ID code: '1H0Q' 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' LKC A 1 alpha beta 13 23 1 10 41 C1' TLN A 2 alpha beta 40 58 42 52 83 C1' LCG A 3 alpha beta 86 99 74 80 118 C1' LCA A 4 alpha beta 121 135 109 115 144 C1' TLN A 5 alpha beta 143 161 145 155 186 C1' LCA A 6 alpha beta 189 203 177 183 212 C1' TLN A 7 alpha beta 211 229 213 223 254 C1' LCG A 8 alpha beta 257 270 245 251 278 C1' LCC A 9 alpha beta 277 298 279 289 319 C1' G B 10 alpha beta 314 337 320 317 354 C1' C B 11 alpha beta 349 369 355 352 385 C1' A B 12 alpha beta 380 402 386 383 418 C1' U B 13 alpha beta 413 433 419 416 448 C1' A B 14 alpha beta 443 465 449 446 481 C1' U B 15 alpha beta 476 496 482 479 511 C1' C B 16 alpha beta 506 526 512 509 542 C1' A B 17 alpha beta 537 559 543 540 575 C1' G B 18 alpha beta 570 593 576 573 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' LKC A 1 OK OK 9 11 24 18 52 C2' TLN A 2 OK OK 41 51 65 53 80 C2' LCG A 3 OK OK 83 72 98 90 115 C2' LCA A 4 OK OK 118 107 132 125 155 C2' TLN A 5 OK OK 144 154 168 156 183 C2' LCA A 6 OK OK 186 175 200 193 223 C2' TLN A 7 OK OK 212 222 236 224 251 C2' LCG A 8 OK OK 254 243 269 261 289 C2' LCC A 9 OK OK 278 288 306 290 317 C2' G B 10 OK OK 319 315 335 318 352 C2' C B 11 OK OK 354 350 367 353 383 C2' A B 12 OK OK 385 381 400 384 416 C2' U B 13 OK OK 418 414 431 417 446 C2' A B 14 OK OK 448 444 463 447 479 C2' U B 15 OK OK 481 477 494 480 509 C2' C B 16 OK OK 511 507 524 510 540 C2' A B 17 OK OK 542 538 557 541 573 C2' G B 18 OK OK 575 571 591 574 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 11 C3' LKC A 1 OK OK 12 25 14 10 51 C3' TLN A 2 OK OK 39 64 54 52 72 C3' LCG A 3 OK OK 82 94 91 80 107 C3' LCA A 4 OK OK 117 128 124 115 154 C3' TLN A 5 OK OK 142 167 157 155 175 C3' LCA A 6 OK OK 185 196 192 183 222 C3' TLN A 7 OK OK 210 235 225 223 243 C3' LCG A 8 OK OK 253 265 262 251 288 C3' LCC A 9 OK OK 276 305 291 289 315 C3' G B 10 OK OK 313 334 316 317 350 C3' C B 11 OK OK 348 366 351 352 381 C3' A B 12 OK OK 379 399 382 383 414 C3' U B 13 OK OK 412 430 415 416 444 C3' A B 14 OK OK 442 462 445 446 477 C3' U B 15 OK OK 475 493 478 479 507 C3' C B 16 OK OK 505 523 508 509 538 C3' A B 17 OK OK 536 556 539 540 571 C3' G B 18 OK OK 569 590 572 573 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 12 C4' LKC A 1 OK 11 15 13 39 C4' TLN A 2 OK 51 38 40 82 C4' LCG A 3 OK 72 71 86 117 C4' LCA A 4 OK 107 106 121 142 C4' TLN A 5 OK 154 141 143 185 C4' LCA A 6 OK 175 174 189 210 C4' TLN A 7 OK 222 209 211 253 C4' LCG A 8 OK 243 242 257 276 C4' LCC A 9 OK 288 275 277 313 C4' G B 10 OK OK 315 333 312 314 348 C4' C B 11 OK OK 350 365 347 349 379 C4' A B 12 OK OK 381 398 378 380 412 C4' U B 13 OK OK 414 429 411 413 442 C4' A B 14 OK OK 444 461 441 443 475 C4' U B 15 OK OK 477 492 474 476 505 C4' C B 16 OK OK 507 522 504 506 536 C4' A B 17 OK OK 538 555 535 537 569 C4' G B 18 OK OK 571 589 568 570 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 15 C5' LKC A 1 OK OK 16 26 27 12 38 C5' TLN A 2 OK OK 37 56 57 39 71 C5' LCG A 3 OK OK 70 92 93 82 106 C5' LCA A 4 OK OK 105 126 127 117 141 C5' TLN A 5 OK OK 140 159 160 142 174 C5' LCA A 6 OK OK 173 194 195 185 209 C5' TLN A 7 OK OK 208 227 228 210 242 C5' LCG A 8 OK OK 241 263 264 253 275 C5' LCC A 9 OK OK 274 296 297 276 312 C5' G B 10 OK OK 311 331 332 313 347 C5' C B 11 distorted distorted 346 363 364 348 378 C5' A B 12 OK OK 377 396 397 379 411 C5' U B 13 OK OK 410 427 428 412 441 C5' A B 14 OK OK 440 459 460 442 474 C5' U B 15 OK OK 473 490 491 475 504 C5' C B 16 OK OK 503 520 521 505 535 C5' A B 17 OK OK 534 553 554 536 568 C5' G B 18 OK OK 567 587 588 569 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 34 P TLN A 2 OK OK 14 35 36 37 68 P LCG A 3 distorted distorted 54 69 87 70 103 P LCA A 4 distorted distorted 91 104 122 105 137 P TLN A 5 OK OK 124 138 139 140 171 P LCA A 6 distorted distorted 157 172 190 173 205 P TLN A 7 OK OK 192 206 207 208 239 P LCG A 8 distorted distorted 225 240 258 241 293 P LCC A 9 distorted distorted 262 294 295 274 343 P C B 11 distorted distorted 316 344 345 346 374 P A B 12 distorted distorted 351 375 376 377 407 P U B 13 distorted distorted 382 408 409 410 437 P A B 14 distorted distorted 415 438 439 440 470 P U B 15 distorted distorted 445 471 472 473 500 P C B 16 distorted distorted 478 501 502 503 531 P A B 17 distorted distorted 508 532 533 534 564 P G B 18 distorted distorted 539 565 566 567 ---------------------------------------------------------------------------------