ID code: '4N5S' 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 235 223 232 253 C1' DG C 204 beta 249 254 252 275 C1' DG C 205 beta 271 276 274 297 C1' DG C 206 beta 293 298 296 319 C1' DC C 207 beta 315 320 318 338 C1' DG C 208 beta 334 339 337 360 C1' DC C 209 beta 356 361 359 379 C1' DC C 210 beta 375 380 378 398 C1' DG C 211 beta 394 399 397 420 C1' DT C 212 beta 416 421 419 440 C1' DG C 213 beta 436 441 439 462 C1' DG C 214 beta 458 463 461 484 C1' DT C 215 beta 480 485 483 504 C1' DC C 216 beta 500 505 503 4816 C1' DCT A 907 beta 4820 4808 4817 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 112 231 233 252 C2' DG C 204 253 250 274 C2' DG C 205 275 272 296 C2' DG C 206 297 294 318 C2' DC C 207 319 316 337 C2' DG C 208 338 335 359 C2' DC C 209 360 357 378 C2' DC C 210 379 376 397 C2' DG C 211 398 395 419 C2' DT C 212 420 417 439 C2' DG C 213 440 437 461 C2' DG C 214 462 459 483 C2' DT C 215 484 481 503 C2' DC C 216 504 501 4817 C2' DCT A 907 4816 4818 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 112 234 232 250 C3' DG C 204 OK 248 251 252 272 C3' DG C 205 OK 270 273 274 294 C3' DG C 206 OK 292 295 296 316 C3' DC C 207 OK 314 317 318 335 C3' DG C 208 OK 333 336 337 357 C3' DC C 209 OK 355 358 359 376 C3' DC C 210 OK 374 377 378 395 C3' DG C 211 OK 393 396 397 417 C3' DT C 212 OK 415 418 419 437 C3' DG C 213 OK 435 438 439 459 C3' DG C 214 OK 457 460 461 481 C3' DT C 215 OK 479 482 483 501 C3' DC C 216 OK 499 502 503 4818 C3' DCT A 907 4819 4817 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 233 236 235 248 C4' DG C 204 OK 250 247 249 270 C4' DG C 205 OK 272 269 271 292 C4' DG C 206 OK 294 291 293 314 C4' DC C 207 OK 316 313 315 333 C4' DG C 208 OK 335 332 334 355 C4' DC C 209 OK 357 354 356 374 C4' DC C 210 OK 376 373 375 393 C4' DG C 211 OK 395 392 394 415 C4' DT C 212 OK 417 414 416 435 C4' DG C 213 OK 437 434 436 457 C4' DG C 214 OK 459 456 458 479 C4' DT C 215 OK 481 478 480 499 C4' DC C 216 OK 501 498 500 4819 C4' DCT A 907 OK 4818 4821 4820 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 112 237 234 247 C5' DG C 204 246 248 269 C5' DG C 205 268 270 291 C5' DG C 206 290 292 313 C5' DC C 207 312 314 332 C5' DG C 208 331 333 354 C5' DC C 209 353 355 373 C5' DC C 210 372 374 392 C5' DG C 211 391 393 414 C5' DT C 212 413 415 434 C5' DG C 213 433 435 456 C5' DG C 214 455 457 478 C5' DT C 215 477 479 498 C5' DC C 216 497 499 4821 C5' DCT A 907 4822 4819 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 212 239 240 237 243 P DG C 204 distorted distorted 242 244 245 246 265 P DG C 205 distorted distorted 251 266 267 268 287 P DG C 206 distorted distorted 273 288 289 290 309 P DC C 207 distorted distorted 295 310 311 312 328 P DG C 208 distorted distorted 317 329 330 331 350 P DC C 209 distorted distorted 336 351 352 353 369 P DC C 210 distorted distorted 358 370 371 372 388 P DG C 211 distorted distorted 377 389 390 391 410 P DT C 212 distorted distorted 396 411 412 413 430 P DG C 213 distorted distorted 418 431 432 433 452 P DG C 214 distorted distorted 438 453 454 455 474 P DT C 215 distorted distorted 460 475 476 477 494 P DC C 216 distorted distorted 482 495 496 497 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