ID code: '4KI4' 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' --------------------------------------------------------------------------------- 7256 C1' DA T 1 beta 7252 7257 7255 7270 C1' DC T 2 beta 7266 7271 7269 7290 C1' A T 3 beta 7285 7291 7288 7312 C1' G T 4 beta 7307 7313 7310 7334 C1' DG T 5 beta 7330 7335 7333 7356 C1' DT T 6 beta 7352 7357 7355 7376 C1' DA T 7 beta 7372 7377 7375 7397 C1' DA T 8 beta 7393 7398 7396 7418 C1' DG T 9 beta 7414 7419 7417 7440 C1' DC T 10 beta 7436 7441 7439 7459 C1' DA T 11 beta 7455 7460 7458 7480 C1' DG T 12 beta 7476 7481 7479 7502 C1' DT T 13 beta 7498 7503 7501 7522 C1' DC T 14 beta 7518 7523 7521 7541 C1' DC T 15 beta 7537 7542 7540 7560 C1' DG T 16 beta 7556 7561 7559 7582 C1' DC T 17 beta 7578 7583 7581 7601 C1' DG T 18 beta 7597 7602 7600 7619 C1' DG P 102 beta 7615 7620 7618 7641 C1' DC P 103 beta 7637 7642 7640 7660 C1' DG P 104 beta 7656 7661 7659 7682 C1' DG P 105 beta 7678 7683 7681 7704 C1' DA P 106 beta 7700 7705 7703 7725 C1' DC P 107 beta 7721 7726 7724 7744 C1' DT P 108 beta 7740 7745 7743 7764 C1' DG P 109 beta 7760 7765 7763 7786 C1' DC P 110 beta 7782 7787 7785 7805 C1' DT P 111 beta 7801 7806 7804 7825 C1' DT P 112 beta 7821 7826 7824 7845 C1' DA P 113 beta 7841 7846 7844 7866 C1' DC P 114 beta 7862 7867 7865 7884 C1' DC P 115 beta 7881 7885 7883 7913 C1' TTP A1001 beta 7909 7914 7912 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7255 C2' DA T 1 7256 7253 7269 C2' DC T 2 7270 7267 7288 C2' A T 3 OK 7290 7286 7289 7310 C2' G T 4 OK 7312 7308 7311 7333 C2' DG T 5 7334 7331 7355 C2' DT T 6 7356 7353 7375 C2' DA T 7 7376 7373 7396 C2' DA T 8 7397 7394 7417 C2' DG T 9 7418 7415 7439 C2' DC T 10 7440 7437 7458 C2' DA T 11 7459 7456 7479 C2' DG T 12 7480 7477 7501 C2' DT T 13 7502 7499 7521 C2' DC T 14 7522 7519 7540 C2' DC T 15 7541 7538 7559 C2' DG T 16 7560 7557 7581 C2' DC T 17 7582 7579 7600 C2' DG T 18 7601 7598 7618 C2' DG P 102 7619 7616 7640 C2' DC P 103 7641 7638 7659 C2' DG P 104 7660 7657 7681 C2' DG P 105 7682 7679 7703 C2' DA P 106 7704 7701 7724 C2' DC P 107 7725 7722 7743 C2' DT P 108 7744 7741 7763 C2' DG P 109 7764 7761 7785 C2' DC P 110 7786 7783 7804 C2' DT P 111 7805 7802 7824 C2' DT P 112 7825 7822 7844 C2' DA P 113 7845 7842 7865 C2' DC P 114 7866 7863 7883 C2' DC P 115 7884 7882 7912 C2' TTP A1001 7913 7910 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7253 C3' DA T 1 OK 7251 7254 7255 7267 C3' DC T 2 OK 7265 7268 7269 7286 C3' A T 3 OK 7284 7287 7288 7308 C3' G T 4 OK 7306 7309 7310 7331 C3' DG T 5 OK 7329 7332 7333 7353 C3' DT T 6 OK 7351 7354 7355 7373 C3' DA T 7 OK 7371 7374 7375 7394 C3' DA T 8 OK 7392 7395 7396 7415 C3' DG T 9 OK 7413 7416 7417 7437 C3' DC T 10 OK 7435 7438 7439 7456 C3' DA T 11 OK 7454 7457 7458 7477 C3' DG T 12 OK 7475 7478 7479 7499 C3' DT T 13 OK 7497 7500 7501 7519 C3' DC T 14 OK 7517 7520 7521 7538 C3' DC T 15 OK 7536 7539 7540 7557 C3' DG T 16 OK 7555 7558 7559 7579 C3' DC T 17 OK 7577 7580 7581 7598 C3' DG T 18 OK 7596 7599 7600 7616 C3' DG P 102 OK 7614 7617 7618 7638 C3' DC P 103 OK 7636 7639 7640 7657 C3' DG P 104 OK 7655 7658 7659 7679 C3' DG P 105 OK 7677 7680 7681 7701 C3' DA P 106 OK 7699 7702 7703 7722 C3' DC P 107 OK 7720 7723 7724 7741 C3' DT P 108 OK 7739 7742 7743 7761 C3' DG P 109 OK 7759 7762 7763 7783 C3' DC P 110 OK 7781 7784 7785 7802 C3' DT P 111 OK 7800 7803 7804 7822 C3' DT P 112 OK 7820 7823 7824 7842 C3' DA P 113 OK 7840 7843 7844 7863 C3' DC P 114 OK 7861 7864 7865 7882 C3' DC P 115 7880 7883 7910 C3' TTP A1001 OK 7908 7911 7912 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7251 C4' DA T 1 OK 7253 7250 7252 7265 C4' DC T 2 OK 7267 7264 7266 7284 C4' A T 3 OK 7286 7283 7285 7306 C4' G T 4 OK 7308 7305 7307 7329 C4' DG T 5 OK 7331 7328 7330 7351 C4' DT T 6 OK 7353 7350 7352 7371 C4' DA T 7 OK 7373 7370 7372 7392 C4' DA T 8 OK 7394 7391 7393 7413 C4' DG T 9 OK 7415 7412 7414 7435 C4' DC T 10 OK 7437 7434 7436 7454 C4' DA T 11 OK 7456 7453 7455 7475 C4' DG T 12 OK 7477 7474 7476 7497 C4' DT T 13 OK 7499 7496 7498 7517 C4' DC T 14 OK 7519 7516 7518 7536 C4' DC T 15 OK 7538 7535 7537 7555 C4' DG T 16 OK 7557 7554 7556 7577 C4' DC T 17 OK 7579 7576 7578 7596 C4' DG T 18 OK 7598 7595 7597 7614 C4' DG P 102 7616 7615 7636 C4' DC P 103 OK 7638 7635 7637 7655 C4' DG P 104 OK 7657 7654 7656 7677 C4' DG P 105 OK 7679 7676 7678 7699 C4' DA P 106 OK 7701 7698 7700 7720 C4' DC P 107 OK 7722 7719 7721 7739 C4' DT P 108 OK 7741 7738 7740 7759 C4' DG P 109 OK 7761 7758 7760 7781 C4' DC P 110 OK 7783 7780 7782 7800 C4' DT P 111 OK 7802 7799 7801 7820 C4' DT P 112 OK 7822 7819 7821 7840 C4' DA P 113 OK 7842 7839 7841 7861 C4' DC P 114 OK 7863 7860 7862 7880 C4' DC P 115 OK 7882 7879 7881 7908 C4' TTP A1001 OK 7910 7907 7909 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7250 C5' DA T 1 7249 7251 7264 C5' DC T 2 7263 7265 7283 C5' A T 3 7282 7284 7305 C5' G T 4 7304 7306 7328 C5' DG T 5 7327 7329 7350 C5' DT T 6 7349 7351 7370 C5' DA T 7 7369 7371 7391 C5' DA T 8 7390 7392 7412 C5' DG T 9 7411 7413 7434 C5' DC T 10 7433 7435 7453 C5' DA T 11 7452 7454 7474 C5' DG T 12 7473 7475 7496 C5' DT T 13 7495 7497 7516 C5' DC T 14 7515 7517 7535 C5' DC T 15 7534 7536 7554 C5' DG T 16 7553 7555 7576 C5' DC T 17 7575 7577 7595 C5' DG T 18 7594 7596 7635 C5' DC P 103 7634 7636 7654 C5' DG P 104 7653 7655 7676 C5' DG P 105 7675 7677 7698 C5' DA P 106 7697 7699 7719 C5' DC P 107 7718 7720 7738 C5' DT P 108 7737 7739 7758 C5' DG P 109 7757 7759 7780 C5' DC P 110 7779 7781 7799 C5' DT P 111 7798 7800 7819 C5' DT P 112 7818 7820 7839 C5' DA P 113 7838 7840 7860 C5' DC P 114 7859 7861 7879 C5' DC P 115 7878 7880 7907 C5' TTP A1001 7906 7908 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7260 P DC T 2 distorted distorted 7254 7261 7262 7263 7279 P A T 3 distorted distorted 7268 7280 7281 7282 7301 P G T 4 distorted distorted 7287 7302 7303 7304 7324 P DG T 5 distorted distorted 7309 7325 7326 7327 7346 P DT T 6 distorted distorted 7332 7347 7348 7349 7366 P DA T 7 distorted distorted 7354 7367 7368 7369 7387 P DA T 8 distorted distorted 7374 7388 7389 7390 7408 P DG T 9 distorted distorted 7395 7409 7410 7411 7430 P DC T 10 distorted distorted 7416 7431 7432 7433 7449 P DA T 11 distorted distorted 7438 7450 7451 7452 7470 P DG T 12 distorted distorted 7457 7471 7472 7473 7492 P DT T 13 distorted distorted 7478 7493 7494 7495 7512 P DC T 14 distorted distorted 7500 7513 7514 7515 7531 P DC T 15 distorted distorted 7520 7532 7533 7534 7550 P DG T 16 distorted distorted 7539 7551 7552 7553 7572 P DC T 17 distorted distorted 7558 7573 7574 7575 7591 P DG T 18 distorted distorted 7580 7592 7593 7594 7631 P DC P 103 distorted distorted 7617 7632 7633 7634 7650 P DG P 104 distorted distorted 7639 7651 7652 7653 7672 P DG P 105 distorted distorted 7658 7673 7674 7675 7694 P DA P 106 distorted distorted 7680 7695 7696 7697 7715 P DC P 107 distorted distorted 7702 7716 7717 7718 7734 P DT P 108 distorted distorted 7723 7735 7736 7737 7754 P DG P 109 distorted distorted 7742 7755 7756 7757 7776 P DC P 110 distorted distorted 7762 7777 7778 7779 7795 P DT P 111 distorted distorted 7784 7796 7797 7798 7815 P DT P 112 distorted distorted 7803 7816 7817 7818 7835 P DA P 113 distorted distorted 7823 7836 7837 7838 7856 P DC P 114 distorted distorted 7843 7857 7858 7859 7875 P DC P 115 distorted distorted 7864 7876 7877 7878 ---------------------------------------------------------------------------------