ID code: '1JKP' 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' T A 4 beta 29 34 32 53 C1' T A 5 beta 49 54 52 73 C1' T A 6 beta 69 74 72 93 C1' T A 7 beta 89 94 92 113 C1' T A 8 beta 109 114 112 133 C1' G A 9 beta 129 134 132 155 C1' A A 10 beta 151 156 154 176 C1' G A 11 beta 172 177 175 198 C1' A A 12 beta 194 199 197 219 C1' A A 13 beta 215 220 218 240 C1' G A 14 beta 236 241 239 263 C1' C B 18 beta 259 264 262 282 C1' T B 19 beta 278 283 281 302 C1' T B 20 beta 298 303 301 322 C1' C B 21 beta 318 323 321 341 C1' T B 22 beta 337 342 340 361 C1' C B 23 beta 357 362 360 380 C1' A B 24 beta 376 381 379 401 C1' A B 25 beta 397 402 400 422 C1' A B 26 beta 418 423 421 443 C1' A B 27 beta 439 444 442 464 C1' A B 28 beta 460 465 463 485 C1' C B 29 beta 481 486 484 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' T A 4 33 30 52 C2' T A 5 53 50 72 C2' T A 6 73 70 92 C2' T A 7 93 90 112 C2' T A 8 113 110 132 C2' G A 9 133 130 154 C2' A A 10 155 152 175 C2' G A 11 176 173 197 C2' A A 12 198 195 218 C2' A A 13 219 216 239 C2' G A 14 240 237 262 C2' C B 18 263 260 281 C2' T B 19 282 279 301 C2' T B 20 302 299 321 C2' C B 21 322 319 340 C2' T B 22 341 338 360 C2' C B 23 361 358 379 C2' A B 24 380 377 400 C2' A B 25 401 398 421 C2' A B 26 422 419 442 C2' A B 27 443 440 463 C2' A B 28 464 461 484 C2' C B 29 485 482 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 3 OK 6 9 10 30 C3' T A 4 OK 28 31 32 50 C3' T A 5 OK 48 51 52 70 C3' T A 6 OK 68 71 72 90 C3' T A 7 OK 88 91 92 110 C3' T A 8 OK 108 111 112 130 C3' G A 9 OK 128 131 132 152 C3' A A 10 OK 150 153 154 173 C3' G A 11 OK 171 174 175 195 C3' A A 12 OK 193 196 197 216 C3' A A 13 OK 214 217 218 237 C3' G A 14 OK 235 238 239 260 C3' C B 18 OK 258 261 262 279 C3' T B 19 OK 277 280 281 299 C3' T B 20 OK 297 300 301 319 C3' C B 21 OK 317 320 321 338 C3' T B 22 OK 336 339 340 358 C3' C B 23 OK 356 359 360 377 C3' A B 24 OK 375 378 379 398 C3' A B 25 OK 396 399 400 419 C3' A B 26 OK 417 420 421 440 C3' A B 27 OK 438 441 442 461 C3' A B 28 OK 459 462 463 482 C3' C B 29 OK 480 483 484 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 3 OK 8 5 7 28 C4' T A 4 OK 30 27 29 48 C4' T A 5 OK 50 47 49 68 C4' T A 6 OK 70 67 69 88 C4' T A 7 OK 90 87 89 108 C4' T A 8 OK 110 107 109 128 C4' G A 9 OK 130 127 129 150 C4' A A 10 OK 152 149 151 171 C4' G A 11 OK 173 170 172 193 C4' A A 12 OK 195 192 194 214 C4' A A 13 OK 216 213 215 235 C4' G A 14 OK 237 234 236 258 C4' C B 18 OK 260 257 259 277 C4' T B 19 OK 279 276 278 297 C4' T B 20 OK 299 296 298 317 C4' C B 21 OK 319 316 318 336 C4' T B 22 OK 338 335 337 356 C4' C B 23 OK 358 355 357 375 C4' A B 24 OK 377 374 376 396 C4' A B 25 OK 398 395 397 417 C4' A B 26 OK 419 416 418 438 C4' A B 27 OK 440 437 439 459 C4' A B 28 OK 461 458 460 480 C4' C B 29 OK 482 479 481 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 3 4 6 27 C5' T A 4 26 28 47 C5' T A 5 46 48 67 C5' T A 6 66 68 87 C5' T A 7 86 88 107 C5' T A 8 106 108 127 C5' G A 9 126 128 149 C5' A A 10 148 150 170 C5' G A 11 169 171 192 C5' A A 12 191 193 213 C5' A A 13 212 214 234 C5' G A 14 233 235 257 C5' C B 18 256 258 276 C5' T B 19 275 277 296 C5' T B 20 295 297 316 C5' C B 21 315 317 335 C5' T B 22 334 336 355 C5' C B 23 354 356 374 C5' A B 24 373 375 395 C5' A B 25 394 396 416 C5' A B 26 415 417 437 C5' A B 27 436 438 458 C5' A B 28 457 459 479 C5' C B 29 478 480 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 3 distorted distorted 2 3 4 23 P T A 4 distorted distorted 9 24 25 26 43 P T A 5 distorted distorted 31 44 45 46 63 P T A 6 distorted distorted 51 64 65 66 83 P T A 7 distorted distorted 71 84 85 86 103 P T A 8 distorted distorted 91 104 105 106 123 P G A 9 distorted distorted 111 124 125 126 145 P A A 10 distorted distorted 131 146 147 148 166 P G A 11 distorted distorted 153 167 168 169 188 P A A 12 distorted distorted 174 189 190 191 209 P A A 13 distorted distorted 196 210 211 212 230 P G A 14 distorted distorted 217 231 232 233 253 P C B 18 distorted distorted 254 255 256 272 P T B 19 distorted distorted 261 273 274 275 292 P T B 20 distorted distorted 280 293 294 295 312 P C B 21 distorted distorted 300 313 314 315 331 P T B 22 distorted distorted 320 332 333 334 351 P C B 23 distorted distorted 339 352 353 354 370 P A B 24 distorted distorted 359 371 372 373 391 P A B 25 distorted distorted 378 392 393 394 412 P A B 26 distorted distorted 399 413 414 415 433 P A B 27 distorted distorted 420 434 435 436 454 P A B 28 distorted distorted 441 455 456 457 475 P C B 29 distorted distorted 462 476 477 478 ---------------------------------------------------------------------------------