ID code: '1SKR' 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' DG P 12 beta 7 12 10 33 C1' DC P 13 beta 29 34 32 52 C1' DC P 14 beta 48 53 51 71 C1' DA P 15 beta 67 72 70 92 C1' DG P 16 beta 88 93 91 114 C1' DT P 17 beta 110 115 113 134 C1' DG P 18 beta 130 135 133 156 C1' DC P 19 beta 152 157 155 175 C1' DC P 20 beta 171 176 174 194 C1' DA P 21 beta 190 195 193 214 C1' 2DA P 22 beta 211 215 213 236 C1' DC T 3 beta 232 237 235 255 C1' DT T 4 beta 251 256 254 275 C1' DT T 5 beta 271 276 274 295 C1' DT T 6 beta 291 296 294 315 C1' DG T 7 beta 311 316 314 337 C1' DG T 8 beta 333 338 336 359 C1' DC T 9 beta 355 360 358 378 C1' DA T 10 beta 374 379 377 399 C1' DC T 11 beta 395 400 398 418 C1' DT T 12 beta 414 419 417 438 C1' DG T 13 beta 434 439 437 460 C1' DG T 14 beta 456 461 459 482 C1' DC T 15 beta 478 483 481 6625 C1' DAD A4004 beta 6622 6626 6624 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' DG P 12 11 8 32 C2' DC P 13 33 30 51 C2' DC P 14 52 49 70 C2' DA P 15 71 68 91 C2' DG P 16 92 89 113 C2' DT P 17 114 111 133 C2' DG P 18 134 131 155 C2' DC P 19 156 153 174 C2' DC P 20 175 172 193 C2' DA P 21 194 191 213 C2' 2DA P 22 214 212 235 C2' DC T 3 236 233 254 C2' DT T 4 255 252 274 C2' DT T 5 275 272 294 C2' DT T 6 295 292 314 C2' DG T 7 315 312 336 C2' DG T 8 337 334 358 C2' DC T 9 359 356 377 C2' DA T 10 378 375 398 C2' DC T 11 399 396 417 C2' DT T 12 418 415 437 C2' DG T 13 438 435 459 C2' DG T 14 460 457 481 C2' DC T 15 482 479 6624 C2' DAD A4004 6625 6623 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' DG P 12 OK 6 9 10 30 C3' DC P 13 OK 28 31 32 49 C3' DC P 14 OK 47 50 51 68 C3' DA P 15 OK 66 69 70 89 C3' DG P 16 OK 87 90 91 111 C3' DT P 17 OK 109 112 113 131 C3' DG P 18 OK 129 132 133 153 C3' DC P 19 OK 151 154 155 172 C3' DC P 20 OK 170 173 174 191 C3' DA P 21 OK 189 192 193 212 C3' 2DA P 22 210 213 233 C3' DC T 3 OK 231 234 235 252 C3' DT T 4 OK 250 253 254 272 C3' DT T 5 OK 270 273 274 292 C3' DT T 6 OK 290 293 294 312 C3' DG T 7 OK 310 313 314 334 C3' DG T 8 OK 332 335 336 356 C3' DC T 9 OK 354 357 358 375 C3' DA T 10 OK 373 376 377 396 C3' DC T 11 OK 394 397 398 415 C3' DT T 12 OK 413 416 417 435 C3' DG T 13 OK 433 436 437 457 C3' DG T 14 OK 455 458 459 479 C3' DC T 15 OK 477 480 481 6623 C3' DAD A4004 6621 6624 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' DG P 12 OK 8 5 7 28 C4' DC P 13 OK 30 27 29 47 C4' DC P 14 OK 49 46 48 66 C4' DA P 15 OK 68 65 67 87 C4' DG P 16 OK 89 86 88 109 C4' DT P 17 OK 111 108 110 129 C4' DG P 18 OK 131 128 130 151 C4' DC P 19 OK 153 150 152 170 C4' DC P 20 OK 172 169 171 189 C4' DA P 21 OK 191 188 190 210 C4' 2DA P 22 OK 212 209 211 231 C4' DC T 3 OK 233 230 232 250 C4' DT T 4 OK 252 249 251 270 C4' DT T 5 OK 272 269 271 290 C4' DT T 6 OK 292 289 291 310 C4' DG T 7 OK 312 309 311 332 C4' DG T 8 OK 334 331 333 354 C4' DC T 9 OK 356 353 355 373 C4' DA T 10 OK 375 372 374 394 C4' DC T 11 OK 396 393 395 413 C4' DT T 12 OK 415 412 414 433 C4' DG T 13 OK 435 432 434 455 C4' DG T 14 OK 457 454 456 477 C4' DC T 15 OK 479 476 478 6621 C4' DAD A4004 OK 6623 6620 6622 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' DG P 12 4 6 27 C5' DC P 13 26 28 46 C5' DC P 14 45 47 65 C5' DA P 15 64 66 86 C5' DG P 16 85 87 108 C5' DT P 17 107 109 128 C5' DG P 18 127 129 150 C5' DC P 19 149 151 169 C5' DC P 20 168 170 188 C5' DA P 21 187 189 209 C5' 2DA P 22 208 210 230 C5' DC T 3 229 231 249 C5' DT T 4 248 250 269 C5' DT T 5 268 270 289 C5' DT T 6 288 290 309 C5' DG T 7 308 310 331 C5' DG T 8 330 332 353 C5' DC T 9 352 354 372 C5' DA T 10 371 373 393 C5' DC T 11 392 394 412 C5' DT T 12 411 413 432 C5' DG T 13 431 433 454 C5' DG T 14 453 455 476 C5' DC T 15 475 477 6620 C5' DAD A4004 6619 6621 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P DG P 12 OK OK 2 3 4 23 P DC P 13 distorted distorted 9 24 25 26 42 P DC P 14 distorted distorted 31 43 44 45 61 P DA P 15 distorted distorted 50 62 63 64 82 P DG P 16 distorted distorted 69 83 84 85 104 P DT P 17 distorted distorted 90 105 106 107 124 P DG P 18 distorted distorted 112 125 126 127 146 P DC P 19 distorted distorted 132 147 148 149 165 P DC P 20 distorted distorted 154 166 167 168 184 P DA P 21 distorted distorted 173 185 186 187 205 P 2DA P 22 distorted distorted 192 206 207 208 226 P DC T 3 OK OK 227 228 229 245 P DT T 4 distorted distorted 234 246 247 248 265 P DT T 5 distorted distorted 253 266 267 268 285 P DT T 6 distorted distorted 273 286 287 288 305 P DG T 7 distorted distorted 293 306 307 308 327 P DG T 8 distorted distorted 313 328 329 330 349 P DC T 9 distorted distorted 335 350 351 352 368 P DA T 10 distorted distorted 357 369 370 371 389 P DC T 11 distorted distorted 376 390 391 392 408 P DT T 12 distorted distorted 397 409 410 411 428 P DG T 13 distorted distorted 416 429 430 431 450 P DG T 14 distorted distorted 436 451 452 453 472 P DC T 15 distorted distorted 458 473 474 475 ---------------------------------------------------------------------------------