ID code: '1T0K' 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 C 6 beta 4 10 7 32 C1' A C 7 beta 27 33 30 54 C1' C C 8 beta 49 55 52 74 C1' C C 9 beta 69 75 72 94 C1' G C 10 beta 89 95 92 117 C1' G C 11 beta 112 118 115 140 C1' A C 12 beta 135 141 138 162 C1' G C 13 beta 157 163 160 185 C1' U C 14 beta 180 186 183 205 C1' G C 15 beta 200 206 203 228 C1' U C 16 beta 223 229 226 248 C1' C C 17 beta 243 249 246 266 C1' G D 50 beta 261 267 264 289 C1' A D 51 beta 284 290 287 311 C1' C D 52 beta 306 312 309 331 C1' G D 53 beta 326 332 329 354 C1' C D 54 beta 349 355 352 374 C1' A D 55 beta 369 375 372 396 C1' G D 56 beta 391 397 394 419 C1' A D 57 beta 414 420 417 441 C1' G D 58 beta 436 442 439 464 C1' A D 59 beta 459 465 462 486 C1' U D 60 beta 481 487 484 506 C1' G D 61 beta 501 507 504 529 C1' G D 62 beta 524 530 527 552 C1' U D 63 beta 547 553 550 572 C1' C D 64 beta 567 573 570 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G C 6 OK 9 5 8 30 C2' A C 7 OK 32 28 31 52 C2' C C 8 OK 54 50 53 72 C2' C C 9 OK 74 70 73 92 C2' G C 10 OK 94 90 93 115 C2' G C 11 OK 117 113 116 138 C2' A C 12 OK 140 136 139 160 C2' G C 13 OK 162 158 161 183 C2' U C 14 OK 185 181 184 203 C2' G C 15 OK 205 201 204 226 C2' U C 16 OK 228 224 227 246 C2' C C 17 OK 248 244 247 264 C2' G D 50 OK 266 262 265 287 C2' A D 51 OK 289 285 288 309 C2' C D 52 OK 311 307 310 329 C2' G D 53 OK 331 327 330 352 C2' C D 54 OK 354 350 353 372 C2' A D 55 OK 374 370 373 394 C2' G D 56 OK 396 392 395 417 C2' A D 57 OK 419 415 418 439 C2' G D 58 OK 441 437 440 462 C2' A D 59 OK 464 460 463 484 C2' U D 60 OK 486 482 485 504 C2' G D 61 OK 506 502 505 527 C2' G D 62 OK 529 525 528 550 C2' U D 63 OK 552 548 551 570 C2' C D 64 OK 572 568 571 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G C 6 OK 3 6 7 28 C3' A C 7 OK 26 29 30 50 C3' C C 8 OK 48 51 52 70 C3' C C 9 OK 68 71 72 90 C3' G C 10 OK 88 91 92 113 C3' G C 11 OK 111 114 115 136 C3' A C 12 OK 134 137 138 158 C3' G C 13 OK 156 159 160 181 C3' U C 14 OK 179 182 183 201 C3' G C 15 OK 199 202 203 224 C3' U C 16 OK 222 225 226 244 C3' C C 17 OK 242 245 246 262 C3' G D 50 OK 260 263 264 285 C3' A D 51 OK 283 286 287 307 C3' C D 52 OK 305 308 309 327 C3' G D 53 OK 325 328 329 350 C3' C D 54 OK 348 351 352 370 C3' A D 55 OK 368 371 372 392 C3' G D 56 OK 390 393 394 415 C3' A D 57 OK 413 416 417 437 C3' G D 58 OK 435 438 439 460 C3' A D 59 OK 458 461 462 482 C3' U D 60 OK 480 483 484 502 C3' G D 61 OK 500 503 504 525 C3' G D 62 OK 523 526 527 548 C3' U D 63 OK 546 549 550 568 C3' C D 64 OK 566 569 570 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G C 6 OK 5 2 4 26 C4' A C 7 OK 28 25 27 48 C4' C C 8 OK 50 47 49 68 C4' C C 9 OK 70 67 69 88 C4' G C 10 OK 90 87 89 111 C4' G C 11 OK 113 110 112 134 C4' A C 12 OK 136 133 135 156 C4' G C 13 OK 158 155 157 179 C4' U C 14 OK 181 178 180 199 C4' G C 15 OK 201 198 200 222 C4' U C 16 OK 224 221 223 242 C4' C C 17 OK 244 241 243 260 C4' G D 50 OK 262 259 261 283 C4' A D 51 OK 285 282 284 305 C4' C D 52 OK 307 304 306 325 C4' G D 53 OK 327 324 326 348 C4' C D 54 OK 350 347 349 368 C4' A D 55 OK 370 367 369 390 C4' G D 56 OK 392 389 391 413 C4' A D 57 OK 415 412 414 435 C4' G D 58 OK 437 434 436 458 C4' A D 59 OK 460 457 459 480 C4' U D 60 OK 482 479 481 500 C4' G D 61 OK 502 499 501 523 C4' G D 62 OK 525 522 524 546 C4' U D 63 OK 548 545 547 566 C4' C D 64 OK 568 565 567 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G C 6 1 3 25 C5' A C 7 24 26 47 C5' C C 8 46 48 67 C5' C C 9 66 68 87 C5' G C 10 86 88 110 C5' G C 11 109 111 133 C5' A C 12 132 134 155 C5' G C 13 154 156 178 C5' U C 14 177 179 198 C5' G C 15 197 199 221 C5' U C 16 220 222 241 C5' C C 17 240 242 259 C5' G D 50 258 260 282 C5' A D 51 281 283 304 C5' C D 52 303 305 324 C5' G D 53 323 325 347 C5' C D 54 346 348 367 C5' A D 55 366 368 389 C5' G D 56 388 390 412 C5' A D 57 411 413 434 C5' G D 58 433 435 457 C5' A D 59 456 458 479 C5' U D 60 478 480 499 C5' G D 61 498 500 522 C5' G D 62 521 523 545 C5' U D 63 544 546 565 C5' C D 64 564 566 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P A C 7 distorted distorted 6 22 23 24 43 P C C 8 distorted distorted 29 44 45 46 63 P C C 9 distorted distorted 51 64 65 66 83 P G C 10 distorted distorted 71 84 85 86 106 P G C 11 distorted distorted 91 107 108 109 129 P A C 12 distorted distorted 114 130 131 132 151 P G C 13 distorted distorted 137 152 153 154 174 P U C 14 distorted distorted 159 175 176 177 194 P G C 15 distorted distorted 182 195 196 197 217 P U C 16 distorted distorted 202 218 219 220 237 P C C 17 distorted distorted 225 238 239 240 278 P A D 51 distorted distorted 263 279 280 281 300 P C D 52 distorted distorted 286 301 302 303 320 P G D 53 distorted distorted 308 321 322 323 343 P C D 54 distorted distorted 328 344 345 346 363 P A D 55 distorted distorted 351 364 365 366 385 P G D 56 distorted distorted 371 386 387 388 408 P A D 57 distorted distorted 393 409 410 411 430 P G D 58 distorted distorted 416 431 432 433 453 P A D 59 distorted distorted 438 454 455 456 475 P U D 60 distorted distorted 461 476 477 478 495 P G D 61 distorted distorted 483 496 497 498 518 P G D 62 distorted distorted 503 519 520 521 541 P U D 63 distorted distorted 526 542 543 544 561 P C D 64 distorted distorted 549 562 563 564 ---------------------------------------------------------------------------------