ID code: '1JWL' 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 D 6 beta 4 9 7 28 C1' G D 7 beta 24 29 27 50 C1' T D 8 beta 46 51 49 70 C1' G D 9 beta 66 71 69 92 C1' A D 10 beta 88 93 91 113 C1' G D 11 beta 109 114 112 135 C1' C D 12 beta 131 136 134 154 C1' G D 13 beta 150 155 153 176 C1' G D 14 beta 172 177 175 198 C1' A D 15 beta 194 199 197 219 C1' T D 16 beta 215 220 218 239 C1' A D 17 beta 235 240 238 260 C1' A D 18 beta 256 261 259 281 C1' C D 19 beta 277 282 280 301 C1' G E 6 beta 297 302 300 323 C1' T E 7 beta 319 324 322 343 C1' T E 8 beta 339 344 342 363 C1' A E 9 beta 359 364 362 384 C1' T E 10 alpha 380 385 383 404 C1' C E 11 beta 400 405 403 423 C1' C E 12 beta 419 424 422 442 C1' G E 13 beta 438 443 441 464 C1' C E 14 beta 460 465 463 483 C1' T E 15 beta 479 484 482 503 C1' C E 16 beta 499 504 502 522 C1' A E 17 beta 518 523 521 543 C1' C E 18 beta 539 544 542 562 C1' A E 19 beta 558 563 561 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' T D 6 8 5 27 C2' G D 7 28 25 49 C2' T D 8 50 47 69 C2' G D 9 70 67 91 C2' A D 10 92 89 112 C2' G D 11 113 110 134 C2' C D 12 135 132 153 C2' G D 13 154 151 175 C2' G D 14 176 173 197 C2' A D 15 198 195 218 C2' T D 16 219 216 238 C2' A D 17 239 236 259 C2' A D 18 260 257 280 C2' C D 19 281 278 300 C2' G E 6 301 298 322 C2' T E 7 323 320 342 C2' T E 8 343 340 362 C2' A E 9 363 360 383 C2' T E 10 384 381 403 C2' C E 11 404 401 422 C2' C E 12 423 420 441 C2' G E 13 442 439 463 C2' C E 14 464 461 482 C2' T E 15 483 480 502 C2' C E 16 503 500 521 C2' A E 17 522 519 542 C2' C E 18 543 540 561 C2' A E 19 562 559 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' T D 6 OK 3 6 7 25 C3' G D 7 OK 23 26 27 47 C3' T D 8 OK 45 48 49 67 C3' G D 9 OK 65 68 69 89 C3' A D 10 OK 87 90 91 110 C3' G D 11 OK 108 111 112 132 C3' C D 12 OK 130 133 134 151 C3' G D 13 OK 149 152 153 173 C3' G D 14 OK 171 174 175 195 C3' A D 15 OK 193 196 197 216 C3' T D 16 OK 214 217 218 236 C3' A D 17 OK 234 237 238 257 C3' A D 18 OK 255 258 259 278 C3' C D 19 OK 276 279 280 298 C3' G E 6 OK 296 299 300 320 C3' T E 7 OK 318 321 322 340 C3' T E 8 OK 338 341 342 360 C3' A E 9 OK 358 361 362 381 C3' T E 10 OK 379 382 383 401 C3' C E 11 OK 399 402 403 420 C3' C E 12 OK 418 421 422 439 C3' G E 13 OK 437 440 441 461 C3' C E 14 OK 459 462 463 480 C3' T E 15 OK 478 481 482 500 C3' C E 16 OK 498 501 502 519 C3' A E 17 OK 517 520 521 540 C3' C E 18 OK 538 541 542 559 C3' A E 19 OK 557 560 561 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' T D 6 OK 5 2 4 23 C4' G D 7 OK 25 22 24 45 C4' T D 8 OK 47 44 46 65 C4' G D 9 OK 67 64 66 87 C4' A D 10 OK 89 86 88 108 C4' G D 11 OK 110 107 109 130 C4' C D 12 OK 132 129 131 149 C4' G D 13 OK 151 148 150 171 C4' G D 14 OK 173 170 172 193 C4' A D 15 OK 195 192 194 214 C4' T D 16 OK 216 213 215 234 C4' A D 17 OK 236 233 235 255 C4' A D 18 OK 257 254 256 276 C4' C D 19 OK 278 275 277 296 C4' G E 6 OK 298 295 297 318 C4' T E 7 OK 320 317 319 338 C4' T E 8 OK 340 337 339 358 C4' A E 9 OK 360 357 359 379 C4' T E 10 OK 381 378 380 399 C4' C E 11 OK 401 398 400 418 C4' C E 12 OK 420 417 419 437 C4' G E 13 OK 439 436 438 459 C4' C E 14 OK 461 458 460 478 C4' T E 15 OK 480 477 479 498 C4' C E 16 OK 500 497 499 517 C4' A E 17 OK 519 516 518 538 C4' C E 18 OK 540 537 539 557 C4' A E 19 OK 559 556 558 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' T D 6 1 3 22 C5' G D 7 21 23 44 C5' T D 8 43 45 64 C5' G D 9 63 65 86 C5' A D 10 85 87 107 C5' G D 11 106 108 129 C5' C D 12 128 130 148 C5' G D 13 147 149 170 C5' G D 14 169 171 192 C5' A D 15 191 193 213 C5' T D 16 212 214 233 C5' A D 17 232 234 254 C5' A D 18 253 255 275 C5' C D 19 274 276 295 C5' G E 6 294 296 317 C5' T E 7 316 318 337 C5' T E 8 336 338 357 C5' A E 9 356 358 378 C5' T E 10 377 379 398 C5' C E 11 397 399 417 C5' C E 12 416 418 436 C5' G E 13 435 437 458 C5' C E 14 457 459 477 C5' T E 15 476 478 497 C5' C E 16 496 498 516 C5' A E 17 515 517 537 C5' C E 18 536 538 556 C5' A E 19 555 557 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P G D 7 distorted distorted 6 19 20 21 40 P T D 8 distorted distorted 26 41 42 43 60 P G D 9 distorted distorted 48 61 62 63 82 P A D 10 distorted distorted 68 83 84 85 103 P G D 11 distorted distorted 90 104 105 106 125 P C D 12 distorted distorted 111 126 127 128 144 P G D 13 distorted distorted 133 145 146 147 166 P G D 14 distorted distorted 152 167 168 169 188 P A D 15 distorted distorted 174 189 190 191 209 P T D 16 distorted distorted 196 210 211 212 229 P A D 17 distorted distorted 217 230 231 232 250 P A D 18 distorted distorted 237 251 252 253 271 P C D 19 distorted distorted 258 272 273 274 291 P G E 6 OK OK 292 293 294 313 P T E 7 distorted distorted 299 314 315 316 333 P T E 8 distorted distorted 321 334 335 336 353 P A E 9 distorted distorted 341 354 355 356 374 P T E 10 distorted distorted 361 375 376 377 394 P C E 11 distorted distorted 382 395 396 397 413 P C E 12 distorted distorted 402 414 415 416 432 P G E 13 distorted distorted 421 433 434 435 454 P C E 14 distorted distorted 440 455 456 457 473 P T E 15 distorted distorted 462 474 475 476 493 P C E 16 distorted distorted 481 494 495 496 512 P A E 17 distorted distorted 501 513 514 515 533 P C E 18 distorted distorted 520 534 535 536 552 P A E 19 distorted distorted 541 553 554 555 ---------------------------------------------------------------------------------