ID code: '1QLN' 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 T 10 beta 7 12 10 33 C1' T T 11 beta 29 34 32 53 C1' G T 12 beta 49 54 52 75 C1' A T 13 beta 71 76 74 96 C1' G T 14 beta 92 97 95 118 C1' T T 15 beta 114 119 117 138 C1' C T 16 beta 134 139 137 157 C1' G T 17 beta 153 158 156 179 C1' T T 18 beta 175 180 178 199 C1' A T 19 beta 195 200 198 220 C1' T T 20 beta 216 221 219 240 C1' T T 21 beta 236 241 239 260 C1' A T 22 beta 256 261 259 282 C1' T N 101 beta 278 283 281 302 C1' A N 102 beta 298 303 301 323 C1' A N 103 beta 319 324 322 344 C1' T N 104 beta 340 345 343 364 C1' A N 105 beta 360 365 363 385 C1' C N 106 beta 381 386 384 404 C1' G N 107 beta 400 405 403 426 C1' A N 108 beta 422 427 425 447 C1' C N 109 beta 443 448 446 466 C1' T N 110 beta 462 467 465 486 C1' C N 111 beta 482 487 485 505 C1' A N 112 beta 501 506 504 526 C1' C N 113 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 T 10 11 8 32 C2' T T 11 33 30 52 C2' G T 12 53 50 74 C2' A T 13 75 72 95 C2' G T 14 96 93 117 C2' T T 15 118 115 137 C2' C T 16 138 135 156 C2' G T 17 157 154 178 C2' T T 18 179 176 198 C2' A T 19 199 196 219 C2' T T 20 220 217 239 C2' T T 21 240 237 259 C2' A T 22 260 257 281 C2' T N 101 282 279 301 C2' A N 102 302 299 322 C2' A N 103 323 320 343 C2' T N 104 344 341 363 C2' A N 105 364 361 384 C2' C N 106 385 382 403 C2' G N 107 404 401 425 C2' A N 108 426 423 446 C2' C N 109 447 444 465 C2' T N 110 466 463 485 C2' C N 111 486 483 504 C2' A N 112 505 502 525 C2' C N 113 526 523 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G T 10 OK 6 9 10 30 C3' T T 11 OK 28 31 32 50 C3' G T 12 OK 48 51 52 72 C3' A T 13 OK 70 73 74 93 C3' G T 14 OK 91 94 95 115 C3' T T 15 OK 113 116 117 135 C3' C T 16 OK 133 136 137 154 C3' G T 17 OK 152 155 156 176 C3' T T 18 OK 174 177 178 196 C3' A T 19 OK 194 197 198 217 C3' T T 20 OK 215 218 219 237 C3' T T 21 OK 235 238 239 257 C3' A T 22 OK 255 258 259 279 C3' T N 101 OK 277 280 281 299 C3' A N 102 OK 297 300 301 320 C3' A N 103 OK 318 321 322 341 C3' T N 104 OK 339 342 343 361 C3' A N 105 OK 359 362 363 382 C3' C N 106 OK 380 383 384 401 C3' G N 107 OK 399 402 403 423 C3' A N 108 OK 421 424 425 444 C3' C N 109 OK 442 445 446 463 C3' T N 110 OK 461 464 465 483 C3' C N 111 OK 481 484 485 502 C3' A N 112 OK 500 503 504 523 C3' C N 113 OK 521 524 525 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G T 10 OK 8 5 7 28 C4' T T 11 OK 30 27 29 48 C4' G T 12 OK 50 47 49 70 C4' A T 13 OK 72 69 71 91 C4' G T 14 OK 93 90 92 113 C4' T T 15 OK 115 112 114 133 C4' C T 16 OK 135 132 134 152 C4' G T 17 OK 154 151 153 174 C4' T T 18 OK 176 173 175 194 C4' A T 19 OK 196 193 195 215 C4' T T 20 OK 217 214 216 235 C4' T T 21 OK 237 234 236 255 C4' A T 22 OK 257 254 256 277 C4' T N 101 OK 279 276 278 297 C4' A N 102 OK 299 296 298 318 C4' A N 103 OK 320 317 319 339 C4' T N 104 OK 341 338 340 359 C4' A N 105 OK 361 358 360 380 C4' C N 106 OK 382 379 381 399 C4' G N 107 OK 401 398 400 421 C4' A N 108 OK 423 420 422 442 C4' C N 109 OK 444 441 443 461 C4' T N 110 OK 463 460 462 481 C4' C N 111 OK 483 480 482 500 C4' A N 112 OK 502 499 501 521 C4' C N 113 OK 523 520 522 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G T 10 4 6 27 C5' T T 11 26 28 47 C5' G T 12 46 48 69 C5' A T 13 68 70 90 C5' G T 14 89 91 112 C5' T T 15 111 113 132 C5' C T 16 131 133 151 C5' G T 17 150 152 173 C5' T T 18 172 174 193 C5' A T 19 192 194 214 C5' T T 20 213 215 234 C5' T T 21 233 235 254 C5' A T 22 253 255 276 C5' T N 101 275 277 296 C5' A N 102 295 297 317 C5' A N 103 316 318 338 C5' T N 104 337 339 358 C5' A N 105 357 359 379 C5' C N 106 378 380 398 C5' G N 107 397 399 420 C5' A N 108 419 421 441 C5' C N 109 440 442 460 C5' T N 110 459 461 480 C5' C N 111 479 481 499 C5' A N 112 498 500 520 C5' C N 113 519 521 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G T 10 distorted distorted 2 3 4 23 P T T 11 distorted distorted 9 24 25 26 43 P G T 12 distorted distorted 31 44 45 46 65 P A T 13 distorted distorted 51 66 67 68 86 P G T 14 distorted distorted 73 87 88 89 108 P T T 15 distorted distorted 94 109 110 111 128 P C T 16 distorted distorted 116 129 130 131 147 P G T 17 distorted distorted 136 148 149 150 169 P T T 18 distorted distorted 155 170 171 172 189 P A T 19 distorted distorted 177 190 191 192 210 P T T 20 distorted distorted 197 211 212 213 230 P T T 21 distorted distorted 218 231 232 233 250 P A T 22 distorted distorted 238 251 252 253 272 P T N 101 distorted distorted 273 274 275 292 P A N 102 distorted distorted 280 293 294 295 313 P A N 103 distorted distorted 300 314 315 316 334 P T N 104 distorted distorted 321 335 336 337 354 P A N 105 distorted distorted 342 355 356 357 375 P C N 106 distorted distorted 362 376 377 378 394 P G N 107 OK OK 383 395 396 397 416 P A N 108 distorted distorted 402 417 418 419 437 P C N 109 distorted distorted 424 438 439 440 456 P T N 110 distorted distorted 445 457 458 459 476 P C N 111 distorted distorted 464 477 478 479 495 P A N 112 distorted distorted 484 496 497 498 516 P C N 113 distorted distorted 503 517 518 519 ---------------------------------------------------------------------------------