ID code: '3CGR' 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' --------------------------------------------------------------------------------- 9 C1' G A 1 beta 4 10 7 32 C1' C A 2 beta 27 33 30 52 C1' G A 3 beta 47 53 50 75 C1' C A 4 beta 70 76 73 95 C1' G A 5 beta 90 96 93 118 C1' G A 6 beta 113 119 116 138 C1' PSU A 7 beta 144 134 139 161 C1' A A 8 beta 156 162 159 183 C1' G A 9 beta 178 184 181 206 C1' U A 10 beta 201 207 204 226 C1' G A 11 beta 221 227 224 249 C1' C A 12 beta 244 250 247 267 C1' C B 13 beta 262 268 265 287 C1' G B 14 beta 282 288 285 310 C1' C B 15 beta 305 311 308 330 C1' A B 16 beta 325 331 328 352 C1' C B 17 beta 347 353 350 372 C1' U B 18 beta 367 373 370 392 C1' A B 19 beta 387 393 390 414 C1' A B 20 beta 409 415 412 436 C1' C B 21 beta 431 437 434 456 C1' C B 22 beta 451 457 454 476 C1' G B 23 beta 471 477 474 499 C1' C B 24 beta 494 500 497 519 C1' G B 25 beta 514 520 517 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK 9 5 8 30 C2' C A 2 OK 32 28 31 50 C2' G A 3 OK 52 48 51 73 C2' C A 4 OK 75 71 74 93 C2' G A 5 OK 95 91 94 116 C2' G A 6 OK 118 114 117 139 C2' PSU A 7 OK 138 141 140 159 C2' A A 8 OK 161 157 160 181 C2' G A 9 OK 183 179 182 204 C2' U A 10 OK 206 202 205 224 C2' G A 11 OK 226 222 225 247 C2' C A 12 OK 249 245 248 265 C2' C B 13 OK 267 263 266 285 C2' G B 14 OK 287 283 286 308 C2' C B 15 OK 310 306 309 328 C2' A B 16 OK 330 326 329 350 C2' C B 17 OK 352 348 351 370 C2' U B 18 OK 372 368 371 390 C2' A B 19 OK 392 388 391 412 C2' A B 20 OK 414 410 413 434 C2' C B 21 OK 436 432 435 454 C2' C B 22 OK 456 452 455 474 C2' G B 23 OK 476 472 475 497 C2' C B 24 OK 499 495 498 517 C2' G B 25 OK 519 515 518 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 28 C3' C A 2 OK 26 29 30 48 C3' G A 3 OK 46 49 50 71 C3' C A 4 OK 69 72 73 91 C3' G A 5 OK 89 92 93 114 C3' G A 6 OK 112 115 116 141 C3' PSU A 7 OK 142 143 139 157 C3' A A 8 OK 155 158 159 179 C3' G A 9 OK 177 180 181 202 C3' U A 10 OK 200 203 204 222 C3' G A 11 OK 220 223 224 245 C3' C A 12 OK 243 246 247 263 C3' C B 13 OK 261 264 265 283 C3' G B 14 OK 281 284 285 306 C3' C B 15 OK 304 307 308 326 C3' A B 16 OK 324 327 328 348 C3' C B 17 OK 346 349 350 368 C3' U B 18 OK 366 369 370 388 C3' A B 19 OK 386 389 390 410 C3' A B 20 OK 408 411 412 432 C3' C B 21 OK 430 433 434 452 C3' C B 22 OK 450 453 454 472 C3' G B 23 OK 470 473 474 495 C3' C B 24 OK 493 496 497 515 C3' G B 25 OK 513 516 517 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 26 C4' C A 2 OK 28 25 27 46 C4' G A 3 OK 48 45 47 69 C4' C A 4 OK 71 68 70 89 C4' G A 5 OK 91 88 90 112 C4' G A 6 OK 114 111 113 142 C4' PSU A 7 OK 141 145 144 155 C4' A A 8 OK 157 154 156 177 C4' G A 9 OK 179 176 178 200 C4' U A 10 OK 202 199 201 220 C4' G A 11 OK 222 219 221 243 C4' C A 12 OK 245 242 244 261 C4' C B 13 OK 263 260 262 281 C4' G B 14 OK 283 280 282 304 C4' C B 15 OK 306 303 305 324 C4' A B 16 OK 326 323 325 346 C4' C B 17 OK 348 345 347 366 C4' U B 18 OK 368 365 367 386 C4' A B 19 OK 388 385 387 408 C4' A B 20 OK 410 407 409 430 C4' C B 21 OK 432 429 431 450 C4' C B 22 OK 452 449 451 470 C4' G B 23 OK 472 469 471 493 C4' C B 24 OK 495 492 494 513 C4' G B 25 OK 515 512 514 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 25 C5' C A 2 24 26 45 C5' G A 3 44 46 68 C5' C A 4 67 69 88 C5' G A 5 87 89 111 C5' G A 6 110 112 145 C5' PSU A 7 146 142 154 C5' A A 8 153 155 176 C5' G A 9 175 177 199 C5' U A 10 198 200 219 C5' G A 11 218 220 242 C5' C A 12 241 243 260 C5' C B 13 259 261 280 C5' G B 14 279 281 303 C5' C B 15 302 304 323 C5' A B 16 322 324 345 C5' C B 17 344 346 365 C5' U B 18 364 366 385 C5' A B 19 384 386 407 C5' A B 20 406 408 429 C5' C B 21 428 430 449 C5' C B 22 448 450 469 C5' G B 23 468 470 492 C5' C B 24 491 493 512 C5' G B 25 511 513 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P C A 2 distorted distorted 6 22 23 24 41 P G A 3 distorted distorted 29 42 43 44 64 P C A 4 distorted distorted 49 65 66 67 84 P G A 5 distorted distorted 72 85 86 87 107 P G A 6 distorted distorted 92 108 109 110 147 P PSU A 7 distorted distorted 115 148 149 146 150 P A A 8 distorted distorted 143 151 152 153 172 P G A 9 distorted distorted 158 173 174 175 195 P U A 10 distorted distorted 180 196 197 198 215 P G A 11 distorted distorted 203 216 217 218 238 P C A 12 distorted distorted 223 239 240 241 276 P G B 14 distorted distorted 264 277 278 279 299 P C B 15 distorted distorted 284 300 301 302 319 P A B 16 distorted distorted 307 320 321 322 341 P C B 17 distorted distorted 327 342 343 344 361 P U B 18 distorted distorted 349 362 363 364 381 P A B 19 distorted distorted 369 382 383 384 403 P A B 20 distorted distorted 389 404 405 406 425 P C B 21 distorted distorted 411 426 427 428 445 P C B 22 distorted distorted 433 446 447 448 465 P G B 23 distorted distorted 453 466 467 468 488 P C B 24 distorted distorted 473 489 490 491 508 P G B 25 distorted distorted 496 509 510 511 ---------------------------------------------------------------------------------