ID code: '1K7A' 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 B 2 beta 7 12 10 32 C1' G B 3 beta 28 33 31 54 C1' T B 4 beta 50 55 53 74 C1' G B 5 beta 70 75 73 96 C1' C B 6 beta 92 97 95 115 C1' C B 7 beta 111 116 114 134 C1' G B 8 beta 130 135 133 156 C1' G B 9 beta 152 157 155 178 C1' A B 10 beta 174 179 177 199 C1' G B 11 beta 195 200 198 221 C1' A B 12 beta 217 222 220 242 C1' T B 13 beta 238 243 241 262 C1' G B 14 beta 258 263 261 285 C1' C C 3 beta 281 286 284 304 C1' A C 4 beta 300 305 303 325 C1' T C 5 beta 321 326 324 345 C1' C C 6 beta 341 346 344 364 C1' T C 7 beta 360 365 363 384 C1' C C 8 beta 380 385 383 403 C1' C C 9 beta 399 404 402 422 C1' G C 10 beta 418 423 421 444 C1' G C 11 beta 440 445 443 466 C1' C C 12 beta 462 467 465 485 C1' A C 13 beta 481 486 484 506 C1' C C 14 beta 502 507 505 525 C1' T C 15 beta 521 526 524 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' A B 2 11 8 31 C2' G B 3 32 29 53 C2' T B 4 54 51 73 C2' G B 5 74 71 95 C2' C B 6 96 93 114 C2' C B 7 115 112 133 C2' G B 8 134 131 155 C2' G B 9 156 153 177 C2' A B 10 178 175 198 C2' G B 11 199 196 220 C2' A B 12 221 218 241 C2' T B 13 242 239 261 C2' G B 14 262 259 284 C2' C C 3 285 282 303 C2' A C 4 304 301 324 C2' T C 5 325 322 344 C2' C C 6 345 342 363 C2' T C 7 364 361 383 C2' C C 8 384 381 402 C2' C C 9 403 400 421 C2' G C 10 422 419 443 C2' G C 11 444 441 465 C2' C C 12 466 463 484 C2' A C 13 485 482 505 C2' C C 14 506 503 524 C2' T C 15 525 522 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A B 2 OK 6 9 10 29 C3' G B 3 OK 27 30 31 51 C3' T B 4 OK 49 52 53 71 C3' G B 5 OK 69 72 73 93 C3' C B 6 OK 91 94 95 112 C3' C B 7 OK 110 113 114 131 C3' G B 8 OK 129 132 133 153 C3' G B 9 OK 151 154 155 175 C3' A B 10 OK 173 176 177 196 C3' G B 11 OK 194 197 198 218 C3' A B 12 OK 216 219 220 239 C3' T B 13 OK 237 240 241 259 C3' G B 14 OK 257 260 261 282 C3' C C 3 OK 280 283 284 301 C3' A C 4 OK 299 302 303 322 C3' T C 5 OK 320 323 324 342 C3' C C 6 OK 340 343 344 361 C3' T C 7 OK 359 362 363 381 C3' C C 8 OK 379 382 383 400 C3' C C 9 OK 398 401 402 419 C3' G C 10 OK 417 420 421 441 C3' G C 11 OK 439 442 443 463 C3' C C 12 OK 461 464 465 482 C3' A C 13 OK 480 483 484 503 C3' C C 14 OK 501 504 505 522 C3' T C 15 OK 520 523 524 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A B 2 OK 8 5 7 27 C4' G B 3 OK 29 26 28 49 C4' T B 4 OK 51 48 50 69 C4' G B 5 OK 71 68 70 91 C4' C B 6 OK 93 90 92 110 C4' C B 7 OK 112 109 111 129 C4' G B 8 OK 131 128 130 151 C4' G B 9 OK 153 150 152 173 C4' A B 10 OK 175 172 174 194 C4' G B 11 OK 196 193 195 216 C4' A B 12 OK 218 215 217 237 C4' T B 13 OK 239 236 238 257 C4' G B 14 OK 259 256 258 280 C4' C C 3 OK 282 279 281 299 C4' A C 4 OK 301 298 300 320 C4' T C 5 OK 322 319 321 340 C4' C C 6 OK 342 339 341 359 C4' T C 7 OK 361 358 360 379 C4' C C 8 OK 381 378 380 398 C4' C C 9 OK 400 397 399 417 C4' G C 10 OK 419 416 418 439 C4' G C 11 OK 441 438 440 461 C4' C C 12 OK 463 460 462 480 C4' A C 13 OK 482 479 481 501 C4' C C 14 OK 503 500 502 520 C4' T C 15 OK 522 519 521 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A B 2 4 6 26 C5' G B 3 25 27 48 C5' T B 4 47 49 68 C5' G B 5 67 69 90 C5' C B 6 89 91 109 C5' C B 7 108 110 128 C5' G B 8 127 129 150 C5' G B 9 149 151 172 C5' A B 10 171 173 193 C5' G B 11 192 194 215 C5' A B 12 214 216 236 C5' T B 13 235 237 256 C5' G B 14 255 257 279 C5' C C 3 278 280 298 C5' A C 4 297 299 319 C5' T C 5 318 320 339 C5' C C 6 338 340 358 C5' T C 7 357 359 378 C5' C C 8 377 379 397 C5' C C 9 396 398 416 C5' G C 10 415 417 438 C5' G C 11 437 439 460 C5' C C 12 459 461 479 C5' A C 13 478 480 500 C5' C C 14 499 501 519 C5' T C 15 518 520 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A B 2 distorted distorted 2 3 4 22 P G B 3 distorted distorted 9 23 24 25 44 P T B 4 distorted distorted 30 45 46 47 64 P G B 5 distorted distorted 52 65 66 67 86 P C B 6 distorted distorted 72 87 88 89 105 P C B 7 distorted distorted 94 106 107 108 124 P G B 8 distorted distorted 113 125 126 127 146 P G B 9 distorted distorted 132 147 148 149 168 P A B 10 distorted distorted 154 169 170 171 189 P G B 11 distorted distorted 176 190 191 192 211 P A B 12 distorted distorted 197 212 213 214 232 P T B 13 distorted distorted 219 233 234 235 252 P G B 14 distorted distorted 240 253 254 255 275 P C C 3 distorted distorted 276 277 278 294 P A C 4 distorted distorted 283 295 296 297 315 P T C 5 distorted distorted 302 316 317 318 335 P C C 6 distorted distorted 323 336 337 338 354 P T C 7 distorted distorted 343 355 356 357 374 P C C 8 distorted distorted 362 375 376 377 393 P C C 9 distorted distorted 382 394 395 396 412 P G C 10 distorted distorted 401 413 414 415 434 P G C 11 distorted distorted 420 435 436 437 456 P C C 12 distorted distorted 442 457 458 459 475 P A C 13 distorted distorted 464 476 477 478 496 P C C 14 distorted distorted 483 497 498 499 515 P T C 15 distorted distorted 504 516 517 518 ---------------------------------------------------------------------------------