1' G E1497 beta 45 50 48 71 C1' G E1498 beta 67 72 70 93 C1' T E1499 beta 89 94 92 113 C1' C E1500 beta 109 114 112 132 C1' A E1501 beta 128 133 131 153 C1' A E1502 beta 149 154 152 174 C1' A E1503 beta 170 175 173 195 C1' G E1504 beta 191 196 194 217 C1' G E1505 beta 213 218 216 239 C1' T E1506 beta 235 240 238 259 C1' C E1507 beta 255 260 258 278 C1' A E1508 beta 274 279 277 299 C1' G E1509 beta 295 300 298 319 C1' C F1531 beta 315 320 318 338 C1' T F1532 beta 334 339 337 358 C1' G F1533 beta 354 359 357 380 C1' A F1534 beta 376 381 379 401 C1' C F1535 beta 397 402 400 420 C1' C F1536 beta 416 421 419 439 C1' T F1537 beta 435 440 438 459 C1' T F1538 beta 455 460 458 479 C1' T F1539 beta 475 480 478 499 C1' G F1540 beta 495 500 498 521 C1' A F1541 beta 517 522 520 542 C1' C F1542 beta 538 543 541 561 C1' C F1543 beta 557 562 560 580 C1' T F1544 beta 576 581 579 600 C1' A F1545 beta 596 601 599 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' T E1495 8 5 27 C2' A E1496 28 25 48 C2' G E1497 49 46 70 C2' G E1498 71 68 92 C2' T E1499 93 90 112 C2' C E1500 113 110 131 C2' A E1501 132 129 152 C2' A E1502 153 150 173 C2' A E1503 174 171 194 C2' G E1504 195 192 216 C2' G E1505 217 214 238 C2' T E1506 239 236 258 C2' C E1507 259 256 277 C2' A E1508 278 275 298 C2' G E1509 299 296 318 C2' C F1531 319 316 337 C2' T F1532 338 335 357 C2' G F1533 358 355 379 C2' A F1534 380 377 400 C2' C F1535 401 398 419 C2' C F1536 420 417 438 C2' T F1537 439 436 458 C2' T F1538 459 456 478 C2' T F1539 479 476 498 C2' G F1540 499 496 520 C2' A F1541 521 518 541 C2' C F1542 542 539 560 C2' C F1543 561 558 579 C2' T F1544 580 577 599 C2' A F1545 600 597 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' T E1495 OK 3 6 7 25 C3' A E1496 OK 23 26 27 46 C3' G E1497 OK 44 47 48 68 C3' G E1498 OK 66 69 70 90 C3' T E1499 OK 88 91 92 110 C3' C E1500 OK 108 111 112 129 C3' A E1501 OK 127 130 131 150 C3' A E1502 OK 148 151 152 171 C3' A E1503 OK 169 172 173 192 C3' G E1504 OK 190 193 194 214 C3' G E1505 OK 212 215 216 236 C3' T E1506 OK 234 237 238 256 C3' C E1507 OK 254 257 258 275 C3' A E1508 OK 273 276 277 296 C3' G E1509 OK 294 297 298 316 C3' C F1531 OK 314 317 318 335 C3' T F1532 OK 333 336 337 355 C3' G F1533 OK 353 356 357 377 C3' A F1534 OK 375 378 379 398 C3' C F1535 OK 396 399 400 417 C3' C F1536 OK 415 418 419 436 C3' T F1537 OK 434 437 438 456 C3' T F1538 OK 454 457 458 476 C3' T F1539 OK 474 477 478 496 C3' G F1540 OK 494 497 498 518 C3' A F1541 OK 516 519 520 539 C3' C F1542 OK 537 540 541 558 C3' C F1543 OK 556 559 560 577 C3' T F1544 OK 575 578 579 597 C3' A F1545 OK 595 598 599 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' T E1495 OK 5 2 4 23 C4' A E1496 OK 25 22 24 44 C4' G E1497 OK 46 43 45 66 C4' G E1498 OK 68 65 67 88 C4' T E1499 OK 90 87 89 108 C4' C E1500 OK 110 107 109 127 C4' A E1501 OK 129 126 128 148 C4' A E1502 OK 150 147 149 169 C4' A E1503 OK 171 168 170 190 C4' G E1504 OK 192 189 191 212 C4' G E1505 OK 214 211 213 234 C4' T E1506 OK 236 233 235 254 C4' C E1507 OK 256 253 255 273 C4' A E1508 OK 275 272 274 294 C4' G E1509 OK 296 293 295 314 C4' C F1531 OK 316 313 315 333 C4' T F1532 OK 335 332 334 353 C4' G F1533 OK 355 352 354 375 C4' A F1534 OK 377 374 376 396 C4' C F1535 OK 398 395 397 415 C4' C F1536 OK 417 414 416 434 C4' T F1537 OK 436 433 435 454 C4' T F1538 OK 456 453 455 474 C4' T F1539 OK 476 473 475 494 C4' G F1540 OK 496 493 495 516 C4' A F1541 OK 518 515 517 537 C4' C F1542 OK 539 536 538 556 C4' C F1543 OK 558 555 557 575 C4' T F1544 OK 577 574 576 595 C4' A F1545 OK 597 594 596 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' T E1495 1 3 22 C5' A E1496 21 23 43 C5' G E1497 42 44 65 C5' G E1498 64 66 87 C5' T E1499 86 88 107 C5' C E1500 106 108 126 C5' A E1501 125 127 147 C5' A E1502 146 148 168 C5' A E1503 167 169 189 C5' G E1504 188 190 211 C5' G E1505 210 212 233 C5' T E1506 232 234 253 C5' C E1507 252 254 272 C5' A E1508 271 273 293 C5' G E1509 292 294 313 C5' C F1531 312 314 332 C5' T F1532 331 333 352 C5' G F1533 351 353 374 C5' A F1534 373 375 395 C5' C F1535 394 396 414 C5' C F1536 413 415 433 C5' T F1537 432 434 453 C5' T F1538 452 454 473 C5' T F1539 472 474 493 C5' G F1540 492 494 515 C5' A F1541 514 516 536 C5' C F1542 535 537 555 C5' C F1543 554 556 574 C5' T F1544 573 575 594 C5' A F1545 593 595 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P A E1496 distorted distorted 6 19 20 21 39 P G E1497 distorted distorted 26 40 41 42 61 P G E1498 distorted distorted 47 62 63 64 83 P T E1499 distorted distorted 69 84 85 86 103 P C E1500 distorted distorted 91 104 105 106 122 P A E1501 distorted distorted 111 123 124 125 143 P A E1502 distorted distorted 130 144 145 146 164 P A E1503 distorted distorted 151 165 166 167 185 P G E1504 distorted distorted 172 186 187 188 207 P G E1505 distorted distorted 193 208 209 210 229 P T E1506 distorted distorted 215 230 231 232 249 P C E1507 distorted distorted 237 250 251 252 268 P A E1508 distorted distorted 257 269 270 271 289 P G E1509 distorted distorted 276 290 291 292 328 P T F1532 distorted distorted 317 329 330 331 348 P G F1533 distorted distorted 336 349 350 351 370 P A F1534 distorted distorted 356 371 372 373 391 P C F1535 distorted distorted 378 392 393 394 410 P C F1536 distorted distorted 399 411 412 413 429 P T F1537 distorted distorted 418 430 431 432 449 P T F1538 distorted distorted 437 450 451 452 469 P T F1539 distorted distorted 457 470 471 472 489 P G F1540 distorted distorted 477 490 491 492 511 P A F1541 distorted distorted 497 512 513 514 532 P C F1542 distorted distorted 519 533 534 535 551 P C F1543 distorted distorted 540 552 553 554 570 P T F1544 distorted distorted 559 571 572 573 590 P A F1545 distorted distorted 578 591 592 593 ---------------------------------------------------------------------------------