ID code: '4XIU' 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' DG B 101 beta 4 9 7 30 C1' DA B 102 beta 26 31 29 51 C1' DC B 103 beta 47 52 50 70 C1' DC B 104 beta 66 71 69 89 C1' DA B 105 beta 85 90 88 110 C1' DC B 106 beta 106 111 109 129 C1' DG B 107 beta 125 130 128 151 C1' DG B 108 beta 147 152 150 173 C1' DC B 109 beta 169 174 172 192 C1' DG B 110 beta 188 193 191 214 C1' DC B 111 beta 210 215 213 231 C1' DOC B 112 beta 235 223 232 252 C1' DT C 203 beta 248 253 251 272 C1' DG C 204 beta 268 273 271 294 C1' DG C 205 beta 290 295 293 316 C1' DG C 206 beta 312 317 315 338 C1' DC C 207 beta 334 339 337 357 C1' DG C 208 beta 353 358 356 379 C1' DC C 209 beta 375 380 378 398 C1' DC C 210 beta 394 399 397 417 C1' DG C 211 beta 413 418 416 439 C1' DT C 212 beta 435 440 438 459 C1' DG C 213 beta 455 460 458 481 C1' DG C 214 beta 477 482 480 503 C1' DT C 215 beta 499 504 502 523 C1' DC C 216 beta 519 524 522 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DG B 101 8 5 29 C2' DA B 102 30 27 50 C2' DC B 103 51 48 69 C2' DC B 104 70 67 88 C2' DA B 105 89 86 109 C2' DC B 106 110 107 128 C2' DG B 107 129 126 150 C2' DG B 108 151 148 172 C2' DC B 109 173 170 191 C2' DG B 110 192 189 213 C2' DC B 111 214 211 232 C2' DOC B 112 231 233 251 C2' DT C 203 252 249 271 C2' DG C 204 272 269 293 C2' DG C 205 294 291 315 C2' DG C 206 316 313 337 C2' DC C 207 338 335 356 C2' DG C 208 357 354 378 C2' DC C 209 379 376 397 C2' DC C 210 398 395 416 C2' DG C 211 417 414 438 C2' DT C 212 439 436 458 C2' DG C 213 459 456 480 C2' DG C 214 481 478 502 C2' DT C 215 503 500 522 C2' DC C 216 523 520 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DG B 101 OK 3 6 7 27 C3' DA B 102 OK 25 28 29 48 C3' DC B 103 OK 46 49 50 67 C3' DC B 104 OK 65 68 69 86 C3' DA B 105 OK 84 87 88 107 C3' DC B 106 OK 105 108 109 126 C3' DG B 107 OK 124 127 128 148 C3' DG B 108 OK 146 149 150 170 C3' DC B 109 OK 168 171 172 189 C3' DG B 110 OK 187 190 191 211 C3' DC B 111 OK 209 212 213 233 C3' DOC B 112 234 232 249 C3' DT C 203 OK 247 250 251 269 C3' DG C 204 OK 267 270 271 291 C3' DG C 205 OK 289 292 293 313 C3' DG C 206 OK 311 314 315 335 C3' DC C 207 OK 333 336 337 354 C3' DG C 208 OK 352 355 356 376 C3' DC C 209 OK 374 377 378 395 C3' DC C 210 OK 393 396 397 414 C3' DG C 211 OK 412 415 416 436 C3' DT C 212 OK 434 437 438 456 C3' DG C 213 OK 454 457 458 478 C3' DG C 214 OK 476 479 480 500 C3' DT C 215 OK 498 501 502 520 C3' DC C 216 OK 518 521 522 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DG B 101 OK 5 2 4 25 C4' DA B 102 OK 27 24 26 46 C4' DC B 103 OK 48 45 47 65 C4' DC B 104 OK 67 64 66 84 C4' DA B 105 OK 86 83 85 105 C4' DC B 106 OK 107 104 106 124 C4' DG B 107 OK 126 123 125 146 C4' DG B 108 OK 148 145 147 168 C4' DC B 109 OK 170 167 169 187 C4' DG B 110 OK 189 186 188 209 C4' DC B 111 OK 211 208 210 234 C4' DOC B 112 OK 233 236 235 247 C4' DT C 203 OK 249 246 248 267 C4' DG C 204 OK 269 266 268 289 C4' DG C 205 OK 291 288 290 311 C4' DG C 206 OK 313 310 312 333 C4' DC C 207 OK 335 332 334 352 C4' DG C 208 OK 354 351 353 374 C4' DC C 209 OK 376 373 375 393 C4' DC C 210 OK 395 392 394 412 C4' DG C 211 OK 414 411 413 434 C4' DT C 212 OK 436 433 435 454 C4' DG C 213 OK 456 453 455 476 C4' DG C 214 OK 478 475 477 498 C4' DT C 215 OK 500 497 499 518 C4' DC C 216 OK 520 517 519 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DG B 101 1 3 24 C5' DA B 102 23 25 45 C5' DC B 103 44 46 64 C5' DC B 104 63 65 83 C5' DA B 105 82 84 104 C5' DC B 106 103 105 123 C5' DG B 107 122 124 145 C5' DG B 108 144 146 167 C5' DC B 109 166 168 186 C5' DG B 110 185 187 208 C5' DC B 111 207 209 236 C5' DOC B 112 237 234 246 C5' DT C 203 245 247 266 C5' DG C 204 265 267 288 C5' DG C 205 287 289 310 C5' DG C 206 309 311 332 C5' DC C 207 331 333 351 C5' DG C 208 350 352 373 C5' DC C 209 372 374 392 C5' DC C 210 391 393 411 C5' DG C 211 410 412 433 C5' DT C 212 432 434 453 C5' DG C 213 452 454 475 C5' DG C 214 474 476 497 C5' DT C 215 496 498 517 C5' DC C 216 516 518 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P DA B 102 distorted distorted 6 21 22 23 41 P DC B 103 distorted distorted 28 42 43 44 60 P DC B 104 distorted distorted 49 61 62 63 79 P DA B 105 distorted distorted 68 80 81 82 100 P DC B 106 distorted distorted 87 101 102 103 119 P DG B 107 distorted distorted 108 120 121 122 141 P DG B 108 distorted distorted 127 142 143 144 163 P DC B 109 distorted distorted 149 164 165 166 182 P DG B 110 distorted distorted 171 183 184 185 204 P DC B 111 distorted distorted 190 205 206 207 238 P DOC B 112 distorted distorted 212 239 240 237 242 P DT C 203 distorted distorted 243 244 245 262 P DG C 204 distorted distorted 250 263 264 265 284 P DG C 205 distorted distorted 270 285 286 287 306 P DG C 206 distorted distorted 292 307 308 309 328 P DC C 207 distorted distorted 314 329 330 331 347 P DG C 208 distorted distorted 336 348 349 350 369 P DC C 209 distorted distorted 355 370 371 372 388 P DC C 210 distorted distorted 377 389 390 391 407 P DG C 211 distorted distorted 396 408 409 410 429 P DT C 212 distorted distorted 415 430 431 432 449 P DG C 213 distorted distorted 437 450 451 452 471 P DG C 214 distorted distorted 457 472 473 474 493 P DT C 215 distorted distorted 479 494 495 496 513 P DC C 216 distorted distorted 501 514 515 516 ---------------------------------------------------------------------------------