ID code: '1SKS' 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 P 11 4 7 19 C1' DG P 12 15 18 30 C1' DC P 13 beta 26 31 29 49 C1' DC P 14 beta 45 50 48 68 C1' DA P 15 beta 64 69 67 89 C1' DG P 16 beta 85 90 88 111 C1' DT P 17 beta 107 112 110 131 C1' DG P 18 beta 127 132 130 153 C1' DC P 19 beta 149 154 152 172 C1' DC P 20 beta 168 173 171 198 C1' 2DT P 21 beta 197 185 194 211 C1' TTD T 5 beta 207 212 210 251 C1' DA T 6 beta 247 252 250 272 C1' DG T 7 beta 268 273 271 294 C1' DG T 8 beta 290 295 293 316 C1' DC T 9 beta 312 317 315 335 C1' DA T 10 beta 331 336 334 356 C1' DC T 11 beta 352 357 355 375 C1' DT T 12 beta 371 376 374 395 C1' DG T 13 beta 391 396 394 417 C1' DG T 14 beta 413 418 416 439 C1' DC T 15 beta 435 440 438 458 C1' DC T 16 beta 454 459 457 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DG P 11 8 5 18 C2' DG P 12 19 16 29 C2' DC P 13 30 27 48 C2' DC P 14 49 46 67 C2' DA P 15 68 65 88 C2' DG P 16 89 86 110 C2' DT P 17 111 108 130 C2' DG P 18 131 128 152 C2' DC P 19 153 150 171 C2' DC P 20 172 169 194 C2' 2DT P 21 198 199 210 C2' TTD T 5 211 250 C2' DA T 6 251 248 271 C2' DG T 7 272 269 293 C2' DG T 8 294 291 315 C2' DC T 9 316 313 334 C2' DA T 10 335 332 355 C2' DC T 11 356 353 374 C2' DT T 12 375 372 394 C2' DG T 13 395 392 416 C2' DG T 14 417 414 438 C2' DC T 15 439 436 457 C2' DC T 16 458 455 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DG P 11 OK 3 6 7 16 C3' DG P 12 OK 14 17 18 27 C3' DC P 13 OK 25 28 29 46 C3' DC P 14 OK 44 47 48 65 C3' DA P 15 OK 63 66 67 86 C3' DG P 16 OK 84 87 88 108 C3' DT P 17 OK 106 109 110 128 C3' DG P 18 OK 126 129 130 150 C3' DC P 19 OK 148 151 152 169 C3' DC P 20 OK 167 170 171 199 C3' 2DT P 21 196 194 239 C3' TTD T 5 238 240 248 C3' DA T 6 OK 246 249 250 269 C3' DG T 7 OK 267 270 271 291 C3' DG T 8 OK 289 292 293 313 C3' DC T 9 OK 311 314 315 332 C3' DA T 10 OK 330 333 334 353 C3' DC T 11 OK 351 354 355 372 C3' DT T 12 OK 370 373 374 392 C3' DG T 13 OK 390 393 394 414 C3' DG T 14 OK 412 415 416 436 C3' DC T 15 OK 434 437 438 455 C3' DC T 16 OK 453 456 457 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DG P 11 OK 5 2 4 14 C4' DG P 12 OK 16 13 15 25 C4' DC P 13 OK 27 24 26 44 C4' DC P 14 OK 46 43 45 63 C4' DA P 15 OK 65 62 64 84 C4' DG P 16 OK 86 83 85 106 C4' DT P 17 OK 108 105 107 126 C4' DG P 18 OK 128 125 127 148 C4' DC P 19 OK 150 147 149 167 C4' DC P 20 OK 169 166 168 196 C4' 2DT P 21 OK 199 195 197 238 C4' TTD T 5 239 246 C4' DA T 6 OK 248 245 247 267 C4' DG T 7 OK 269 266 268 289 C4' DG T 8 OK 291 288 290 311 C4' DC T 9 OK 313 310 312 330 C4' DA T 10 OK 332 329 331 351 C4' DC T 11 OK 353 350 352 370 C4' DT T 12 OK 372 369 371 390 C4' DG T 13 OK 392 389 391 412 C4' DG T 14 OK 414 411 413 434 C4' DC T 15 OK 436 433 435 453 C4' DC T 16 OK 455 452 454 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DG P 11 1 3 13 C5' DG P 12 12 14 24 C5' DC P 13 23 25 43 C5' DC P 14 42 44 62 C5' DA P 15 61 63 83 C5' DG P 16 82 84 105 C5' DT P 17 104 106 125 C5' DG P 18 124 126 147 C5' DC P 19 146 148 166 C5' DC P 20 165 167 195 C5' 2DT P 21 184 196 205 C5' TTD T 5 204 245 C5' DA T 6 244 246 266 C5' DG T 7 265 267 288 C5' DG T 8 287 289 310 C5' DC T 9 309 311 329 C5' DA T 10 328 330 350 C5' DC T 11 349 351 369 C5' DT T 12 368 370 389 C5' DG T 13 388 390 411 C5' DG T 14 410 412 433 C5' DC T 15 432 434 452 C5' DC T 16 451 453 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 9 P DG P 12 distorted distorted 6 10 11 12 20 P DC P 13 distorted distorted 17 21 22 23 39 P DC P 14 distorted distorted 28 40 41 42 58 P DA P 15 distorted distorted 47 59 60 61 79 P DG P 16 distorted distorted 66 80 81 82 101 P DT P 17 distorted distorted 87 102 103 104 121 P DG P 18 distorted distorted 109 122 123 124 143 P DC P 19 distorted distorted 129 144 145 146 162 P DC P 20 distorted distorted 151 163 164 165 181 P 2DT P 21 distorted distorted 170 182 183 184 201 P TTD T 5 distorted distorted 202 203 204 241 P DA T 6 distorted distorted 240 242 243 244 262 P DG T 7 distorted distorted 249 263 264 265 284 P DG T 8 distorted distorted 270 285 286 287 306 P DC T 9 distorted distorted 292 307 308 309 325 P DA T 10 distorted distorted 314 326 327 328 346 P DC T 11 distorted distorted 333 347 348 349 365 P DT T 12 distorted distorted 354 366 367 368 385 P DG T 13 distorted distorted 373 386 387 388 407 P DG T 14 distorted distorted 393 408 409 410 429 P DC T 15 distorted distorted 415 430 431 432 448 P DC T 16 distorted distorted 437 449 450 451 ---------------------------------------------------------------------------------