ID code: '1JJ8' 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 A 3 beta 7 12 10 33 C1' +U A 4 beta 29 34 32 52 C1' T A 5 beta 48 53 51 72 C1' T A 6 beta 68 73 71 92 C1' T A 7 beta 88 93 91 112 C1' T A 8 beta 108 113 111 132 C1' G A 9 beta 128 133 131 154 C1' A A 10 beta 150 155 153 175 C1' T A 11 beta 171 176 174 195 C1' A A 12 beta 191 196 194 216 C1' A A 13 beta 212 217 215 237 C1' G A 14 beta 233 238 236 260 C1' C B 18 beta 256 261 259 279 C1' T B 19 beta 275 280 278 299 C1' T B 20 beta 295 300 298 319 C1' A B 21 beta 315 320 318 340 C1' T B 22 beta 336 341 339 360 C1' C B 23 beta 356 361 359 379 C1' A B 24 beta 375 380 378 400 C1' A B 25 beta 396 401 399 421 C1' A B 26 beta 417 422 420 442 C1' A B 27 beta 438 443 441 463 C1' A B 28 beta 459 464 462 484 C1' C B 29 beta 480 485 483 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 3 11 8 32 C2' +U A 4 33 30 51 C2' T A 5 52 49 71 C2' T A 6 72 69 91 C2' T A 7 92 89 111 C2' T A 8 112 109 131 C2' G A 9 132 129 153 C2' A A 10 154 151 174 C2' T A 11 175 172 194 C2' A A 12 195 192 215 C2' A A 13 216 213 236 C2' G A 14 237 234 259 C2' C B 18 260 257 278 C2' T B 19 279 276 298 C2' T B 20 299 296 318 C2' A B 21 319 316 339 C2' T B 22 340 337 359 C2' C B 23 360 357 378 C2' A B 24 379 376 399 C2' A B 25 400 397 420 C2' A B 26 421 418 441 C2' A B 27 442 439 462 C2' A B 28 463 460 483 C2' C B 29 484 481 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 3 OK 6 9 10 30 C3' +U A 4 OK 28 31 32 49 C3' T A 5 OK 47 50 51 69 C3' T A 6 OK 67 70 71 89 C3' T A 7 OK 87 90 91 109 C3' T A 8 OK 107 110 111 129 C3' G A 9 OK 127 130 131 151 C3' A A 10 OK 149 152 153 172 C3' T A 11 OK 170 173 174 192 C3' A A 12 OK 190 193 194 213 C3' A A 13 OK 211 214 215 234 C3' G A 14 OK 232 235 236 257 C3' C B 18 OK 255 258 259 276 C3' T B 19 OK 274 277 278 296 C3' T B 20 OK 294 297 298 316 C3' A B 21 OK 314 317 318 337 C3' T B 22 OK 335 338 339 357 C3' C B 23 OK 355 358 359 376 C3' A B 24 OK 374 377 378 397 C3' A B 25 OK 395 398 399 418 C3' A B 26 OK 416 419 420 439 C3' A B 27 OK 437 440 441 460 C3' A B 28 OK 458 461 462 481 C3' C B 29 OK 479 482 483 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 3 OK 8 5 7 28 C4' +U A 4 OK 30 27 29 47 C4' T A 5 OK 49 46 48 67 C4' T A 6 OK 69 66 68 87 C4' T A 7 OK 89 86 88 107 C4' T A 8 OK 109 106 108 127 C4' G A 9 OK 129 126 128 149 C4' A A 10 OK 151 148 150 170 C4' T A 11 OK 172 169 171 190 C4' A A 12 OK 192 189 191 211 C4' A A 13 OK 213 210 212 232 C4' G A 14 OK 234 231 233 255 C4' C B 18 OK 257 254 256 274 C4' T B 19 OK 276 273 275 294 C4' T B 20 OK 296 293 295 314 C4' A B 21 OK 316 313 315 335 C4' T B 22 OK 337 334 336 355 C4' C B 23 OK 357 354 356 374 C4' A B 24 OK 376 373 375 395 C4' A B 25 OK 397 394 396 416 C4' A B 26 OK 418 415 417 437 C4' A B 27 OK 439 436 438 458 C4' A B 28 OK 460 457 459 479 C4' C B 29 OK 481 478 480 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 3 4 6 27 C5' +U A 4 26 28 46 C5' T A 5 45 47 66 C5' T A 6 65 67 86 C5' T A 7 85 87 106 C5' T A 8 105 107 126 C5' G A 9 125 127 148 C5' A A 10 147 149 169 C5' T A 11 168 170 189 C5' A A 12 188 190 210 C5' A A 13 209 211 231 C5' G A 14 230 232 254 C5' C B 18 253 255 273 C5' T B 19 272 274 293 C5' T B 20 292 294 313 C5' A B 21 312 314 334 C5' T B 22 333 335 354 C5' C B 23 353 355 373 C5' A B 24 372 374 394 C5' A B 25 393 395 415 C5' A B 26 414 416 436 C5' A B 27 435 437 457 C5' A B 28 456 458 478 C5' C B 29 477 479 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 3 distorted distorted 2 3 4 23 P +U A 4 distorted distorted 9 24 25 26 42 P T A 5 distorted distorted 31 43 44 45 62 P T A 6 distorted distorted 50 63 64 65 82 P T A 7 distorted distorted 70 83 84 85 102 P T A 8 distorted distorted 90 103 104 105 122 P G A 9 distorted distorted 110 123 124 125 144 P A A 10 distorted distorted 130 145 146 147 165 P T A 11 distorted distorted 152 166 167 168 185 P A A 12 distorted distorted 173 186 187 188 206 P A A 13 distorted distorted 193 207 208 209 227 P G A 14 distorted distorted 214 228 229 230 250 P C B 18 distorted distorted 251 252 253 269 P T B 19 distorted distorted 258 270 271 272 289 P T B 20 distorted distorted 277 290 291 292 309 P A B 21 distorted distorted 297 310 311 312 330 P T B 22 distorted distorted 317 331 332 333 350 P C B 23 distorted distorted 338 351 352 353 369 P A B 24 distorted distorted 358 370 371 372 390 P A B 25 distorted distorted 377 391 392 393 411 P A B 26 distorted distorted 398 412 413 414 432 P A B 27 distorted distorted 419 433 434 435 453 P A B 28 distorted distorted 440 454 455 456 474 P C B 29 distorted distorted 461 475 476 477 ---------------------------------------------------------------------------------