ID code: '1GTW' 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 C 2 beta 7 12 10 32 C1' T C 3 beta 28 33 31 52 C1' G C 4 beta 48 53 51 74 C1' T C 5 beta 70 75 73 94 C1' G C 6 beta 90 95 93 116 C1' G C 7 beta 112 117 115 138 C1' C C 8 beta 134 139 137 157 C1' G C 9 beta 153 158 156 179 C1' C C 10 beta 175 180 178 198 C1' A C 11 beta 194 199 197 219 C1' A C 12 beta 215 220 218 240 C1' T C 13 beta 236 241 239 260 C1' C C 14 beta 256 261 259 279 C1' C C 15 beta 275 280 278 298 C1' T C 16 beta 294 299 297 319 C1' A D 102 beta 315 320 318 340 C1' G D 103 beta 336 341 339 362 C1' G D 104 beta 358 363 361 384 C1' A D 105 beta 380 385 383 405 C1' T D 106 beta 401 406 404 425 C1' T D 107 beta 421 426 424 445 C1' G D 108 beta 441 446 444 467 C1' C D 109 beta 463 468 466 486 C1' G D 110 beta 482 487 485 508 C1' C D 111 beta 504 509 507 527 C1' C D 112 beta 523 528 526 546 C1' A D 113 beta 542 547 545 567 C1' C D 114 beta 563 568 566 586 C1' A D 115 beta 582 587 585 607 C1' T D 116 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 C 2 11 8 31 C2' T C 3 32 29 51 C2' G C 4 52 49 73 C2' T C 5 74 71 93 C2' G C 6 94 91 115 C2' G C 7 116 113 137 C2' C C 8 138 135 156 C2' G C 9 157 154 178 C2' C C 10 179 176 197 C2' A C 11 198 195 218 C2' A C 12 219 216 239 C2' T C 13 240 237 259 C2' C C 14 260 257 278 C2' C C 15 279 276 297 C2' T C 16 298 295 318 C2' A D 102 319 316 339 C2' G D 103 340 337 361 C2' G D 104 362 359 383 C2' A D 105 384 381 404 C2' T D 106 405 402 424 C2' T D 107 425 422 444 C2' G D 108 445 442 466 C2' C D 109 467 464 485 C2' G D 110 486 483 507 C2' C D 111 508 505 526 C2' C D 112 527 524 545 C2' A D 113 546 543 566 C2' C D 114 567 564 585 C2' A D 115 586 583 606 C2' T D 116 607 604 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A C 2 OK 6 9 10 29 C3' T C 3 OK 27 30 31 49 C3' G C 4 OK 47 50 51 71 C3' T C 5 OK 69 72 73 91 C3' G C 6 OK 89 92 93 113 C3' G C 7 OK 111 114 115 135 C3' C C 8 OK 133 136 137 154 C3' G C 9 OK 152 155 156 176 C3' C C 10 OK 174 177 178 195 C3' A C 11 OK 193 196 197 216 C3' A C 12 OK 214 217 218 237 C3' T C 13 OK 235 238 239 257 C3' C C 14 OK 255 258 259 276 C3' C C 15 OK 274 277 278 295 C3' T C 16 OK 293 296 297 316 C3' A D 102 OK 314 317 318 337 C3' G D 103 OK 335 338 339 359 C3' G D 104 OK 357 360 361 381 C3' A D 105 OK 379 382 383 402 C3' T D 106 OK 400 403 404 422 C3' T D 107 OK 420 423 424 442 C3' G D 108 OK 440 443 444 464 C3' C D 109 OK 462 465 466 483 C3' G D 110 OK 481 484 485 505 C3' C D 111 OK 503 506 507 524 C3' C D 112 OK 522 525 526 543 C3' A D 113 OK 541 544 545 564 C3' C D 114 OK 562 565 566 583 C3' A D 115 OK 581 584 585 604 C3' T D 116 OK 602 605 606 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A C 2 OK 8 5 7 27 C4' T C 3 OK 29 26 28 47 C4' G C 4 OK 49 46 48 69 C4' T C 5 OK 71 68 70 89 C4' G C 6 OK 91 88 90 111 C4' G C 7 OK 113 110 112 133 C4' C C 8 OK 135 132 134 152 C4' G C 9 OK 154 151 153 174 C4' C C 10 OK 176 173 175 193 C4' A C 11 OK 195 192 194 214 C4' A C 12 OK 216 213 215 235 C4' T C 13 OK 237 234 236 255 C4' C C 14 OK 257 254 256 274 C4' C C 15 OK 276 273 275 293 C4' T C 16 OK 295 292 294 314 C4' A D 102 OK 316 313 315 335 C4' G D 103 OK 337 334 336 357 C4' G D 104 OK 359 356 358 379 C4' A D 105 OK 381 378 380 400 C4' T D 106 OK 402 399 401 420 C4' T D 107 OK 422 419 421 440 C4' G D 108 OK 442 439 441 462 C4' C D 109 OK 464 461 463 481 C4' G D 110 OK 483 480 482 503 C4' C D 111 OK 505 502 504 522 C4' C D 112 OK 524 521 523 541 C4' A D 113 OK 543 540 542 562 C4' C D 114 OK 564 561 563 581 C4' A D 115 OK 583 580 582 602 C4' T D 116 OK 604 601 603 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A C 2 4 6 26 C5' T C 3 25 27 46 C5' G C 4 45 47 68 C5' T C 5 67 69 88 C5' G C 6 87 89 110 C5' G C 7 109 111 132 C5' C C 8 131 133 151 C5' G C 9 150 152 173 C5' C C 10 172 174 192 C5' A C 11 191 193 213 C5' A C 12 212 214 234 C5' T C 13 233 235 254 C5' C C 14 253 255 273 C5' C C 15 272 274 292 C5' T C 16 291 293 313 C5' A D 102 312 314 334 C5' G D 103 333 335 356 C5' G D 104 355 357 378 C5' A D 105 377 379 399 C5' T D 106 398 400 419 C5' T D 107 418 420 439 C5' G D 108 438 440 461 C5' C D 109 460 462 480 C5' G D 110 479 481 502 C5' C D 111 501 503 521 C5' C D 112 520 522 540 C5' A D 113 539 541 561 C5' C D 114 560 562 580 C5' A D 115 579 581 601 C5' T D 116 600 602 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A C 2 distorted distorted 2 3 4 22 P T C 3 distorted distorted 9 23 24 25 42 P G C 4 distorted distorted 30 43 44 45 64 P T C 5 distorted distorted 50 65 66 67 84 P G C 6 distorted distorted 72 85 86 87 106 P G C 7 distorted distorted 92 107 108 109 128 P C C 8 distorted distorted 114 129 130 131 147 P G C 9 distorted distorted 136 148 149 150 169 P C C 10 distorted distorted 155 170 171 172 188 P A C 11 distorted distorted 177 189 190 191 209 P A C 12 distorted distorted 196 210 211 212 230 P T C 13 distorted distorted 217 231 232 233 250 P C C 14 distorted distorted 238 251 252 253 269 P C C 15 distorted distorted 258 270 271 272 288 P T C 16 distorted distorted 277 289 290 291 309 P A D 102 distorted distorted 310 311 312 330 P G D 103 distorted distorted 317 331 332 333 352 P G D 104 distorted distorted 338 353 354 355 374 P A D 105 distorted distorted 360 375 376 377 395 P T D 106 distorted distorted 382 396 397 398 415 P T D 107 distorted distorted 403 416 417 418 435 P G D 108 distorted distorted 423 436 437 438 457 P C D 109 distorted distorted 443 458 459 460 476 P G D 110 distorted distorted 465 477 478 479 498 P C D 111 distorted distorted 484 499 500 501 517 P C D 112 distorted distorted 506 518 519 520 536 P A D 113 distorted distorted 525 537 538 539 557 P C D 114 distorted distorted 544 558 559 560 576 P A D 115 distorted distorted 565 577 578 579 597 P T D 116 distorted distorted 584 598 599 600 ---------------------------------------------------------------------------------