ID code: '1JX4' 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' --------------------------------------------------------------------------------- 8 C1' G P 1 beta 4 9 7 30 C1' G P 2 beta 26 31 29 52 C1' G P 3 beta 48 53 51 74 C1' G P 4 beta 70 75 73 96 C1' G P 5 beta 92 97 95 118 C1' A P 6 beta 114 119 117 139 C1' A P 7 beta 135 140 138 160 C1' G P 8 beta 156 161 159 182 C1' G P 9 beta 178 183 181 204 C1' A P 10 beta 200 205 203 225 C1' C P 11 beta 221 226 224 244 C1' T P 12 beta 240 245 243 263 C1' A P 13 beta 260 264 262 285 C1' T T 6 beta 281 286 284 305 C1' A T 7 beta 301 306 304 326 C1' G T 8 beta 322 327 325 348 C1' T T 9 beta 344 349 347 368 C1' C T 10 beta 364 369 367 387 C1' C T 11 beta 383 388 386 406 C1' T T 12 beta 402 407 405 426 C1' T T 13 beta 422 427 425 446 C1' C T 14 beta 442 447 445 465 C1' C T 15 beta 461 466 464 484 C1' C T 16 beta 480 485 483 503 C1' C T 17 beta 499 504 502 522 C1' C T 18 beta 518 523 521 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G P 1 8 5 29 C2' G P 2 30 27 51 C2' G P 3 52 49 73 C2' G P 4 74 71 95 C2' G P 5 96 93 117 C2' A P 6 118 115 138 C2' A P 7 139 136 159 C2' G P 8 160 157 181 C2' G P 9 182 179 203 C2' A P 10 204 201 224 C2' C P 11 225 222 243 C2' T P 12 244 241 262 C2' A P 13 263 261 284 C2' T T 6 285 282 304 C2' A T 7 305 302 325 C2' G T 8 326 323 347 C2' T T 9 348 345 367 C2' C T 10 368 365 386 C2' C T 11 387 384 405 C2' T T 12 406 403 425 C2' T T 13 426 423 445 C2' C T 14 446 443 464 C2' C T 15 465 462 483 C2' C T 16 484 481 502 C2' C T 17 503 500 521 C2' C T 18 522 519 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G P 1 OK 3 6 7 27 C3' G P 2 OK 25 28 29 49 C3' G P 3 OK 47 50 51 71 C3' G P 4 OK 69 72 73 93 C3' G P 5 OK 91 94 95 115 C3' A P 6 OK 113 116 117 136 C3' A P 7 OK 134 137 138 157 C3' G P 8 OK 155 158 159 179 C3' G P 9 OK 177 180 181 201 C3' A P 10 OK 199 202 203 222 C3' C P 11 OK 220 223 224 241 C3' T P 12 OK 239 242 243 261 C3' A P 13 259 262 282 C3' T T 6 OK 280 283 284 302 C3' A T 7 OK 300 303 304 323 C3' G T 8 OK 321 324 325 345 C3' T T 9 OK 343 346 347 365 C3' C T 10 OK 363 366 367 384 C3' C T 11 OK 382 385 386 403 C3' T T 12 OK 401 404 405 423 C3' T T 13 OK 421 424 425 443 C3' C T 14 OK 441 444 445 462 C3' C T 15 OK 460 463 464 481 C3' C T 16 OK 479 482 483 500 C3' C T 17 OK 498 501 502 519 C3' C T 18 OK 517 520 521 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G P 1 OK 5 2 4 25 C4' G P 2 OK 27 24 26 47 C4' G P 3 OK 49 46 48 69 C4' G P 4 OK 71 68 70 91 C4' G P 5 OK 93 90 92 113 C4' A P 6 OK 115 112 114 134 C4' A P 7 OK 136 133 135 155 C4' G P 8 OK 157 154 156 177 C4' G P 9 OK 179 176 178 199 C4' A P 10 201 200 220 C4' C P 11 OK 222 219 221 239 C4' T P 12 OK 241 238 240 259 C4' A P 13 OK 261 258 260 280 C4' T T 6 OK 282 279 281 300 C4' A T 7 OK 302 299 301 321 C4' G T 8 OK 323 320 322 343 C4' T T 9 OK 345 342 344 363 C4' C T 10 OK 365 362 364 382 C4' C T 11 OK 384 381 383 401 C4' T T 12 OK 403 400 402 421 C4' T T 13 OK 423 420 422 441 C4' C T 14 OK 443 440 442 460 C4' C T 15 OK 462 459 461 479 C4' C T 16 OK 481 478 480 498 C4' C T 17 OK 500 497 499 517 C4' C T 18 OK 519 516 518 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G P 1 1 3 24 C5' G P 2 23 25 46 C5' G P 3 45 47 68 C5' G P 4 67 69 90 C5' G P 5 89 91 112 C5' A P 6 111 113 133 C5' A P 7 132 134 154 C5' G P 8 153 155 176 C5' G P 9 175 177 219 C5' C P 11 218 220 238 C5' T P 12 237 239 258 C5' A P 13 257 259 279 C5' T T 6 278 280 299 C5' A T 7 298 300 320 C5' G T 8 319 321 342 C5' T T 9 341 343 362 C5' C T 10 361 363 381 C5' C T 11 380 382 400 C5' T T 12 399 401 420 C5' T T 13 419 421 440 C5' C T 14 439 441 459 C5' C T 15 458 460 478 C5' C T 16 477 479 497 C5' C T 17 496 498 516 C5' C T 18 515 517 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P G P 2 distorted distorted 6 21 22 23 42 P G P 3 distorted distorted 28 43 44 45 64 P G P 4 distorted distorted 50 65 66 67 86 P G P 5 distorted distorted 72 87 88 89 108 P A P 6 distorted distorted 94 109 110 111 129 P A P 7 distorted distorted 116 130 131 132 150 P G P 8 distorted distorted 137 151 152 153 172 P G P 9 distorted distorted 158 173 174 175 194 P A P 10 180 215 P C P 11 distorted distorted 202 216 217 218 234 P T P 12 distorted distorted 223 235 236 237 254 P A P 13 distorted distorted 242 255 256 257 275 P T T 6 distorted distorted 276 277 278 295 P A T 7 distorted distorted 283 296 297 298 316 P G T 8 distorted distorted 303 317 318 319 338 P T T 9 distorted distorted 324 339 340 341 358 P C T 10 distorted distorted 346 359 360 361 377 P C T 11 distorted distorted 366 378 379 380 396 P T T 12 distorted distorted 385 397 398 399 416 P T T 13 distorted distorted 404 417 418 419 436 P C T 14 distorted distorted 424 437 438 439 455 P C T 15 distorted distorted 444 456 457 458 474 P C T 16 distorted distorted 463 475 476 477 493 P C T 17 distorted distorted 482 494 495 496 512 P C T 18 distorted distorted 501 513 514 515 ---------------------------------------------------------------------------------