ID code: '1MNN' 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' G B 2 beta 7 12 10 33 C1' C B 3 beta 29 34 32 52 C1' G B 4 beta 48 53 51 74 C1' A B 5 beta 70 75 73 95 C1' C B 6 beta 91 96 94 114 C1' A B 7 beta 110 115 113 135 C1' C B 8 beta 131 136 134 154 C1' A B 9 beta 150 155 153 175 C1' A B 10 beta 171 176 174 196 C1' A B 11 beta 192 197 195 217 C1' A B 12 beta 213 218 216 238 C1' A B 13 beta 234 239 237 259 C1' C B 14 beta 255 260 258 279 C1' G C 2 beta 275 280 278 301 C1' T C 3 beta 297 302 300 321 C1' T C 4 beta 317 322 320 341 C1' T C 5 beta 337 342 340 361 C1' T C 6 beta 357 362 360 381 C1' T C 7 beta 377 382 380 401 C1' G C 8 beta 397 402 400 423 C1' T C 9 beta 419 424 422 443 C1' G C 10 beta 439 444 442 465 C1' T C 11 beta 461 466 464 485 C1' C C 12 beta 481 486 484 504 C1' G C 13 beta 500 505 503 526 C1' C C 14 beta 522 527 525 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G B 2 11 8 32 C2' C B 3 33 30 51 C2' G B 4 52 49 73 C2' A B 5 74 71 94 C2' C B 6 95 92 113 C2' A B 7 114 111 134 C2' C B 8 135 132 153 C2' A B 9 154 151 174 C2' A B 10 175 172 195 C2' A B 11 196 193 216 C2' A B 12 217 214 237 C2' A B 13 238 235 258 C2' C B 14 259 256 278 C2' G C 2 279 276 300 C2' T C 3 301 298 320 C2' T C 4 321 318 340 C2' T C 5 341 338 360 C2' T C 6 361 358 380 C2' T C 7 381 378 400 C2' G C 8 401 398 422 C2' T C 9 423 420 442 C2' G C 10 443 440 464 C2' T C 11 465 462 484 C2' C C 12 485 482 503 C2' G C 13 504 501 525 C2' C C 14 526 523 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G B 2 OK 6 9 10 30 C3' C B 3 OK 28 31 32 49 C3' G B 4 OK 47 50 51 71 C3' A B 5 OK 69 72 73 92 C3' C B 6 OK 90 93 94 111 C3' A B 7 OK 109 112 113 132 C3' C B 8 OK 130 133 134 151 C3' A B 9 OK 149 152 153 172 C3' A B 10 OK 170 173 174 193 C3' A B 11 OK 191 194 195 214 C3' A B 12 OK 212 215 216 235 C3' A B 13 OK 233 236 237 256 C3' C B 14 OK 254 257 258 276 C3' G C 2 OK 274 277 278 298 C3' T C 3 OK 296 299 300 318 C3' T C 4 OK 316 319 320 338 C3' T C 5 OK 336 339 340 358 C3' T C 6 OK 356 359 360 378 C3' T C 7 OK 376 379 380 398 C3' G C 8 OK 396 399 400 420 C3' T C 9 OK 418 421 422 440 C3' G C 10 OK 438 441 442 462 C3' T C 11 OK 460 463 464 482 C3' C C 12 OK 480 483 484 501 C3' G C 13 OK 499 502 503 523 C3' C C 14 OK 521 524 525 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G B 2 OK 8 5 7 28 C4' C B 3 OK 30 27 29 47 C4' G B 4 OK 49 46 48 69 C4' A B 5 OK 71 68 70 90 C4' C B 6 OK 92 89 91 109 C4' A B 7 OK 111 108 110 130 C4' C B 8 OK 132 129 131 149 C4' A B 9 OK 151 148 150 170 C4' A B 10 OK 172 169 171 191 C4' A B 11 OK 193 190 192 212 C4' A B 12 OK 214 211 213 233 C4' A B 13 OK 235 232 234 254 C4' C B 14 OK 256 253 255 274 C4' G C 2 OK 276 273 275 296 C4' T C 3 OK 298 295 297 316 C4' T C 4 OK 318 315 317 336 C4' T C 5 OK 338 335 337 356 C4' T C 6 OK 358 355 357 376 C4' T C 7 OK 378 375 377 396 C4' G C 8 OK 398 395 397 418 C4' T C 9 OK 420 417 419 438 C4' G C 10 OK 440 437 439 460 C4' T C 11 OK 462 459 461 480 C4' C C 12 OK 482 479 481 499 C4' G C 13 OK 501 498 500 521 C4' C C 14 OK 523 520 522 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G B 2 4 6 27 C5' C B 3 26 28 46 C5' G B 4 45 47 68 C5' A B 5 67 69 89 C5' C B 6 88 90 108 C5' A B 7 107 109 129 C5' C B 8 128 130 148 C5' A B 9 147 149 169 C5' A B 10 168 170 190 C5' A B 11 189 191 211 C5' A B 12 210 212 232 C5' A B 13 231 233 253 C5' C B 14 252 254 273 C5' G C 2 272 274 295 C5' T C 3 294 296 315 C5' T C 4 314 316 335 C5' T C 5 334 336 355 C5' T C 6 354 356 375 C5' T C 7 374 376 395 C5' G C 8 394 396 417 C5' T C 9 416 418 437 C5' G C 10 436 438 459 C5' T C 11 458 460 479 C5' C C 12 478 480 498 C5' G C 13 497 499 520 C5' C C 14 519 521 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G B 2 distorted distorted 2 3 4 23 P C B 3 distorted distorted 9 24 25 26 42 P G B 4 distorted distorted 31 43 44 45 64 P A B 5 distorted distorted 50 65 66 67 85 P C B 6 distorted distorted 72 86 87 88 104 P A B 7 distorted distorted 93 105 106 107 125 P C B 8 distorted distorted 112 126 127 128 144 P A B 9 distorted distorted 133 145 146 147 165 P A B 10 distorted distorted 152 166 167 168 186 P A B 11 distorted distorted 173 187 188 189 207 P A B 12 distorted distorted 194 208 209 210 228 P A B 13 distorted distorted 215 229 230 231 249 P C B 14 distorted distorted 236 250 251 252 269 P G C 2 distorted distorted 270 271 272 291 P T C 3 distorted distorted 277 292 293 294 311 P T C 4 distorted distorted 299 312 313 314 331 P T C 5 distorted distorted 319 332 333 334 351 P T C 6 distorted distorted 339 352 353 354 371 P T C 7 distorted distorted 359 372 373 374 391 P G C 8 distorted distorted 379 392 393 394 413 P T C 9 distorted distorted 399 414 415 416 433 P G C 10 distorted distorted 421 434 435 436 455 P T C 11 distorted distorted 441 456 457 458 475 P C C 12 distorted distorted 463 476 477 478 494 P G C 13 distorted distorted 483 495 496 497 516 P C C 14 distorted distorted 502 517 518 519 ---------------------------------------------------------------------------------