ID code: '1IMH' 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' G A4003 beta 7 12 10 33 C1' C A4004 beta 29 34 32 52 C1' T A4005 beta 48 53 51 72 C1' G A4006 beta 68 73 71 94 C1' G A4007 beta 90 95 93 116 C1' A A4008 beta 112 117 115 137 C1' A A4009 beta 133 138 136 158 C1' A A4010 beta 154 159 157 179 C1' A A4011 beta 175 180 178 200 C1' A A4012 beta 196 201 199 221 C1' T A4013 beta 217 222 220 241 C1' A A4014 beta 237 242 240 262 C1' G A4015 beta 258 263 261 285 C1' C B5003 beta 281 286 284 304 C1' T B5004 beta 300 305 303 324 C1' A B5005 beta 320 325 323 345 C1' T B5006 beta 341 346 344 365 C1' T B5007 beta 361 366 364 385 C1' T B5008 beta 381 386 384 405 C1' T B5009 beta 401 406 404 425 C1' T B5010 beta 421 426 424 445 C1' C B5011 beta 441 446 444 464 C1' C B5012 beta 460 465 463 483 C1' A B5013 beta 479 484 482 504 C1' G B5014 beta 500 505 503 526 C1' C B5015 beta 522 527 525 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A4003 11 8 32 C2' C A4004 33 30 51 C2' T A4005 52 49 71 C2' G A4006 72 69 93 C2' G A4007 94 91 115 C2' A A4008 116 113 136 C2' A A4009 137 134 157 C2' A A4010 158 155 178 C2' A A4011 179 176 199 C2' A A4012 200 197 220 C2' T A4013 221 218 240 C2' A A4014 241 238 261 C2' G A4015 262 259 284 C2' C B5003 285 282 303 C2' T B5004 304 301 323 C2' A B5005 324 321 344 C2' T B5006 345 342 364 C2' T B5007 365 362 384 C2' T B5008 385 382 404 C2' T B5009 405 402 424 C2' T B5010 425 422 444 C2' C B5011 445 442 463 C2' C B5012 464 461 482 C2' A B5013 483 480 503 C2' G B5014 504 501 525 C2' C B5015 526 523 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A4003 OK 6 9 10 30 C3' C A4004 OK 28 31 32 49 C3' T A4005 OK 47 50 51 69 C3' G A4006 OK 67 70 71 91 C3' G A4007 OK 89 92 93 113 C3' A A4008 OK 111 114 115 134 C3' A A4009 OK 132 135 136 155 C3' A A4010 OK 153 156 157 176 C3' A A4011 OK 174 177 178 197 C3' A A4012 OK 195 198 199 218 C3' T A4013 OK 216 219 220 238 C3' A A4014 OK 236 239 240 259 C3' G A4015 OK 257 260 261 282 C3' C B5003 OK 280 283 284 301 C3' T B5004 OK 299 302 303 321 C3' A B5005 OK 319 322 323 342 C3' T B5006 OK 340 343 344 362 C3' T B5007 OK 360 363 364 382 C3' T B5008 OK 380 383 384 402 C3' T B5009 OK 400 403 404 422 C3' T B5010 OK 420 423 424 442 C3' C B5011 OK 440 443 444 461 C3' C B5012 OK 459 462 463 480 C3' A B5013 OK 478 481 482 501 C3' G B5014 OK 499 502 503 523 C3' C B5015 OK 521 524 525 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A4003 OK 8 5 7 28 C4' C A4004 OK 30 27 29 47 C4' T A4005 OK 49 46 48 67 C4' G A4006 OK 69 66 68 89 C4' G A4007 OK 91 88 90 111 C4' A A4008 OK 113 110 112 132 C4' A A4009 OK 134 131 133 153 C4' A A4010 OK 155 152 154 174 C4' A A4011 OK 176 173 175 195 C4' A A4012 OK 197 194 196 216 C4' T A4013 OK 218 215 217 236 C4' A A4014 OK 238 235 237 257 C4' G A4015 OK 259 256 258 280 C4' C B5003 OK 282 279 281 299 C4' T B5004 OK 301 298 300 319 C4' A B5005 OK 321 318 320 340 C4' T B5006 OK 342 339 341 360 C4' T B5007 OK 362 359 361 380 C4' T B5008 OK 382 379 381 400 C4' T B5009 OK 402 399 401 420 C4' T B5010 OK 422 419 421 440 C4' C B5011 OK 442 439 441 459 C4' C B5012 OK 461 458 460 478 C4' A B5013 OK 480 477 479 499 C4' G B5014 OK 501 498 500 521 C4' C B5015 OK 523 520 522 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A4003 4 6 27 C5' C A4004 26 28 46 C5' T A4005 45 47 66 C5' G A4006 65 67 88 C5' G A4007 87 89 110 C5' A A4008 109 111 131 C5' A A4009 130 132 152 C5' A A4010 151 153 173 C5' A A4011 172 174 194 C5' A A4012 193 195 215 C5' T A4013 214 216 235 C5' A A4014 234 236 256 C5' G A4015 255 257 279 C5' C B5003 278 280 298 C5' T B5004 297 299 318 C5' A B5005 317 319 339 C5' T B5006 338 340 359 C5' T B5007 358 360 379 C5' T B5008 378 380 399 C5' T B5009 398 400 419 C5' T B5010 418 420 439 C5' C B5011 438 440 458 C5' C B5012 457 459 477 C5' A B5013 476 478 498 C5' G B5014 497 499 520 C5' C B5015 519 521 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A4003 distorted distorted 2 3 4 23 P C A4004 distorted distorted 9 24 25 26 42 P T A4005 distorted distorted 31 43 44 45 62 P G A4006 distorted distorted 50 63 64 65 84 P G A4007 distorted distorted 70 85 86 87 106 P A A4008 distorted distorted 92 107 108 109 127 P A A4009 distorted distorted 114 128 129 130 148 P A A4010 distorted distorted 135 149 150 151 169 P A A4011 distorted distorted 156 170 171 172 190 P A A4012 distorted distorted 177 191 192 193 211 P T A4013 distorted distorted 198 212 213 214 231 P A A4014 distorted distorted 219 232 233 234 252 P G A4015 distorted distorted 239 253 254 255 275 P C B5003 distorted distorted 276 277 278 294 P T B5004 distorted distorted 283 295 296 297 314 P A B5005 distorted distorted 302 315 316 317 335 P T B5006 distorted distorted 322 336 337 338 355 P T B5007 distorted distorted 343 356 357 358 375 P T B5008 distorted distorted 363 376 377 378 395 P T B5009 distorted distorted 383 396 397 398 415 P T B5010 distorted distorted 403 416 417 418 435 P C B5011 distorted distorted 423 436 437 438 454 P C B5012 distorted distorted 443 455 456 457 473 P A B5013 distorted distorted 462 474 475 476 494 P G B5014 distorted distorted 481 495 496 497 516 P C B5015 distorted distorted 502 517 518 519 ---------------------------------------------------------------------------------