ID code: '1EZH' 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' T A 1 alpha beta 4 24 9 7 41 C1' A A 2 alpha beta 37 56 42 40 73 C1' A A 3 alpha beta 69 88 74 72 105 C1' C A 4 alpha beta 101 118 106 104 135 C1' G A 5 alpha beta 131 151 136 134 167 C1' G A 6 alpha beta 163 183 168 166 200 C1' T A 7 alpha beta 196 216 201 199 232 C1' T A 8 alpha beta 228 248 233 231 264 C1' A A 9 alpha beta 260 280 265 263 295 C1' T B 10 alpha beta 291 311 296 294 328 C1' A B 11 alpha beta 324 343 329 327 360 C1' A B 12 alpha beta 356 375 361 359 392 C1' C B 13 alpha beta 388 405 393 391 422 C1' C B 14 alpha beta 418 435 423 421 452 C1' G B 15 alpha beta 448 468 453 451 485 C1' T B 16 alpha beta 481 501 486 484 517 C1' T B 17 alpha beta 513 533 518 516 549 C1' A B 18 alpha beta 545 565 550 548 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' T A 1 OK OK 8 5 22 23 40 C2' A A 2 OK OK 41 38 62 61 72 C2' A A 3 OK OK 73 70 94 93 104 C2' C A 4 OK OK 105 102 124 123 134 C2' G A 5 OK OK 135 132 156 155 166 C2' G A 6 OK OK 167 164 189 188 199 C2' T A 7 OK OK 200 197 214 215 231 C2' T A 8 OK OK 232 229 246 247 263 C2' A A 9 OK OK 264 261 286 285 294 C2' T B 10 OK OK 295 292 309 310 327 C2' A B 11 OK OK 328 325 349 348 359 C2' A B 12 OK OK 360 357 381 380 391 C2' C B 13 OK OK 392 389 411 410 421 C2' C B 14 OK OK 422 419 441 440 451 C2' G B 15 OK OK 452 449 474 473 484 C2' T B 16 OK OK 485 482 499 500 516 C2' T B 17 OK OK 517 514 531 532 548 C2' A B 18 OK OK 549 546 571 570 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' T A 1 OK OK 3 21 6 7 38 C3' A A 2 OK OK 36 55 39 40 70 C3' A A 3 OK OK 68 87 71 72 102 C3' C A 4 OK OK 100 117 103 104 132 C3' G A 5 OK OK 130 150 133 134 164 C3' G A 6 OK OK 162 182 165 166 197 C3' T A 7 OK OK 195 213 198 199 229 C3' T A 8 OK OK 227 245 230 231 261 C3' A A 9 OK OK 259 278 262 263 292 C3' T B 10 OK OK 290 308 293 294 325 C3' A B 11 OK OK 323 342 326 327 357 C3' A B 12 OK OK 355 374 358 359 389 C3' C B 13 OK OK 387 404 390 391 419 C3' C B 14 OK OK 417 434 420 421 449 C3' G B 15 OK OK 447 467 450 451 482 C3' T B 16 OK OK 480 498 483 484 514 C3' T B 17 OK OK 512 530 515 516 546 C3' A B 18 OK OK 544 563 547 548 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' T A 1 OK OK 5 20 2 4 36 C4' A A 2 OK OK 38 54 35 37 68 C4' A A 3 OK OK 70 86 67 69 100 C4' C A 4 OK OK 102 116 99 101 130 C4' G A 5 OK OK 132 149 129 131 162 C4' G A 6 OK OK 164 181 161 163 195 C4' T A 7 OK OK 197 212 194 196 227 C4' T A 8 OK OK 229 244 226 228 259 C4' A A 9 OK OK 261 277 258 260 290 C4' T B 10 OK OK 292 307 289 291 323 C4' A B 11 OK OK 325 341 322 324 355 C4' A B 12 OK OK 357 373 354 356 387 C4' C B 13 OK OK 389 403 386 388 417 C4' C B 14 OK OK 419 433 416 418 447 C4' G B 15 OK OK 449 466 446 448 480 C4' T B 16 OK OK 482 497 479 481 512 C4' T B 17 OK OK 514 529 511 513 544 C4' A B 18 OK OK 546 562 543 545 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' T A 1 OK OK 1 18 19 3 35 C5' A A 2 OK OK 34 52 53 36 67 C5' A A 3 OK OK 66 84 85 68 99 C5' C A 4 OK OK 98 114 115 100 129 C5' G A 5 OK OK 128 147 148 130 161 C5' G A 6 OK OK 160 179 180 162 194 C5' T A 7 OK OK 193 210 211 195 226 C5' T A 8 OK OK 225 242 243 227 258 C5' A A 9 OK OK 257 275 276 259 289 C5' T B 10 OK OK 288 305 306 290 322 C5' A B 11 OK OK 321 339 340 323 354 C5' A B 12 OK OK 353 371 372 355 386 C5' C B 13 OK OK 385 401 402 387 416 C5' C B 14 OK OK 415 431 432 417 446 C5' G B 15 OK OK 445 464 465 447 479 C5' T B 16 OK OK 478 495 496 480 511 C5' T B 17 OK OK 510 527 528 512 543 C5' A B 18 OK OK 542 560 561 544 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 31 P A A 2 distorted distorted 6 32 33 34 63 P A A 3 distorted distorted 39 64 65 66 95 P C A 4 distorted distorted 71 96 97 98 125 P G A 5 distorted distorted 103 126 127 128 157 P G A 6 distorted distorted 133 158 159 160 190 P T A 7 distorted distorted 165 191 192 193 222 P T A 8 distorted distorted 198 223 224 225 254 P A A 9 distorted distorted 230 255 256 257 318 P A B 11 distorted distorted 293 319 320 321 350 P A B 12 distorted distorted 326 351 352 353 382 P C B 13 distorted distorted 358 383 384 385 412 P C B 14 distorted distorted 390 413 414 415 442 P G B 15 distorted distorted 420 443 444 445 475 P T B 16 distorted distorted 450 476 477 478 507 P T B 17 distorted distorted 483 508 509 510 539 P A B 18 distorted distorted 515 540 541 542 ---------------------------------------------------------------------------------