ID code: '1DRG' 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' --------------------------------------------------------------------------------- 11 C1' A B 2 beta 7 12 10 32 C1' T B 3 beta 28 33 31 52 C1' A B 4 beta 48 53 51 73 C1' A B 5 beta 69 74 72 94 C1' C B 6 beta 90 95 93 113 C1' T B 7 beta 109 114 112 133 C1' T B 8 beta 129 134 132 153 C1' C B 9 beta 149 154 152 172 C1' G B 10 beta 168 173 171 194 C1' T B 11 beta 190 195 193 214 C1' A B 12 beta 210 215 213 235 C1' T B 13 beta 231 236 234 255 C1' A B 14 beta 251 256 254 276 C1' G B 15 beta 272 277 275 298 C1' C B 16 beta 294 299 297 318 C1' G C 5 beta 314 319 317 340 C1' C C 6 beta 336 341 339 359 C1' T C 7 beta 355 360 358 379 C1' A C 8 beta 375 380 378 400 C1' T C 9 beta 396 401 399 420 C1' A C 10 beta 416 421 419 441 C1' C C 11 beta 437 442 440 460 C1' G C 12 beta 456 461 459 482 C1' A C 13 beta 478 483 481 503 C1' A C 14 beta 499 504 502 524 C1' G C 15 beta 520 525 523 546 C1' T C 16 beta 542 547 545 566 C1' T C 17 beta 562 567 565 586 C1' A C 18 beta 582 587 585 607 C1' T C 19 beta 603 608 606 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' A B 2 11 8 31 C2' T B 3 32 29 51 C2' A B 4 52 49 72 C2' A B 5 73 70 93 C2' C B 6 94 91 112 C2' T B 7 113 110 132 C2' T B 8 133 130 152 C2' C B 9 153 150 171 C2' G B 10 172 169 193 C2' T B 11 194 191 213 C2' A B 12 214 211 234 C2' T B 13 235 232 254 C2' A B 14 255 252 275 C2' G B 15 276 273 297 C2' C B 16 298 295 317 C2' G C 5 318 315 339 C2' C C 6 340 337 358 C2' T C 7 359 356 378 C2' A C 8 379 376 399 C2' T C 9 400 397 419 C2' A C 10 420 417 440 C2' C C 11 441 438 459 C2' G C 12 460 457 481 C2' A C 13 482 479 502 C2' A C 14 503 500 523 C2' G C 15 524 521 545 C2' T C 16 546 543 565 C2' T C 17 566 563 585 C2' A C 18 586 583 606 C2' T C 19 607 604 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A B 2 OK 6 9 10 29 C3' T B 3 OK 27 30 31 49 C3' A B 4 OK 47 50 51 70 C3' A B 5 OK 68 71 72 91 C3' C B 6 OK 89 92 93 110 C3' T B 7 OK 108 111 112 130 C3' T B 8 OK 128 131 132 150 C3' C B 9 OK 148 151 152 169 C3' G B 10 OK 167 170 171 191 C3' T B 11 OK 189 192 193 211 C3' A B 12 OK 209 212 213 232 C3' T B 13 OK 230 233 234 252 C3' A B 14 OK 250 253 254 273 C3' G B 15 OK 271 274 275 295 C3' C B 16 OK 293 296 297 315 C3' G C 5 OK 313 316 317 337 C3' C C 6 OK 335 338 339 356 C3' T C 7 OK 354 357 358 376 C3' A C 8 OK 374 377 378 397 C3' T C 9 OK 395 398 399 417 C3' A C 10 OK 415 418 419 438 C3' C C 11 OK 436 439 440 457 C3' G C 12 OK 455 458 459 479 C3' A C 13 OK 477 480 481 500 C3' A C 14 OK 498 501 502 521 C3' G C 15 OK 519 522 523 543 C3' T C 16 OK 541 544 545 563 C3' T C 17 OK 561 564 565 583 C3' A C 18 OK 581 584 585 604 C3' T C 19 OK 602 605 606 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A B 2 OK 8 5 7 27 C4' T B 3 OK 29 26 28 47 C4' A B 4 OK 49 46 48 68 C4' A B 5 OK 70 67 69 89 C4' C B 6 OK 91 88 90 108 C4' T B 7 OK 110 107 109 128 C4' T B 8 OK 130 127 129 148 C4' C B 9 OK 150 147 149 167 C4' G B 10 OK 169 166 168 189 C4' T B 11 OK 191 188 190 209 C4' A B 12 OK 211 208 210 230 C4' T B 13 OK 232 229 231 250 C4' A B 14 OK 252 249 251 271 C4' G B 15 OK 273 270 272 293 C4' C B 16 OK 295 292 294 313 C4' G C 5 OK 315 312 314 335 C4' C C 6 OK 337 334 336 354 C4' T C 7 OK 356 353 355 374 C4' A C 8 OK 376 373 375 395 C4' T C 9 OK 397 394 396 415 C4' A C 10 OK 417 414 416 436 C4' C C 11 OK 438 435 437 455 C4' G C 12 OK 457 454 456 477 C4' A C 13 OK 479 476 478 498 C4' A C 14 OK 500 497 499 519 C4' G C 15 OK 521 518 520 541 C4' T C 16 OK 543 540 542 561 C4' T C 17 OK 563 560 562 581 C4' A C 18 OK 583 580 582 602 C4' T C 19 OK 604 601 603 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A B 2 4 6 26 C5' T B 3 25 27 46 C5' A B 4 45 47 67 C5' A B 5 66 68 88 C5' C B 6 87 89 107 C5' T B 7 106 108 127 C5' T B 8 126 128 147 C5' C B 9 146 148 166 C5' G B 10 165 167 188 C5' T B 11 187 189 208 C5' A B 12 207 209 229 C5' T B 13 228 230 249 C5' A B 14 248 250 270 C5' G B 15 269 271 292 C5' C B 16 291 293 312 C5' G C 5 311 313 334 C5' C C 6 333 335 353 C5' T C 7 352 354 373 C5' A C 8 372 374 394 C5' T C 9 393 395 414 C5' A C 10 413 415 435 C5' C C 11 434 436 454 C5' G C 12 453 455 476 C5' A C 13 475 477 497 C5' A C 14 496 498 518 C5' G C 15 517 519 540 C5' T C 16 539 541 560 C5' T C 17 559 561 580 C5' A C 18 579 581 601 C5' T C 19 600 602 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A B 2 distorted distorted 2 3 4 22 P T B 3 distorted distorted 9 23 24 25 42 P A B 4 distorted distorted 30 43 44 45 63 P A B 5 distorted distorted 50 64 65 66 84 P C B 6 distorted distorted 71 85 86 87 103 P T B 7 distorted distorted 92 104 105 106 123 P T B 8 distorted distorted 111 124 125 126 143 P C B 9 distorted distorted 131 144 145 146 162 P G B 10 distorted distorted 151 163 164 165 184 P T B 11 distorted distorted 170 185 186 187 204 P A B 12 distorted distorted 192 205 206 207 225 P T B 13 distorted distorted 212 226 227 228 245 P A B 14 distorted distorted 233 246 247 248 266 P G B 15 distorted distorted 253 267 268 269 288 P C B 16 distorted distorted 274 289 290 291 308 P G C 5 distorted distorted 309 310 311 330 P C C 6 distorted distorted 316 331 332 333 349 P T C 7 distorted distorted 338 350 351 352 369 P A C 8 distorted distorted 357 370 371 372 390 P T C 9 distorted distorted 377 391 392 393 410 P A C 10 distorted distorted 398 411 412 413 431 P C C 11 distorted distorted 418 432 433 434 450 P G C 12 distorted distorted 439 451 452 453 472 P A C 13 distorted distorted 458 473 474 475 493 P A C 14 distorted distorted 480 494 495 496 514 P G C 15 distorted distorted 501 515 516 517 536 P T C 16 distorted distorted 522 537 538 539 556 P T C 17 distorted distorted 544 557 558 559 576 P A C 18 distorted distorted 564 577 578 579 597 P T C 19 distorted distorted 584 598 599 600 ---------------------------------------------------------------------------------