ID code: '4QOZ' 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' C A 1 beta 4 10 7 29 C1' C A 2 beta 24 30 27 49 C1' A A 3 beta 44 50 47 71 C1' A A 4 beta 66 72 69 93 C1' A A 5 beta 88 94 91 115 C1' G A 6 beta 110 116 113 138 C1' G A 7 beta 133 139 136 161 C1' C A 8 beta 156 162 159 181 C1' U A 9 beta 176 182 179 201 C1' C A 10 beta 196 202 199 221 C1' U A 11 beta 216 222 219 241 C1' U A 12 beta 236 242 239 261 C1' U A 13 beta 256 262 259 281 C1' U A 14 beta 276 282 279 301 C1' C A 15 beta 296 302 299 321 C1' A A 16 beta 316 322 319 343 C1' G A 17 beta 338 344 341 366 C1' A A 18 beta 361 367 364 388 C1' G A 19 beta 383 389 386 411 C1' C A 20 beta 406 412 409 431 C1' C A 21 beta 426 432 429 451 C1' A A 22 beta 446 452 449 473 C1' C A 23 beta 468 474 471 493 C1' C A 24 beta 488 494 491 513 C1' C A 25 beta 508 514 511 533 C1' A A 26 beta 528 534 531 3468 C1' U D 9 beta 3463 3469 3466 3488 C1' C D 10 beta 3483 3489 3486 3508 C1' U D 11 beta 3503 3509 3506 3528 C1' U D 12 beta 3523 3529 3526 3548 C1' U D 13 beta 3543 3549 3546 3568 C1' U D 14 beta 3563 3569 3566 3588 C1' C D 15 beta 3583 3589 3586 3608 C1' A D 16 beta 3603 3609 3606 3630 C1' G D 17 beta 3625 3631 3628 3653 C1' A D 18 beta 3648 3654 3651 3675 C1' G D 19 beta 3670 3676 3673 3698 C1' C D 20 beta 3693 3699 3696 3718 C1' C D 21 beta 3713 3719 3716 3738 C1' A D 22 beta 3733 3739 3736 3760 C1' C D 23 beta 3755 3761 3758 3780 C1' C D 24 beta 3775 3781 3778 3800 C1' C D 25 beta 3795 3801 3798 3820 C1' A D 26 beta 3815 3821 3818 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 1 OK 9 5 8 27 C2' C A 2 OK 29 25 28 47 C2' A A 3 OK 49 45 48 69 C2' A A 4 OK 71 67 70 91 C2' A A 5 OK 93 89 92 113 C2' G A 6 OK 115 111 114 136 C2' G A 7 OK 138 134 137 159 C2' C A 8 OK 161 157 160 179 C2' U A 9 OK 181 177 180 199 C2' C A 10 OK 201 197 200 219 C2' U A 11 OK 221 217 220 239 C2' U A 12 OK 241 237 240 259 C2' U A 13 OK 261 257 260 279 C2' U A 14 OK 281 277 280 299 C2' C A 15 OK 301 297 300 319 C2' A A 16 OK 321 317 320 341 C2' G A 17 OK 343 339 342 364 C2' A A 18 OK 366 362 365 386 C2' G A 19 OK 388 384 387 409 C2' C A 20 OK 411 407 410 429 C2' C A 21 OK 431 427 430 449 C2' A A 22 OK 451 447 450 471 C2' C A 23 OK 473 469 472 491 C2' C A 24 OK 493 489 492 511 C2' C A 25 OK 513 509 512 531 C2' A A 26 OK 533 529 532 3466 C2' U D 9 OK 3468 3464 3467 3486 C2' C D 10 OK 3488 3484 3487 3506 C2' U D 11 OK 3508 3504 3507 3526 C2' U D 12 OK 3528 3524 3527 3546 C2' U D 13 OK 3548 3544 3547 3566 C2' U D 14 OK 3568 3564 3567 3586 C2' C D 15 OK 3588 3584 3587 3606 C2' A D 16 OK 3608 3604 3607 3628 C2' G D 17 OK 3630 3626 3629 3651 C2' A D 18 OK 3653 3649 3652 3673 C2' G D 19 OK 3675 3671 3674 3696 C2' C D 20 OK 3698 3694 3697 3716 C2' C D 21 OK 3718 3714 3717 3736 C2' A D 22 OK 3738 3734 3737 3758 C2' C D 23 OK 3760 3756 3759 3778 C2' C D 24 OK 3780 3776 3779 3798 C2' C D 25 OK 3800 3796 3799 3818 C2' A D 26 OK 3820 3816 3819 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK 3 6 7 25 C3' C A 2 OK 23 26 27 45 C3' A A 3 OK 43 46 47 67 C3' A A 4 OK 65 68 69 89 C3' A A 5 OK 87 90 91 111 C3' G A 6 OK 109 112 113 134 C3' G A 7 OK 132 135 136 157 C3' C A 8 OK 155 158 159 177 C3' U A 9 OK 175 178 179 197 C3' C A 10 OK 195 198 199 217 C3' U A 11 OK 215 218 219 237 C3' U A 12 OK 235 238 239 257 C3' U A 13 OK 255 258 259 277 C3' U A 14 OK 275 278 279 297 C3' C A 15 OK 295 298 299 317 C3' A A 16 OK 315 318 319 339 C3' G A 17 OK 337 340 341 362 C3' A A 18 OK 360 363 364 384 C3' G A 19 OK 382 385 386 407 C3' C A 20 OK 405 408 409 427 C3' C A 21 OK 425 428 429 447 C3' A A 22 OK 445 448 449 469 C3' C A 23 OK 467 470 471 489 C3' C A 24 OK 487 490 491 509 C3' C A 25 OK 507 510 511 529 C3' A A 26 OK 527 530 531 3464 C3' U D 9 OK 3462 3465 3466 3484 C3' C D 10 OK 3482 3485 3486 3504 C3' U D 11 OK 3502 3505 3506 3524 C3' U D 12 OK 3522 3525 3526 3544 C3' U D 13 OK 3542 3545 3546 3564 C3' U D 14 OK 3562 3565 3566 3584 C3' C D 15 OK 3582 3585 3586 3604 C3' A D 16 OK 3602 3605 3606 3626 C3' G D 17 OK 3624 3627 3628 3649 C3' A D 18 OK 3647 3650 3651 3671 C3' G D 19 OK 3669 3672 3673 3694 C3' C D 20 OK 3692 3695 3696 3714 C3' C D 21 OK 3712 3715 3716 3734 C3' A D 22 OK 3732 3735 3736 3756 C3' C D 23 OK 3754 3757 3758 3776 C3' C D 24 OK 3774 3777 3778 3796 C3' C D 25 OK 3794 3797 3798 3816 C3' A D 26 OK 3814 3817 3818 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK 5 2 4 23 C4' C A 2 OK 25 22 24 43 C4' A A 3 OK 45 42 44 65 C4' A A 4 OK 67 64 66 87 C4' A A 5 OK 89 86 88 109 C4' G A 6 OK 111 108 110 132 C4' G A 7 OK 134 131 133 155 C4' C A 8 OK 157 154 156 175 C4' U A 9 OK 177 174 176 195 C4' C A 10 OK 197 194 196 215 C4' U A 11 OK 217 214 216 235 C4' U A 12 OK 237 234 236 255 C4' U A 13 OK 257 254 256 275 C4' U A 14 OK 277 274 276 295 C4' C A 15 OK 297 294 296 315 C4' A A 16 OK 317 314 316 337 C4' G A 17 OK 339 336 338 360 C4' A A 18 OK 362 359 361 382 C4' G A 19 OK 384 381 383 405 C4' C A 20 OK 407 404 406 425 C4' C A 21 OK 427 424 426 445 C4' A A 22 OK 447 444 446 467 C4' C A 23 OK 469 466 468 487 C4' C A 24 OK 489 486 488 507 C4' C A 25 OK 509 506 508 527 C4' A A 26 OK 529 526 528 3462 C4' U D 9 OK 3464 3461 3463 3482 C4' C D 10 OK 3484 3481 3483 3502 C4' U D 11 OK 3504 3501 3503 3522 C4' U D 12 OK 3524 3521 3523 3542 C4' U D 13 OK 3544 3541 3543 3562 C4' U D 14 OK 3564 3561 3563 3582 C4' C D 15 OK 3584 3581 3583 3602 C4' A D 16 OK 3604 3601 3603 3624 C4' G D 17 OK 3626 3623 3625 3647 C4' A D 18 OK 3649 3646 3648 3669 C4' G D 19 OK 3671 3668 3670 3692 C4' C D 20 OK 3694 3691 3693 3712 C4' C D 21 OK 3714 3711 3713 3732 C4' A D 22 OK 3734 3731 3733 3754 C4' C D 23 OK 3756 3753 3755 3774 C4' C D 24 OK 3776 3773 3775 3794 C4' C D 25 OK 3796 3793 3795 3814 C4' A D 26 OK 3816 3813 3815 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 1 3 22 C5' C A 2 21 23 42 C5' A A 3 41 43 64 C5' A A 4 63 65 86 C5' A A 5 85 87 108 C5' G A 6 107 109 131 C5' G A 7 130 132 154 C5' C A 8 153 155 174 C5' U A 9 173 175 194 C5' C A 10 193 195 214 C5' U A 11 213 215 234 C5' U A 12 233 235 254 C5' U A 13 253 255 274 C5' U A 14 273 275 294 C5' C A 15 293 295 314 C5' A A 16 313 315 336 C5' G A 17 335 337 359 C5' A A 18 358 360 381 C5' G A 19 380 382 404 C5' C A 20 403 405 424 C5' C A 21 423 425 444 C5' A A 22 443 445 466 C5' C A 23 465 467 486 C5' C A 24 485 487 506 C5' C A 25 505 507 526 C5' A A 26 525 527 3461 C5' U D 9 3460 3462 3481 C5' C D 10 3480 3482 3501 C5' U D 11 3500 3502 3521 C5' U D 12 3520 3522 3541 C5' U D 13 3540 3542 3561 C5' U D 14 3560 3562 3581 C5' C D 15 3580 3582 3601 C5' A D 16 3600 3602 3623 C5' G D 17 3622 3624 3646 C5' A D 18 3645 3647 3668 C5' G D 19 3667 3669 3691 C5' C D 20 3690 3692 3711 C5' C D 21 3710 3712 3731 C5' A D 22 3730 3732 3753 C5' C D 23 3752 3754 3773 C5' C D 24 3772 3774 3793 C5' C D 25 3792 3794 3813 C5' A D 26 3812 3814 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P C A 2 distorted distorted 6 19 20 21 38 P A A 3 distorted distorted 26 39 40 41 60 P A A 4 distorted distorted 46 61 62 63 82 P A A 5 distorted distorted 68 83 84 85 104 P G A 6 distorted distorted 90 105 106 107 127 P G A 7 distorted distorted 112 128 129 130 150 P C A 8 distorted distorted 135 151 152 153 170 P U A 9 distorted distorted 158 171 172 173 190 P C A 10 distorted distorted 178 191 192 193 210 P U A 11 distorted distorted 198 211 212 213 230 P U A 12 distorted distorted 218 231 232 233 250 P U A 13 distorted distorted 238 251 252 253 270 P U A 14 distorted distorted 258 271 272 273 290 P C A 15 distorted distorted 278 291 292 293 310 P A A 16 distorted distorted 298 311 312 313 332 P G A 17 distorted distorted 318 333 334 335 355 P A A 18 distorted distorted 340 356 357 358 377 P G A 19 distorted distorted 363 378 379 380 400 P C A 20 distorted distorted 385 401 402 403 420 P C A 21 distorted distorted 408 421 422 423 440 P A A 22 distorted distorted 428 441 442 443 462 P C A 23 distorted distorted 448 463 464 465 482 P C A 24 distorted distorted 470 483 484 485 502 P C A 25 distorted distorted 490 503 504 505 522 P A A 26 distorted distorted 510 523 524 525 3193 P TPO C 171 3194 3195 3457 P U D 9 OK OK 3458 3459 3460 3477 P C D 10 distorted distorted 3465 3478 3479 3480 3497 P U D 11 distorted distorted 3485 3498 3499 3500 3517 P U D 12 distorted distorted 3505 3518 3519 3520 3537 P U D 13 distorted distorted 3525 3538 3539 3540 3557 P U D 14 distorted distorted 3545 3558 3559 3560 3577 P C D 15 distorted distorted 3565 3578 3579 3580 3597 P A D 16 distorted distorted 3585 3598 3599 3600 3619 P G D 17 distorted distorted 3605 3620 3621 3622 3642 P A D 18 distorted distorted 3627 3643 3644 3645 3664 P G D 19 distorted distorted 3650 3665 3666 3667 3687 P C D 20 distorted distorted 3672 3688 3689 3690 3707 P C D 21 distorted distorted 3695 3708 3709 3710 3727 P A D 22 distorted distorted 3715 3728 3729 3730 3749 P C D 23 distorted distorted 3735 3750 3751 3752 3769 P C D 24 distorted distorted 3757 3770 3771 3772 3789 P C D 25 distorted distorted 3777 3790 3791 3792 3809 P A D 26 distorted distorted 3797 3810 3811 3812 ---------------------------------------------------------------------------------