####################################################### # # # LGA # # --------------- # # # # Local-Global Alignment # # A Method for Finding 3-D Similarities # # in Protein Structures # # # # ------------ 09/2011 # # # # Adam Zemla (adamz@llnl.gov) # # Lawrence Livermore National Laboratory, CA # # # ####################################################### # Molecule1: number of CA atoms 30 ( 199), selected 30 , name pdb1h9iI # Molecule2: number of CA atoms 32 ( 200), selected 32 , name T0711.pdb # PARAMETERS: -4 -ie -o1 -sia -d:4 -swap -gdc_sc 1h9iI.T0711.pdb # Search for Atom-Atom correspondence # Structure alignment analysis # Checking swapping # Molecule1 Molecule2 DISTANCE Mis MC All Dist_max GDC_mc GDC_all Dist_at LGA G 1 C 2 3.041 2 0.224 0.224 4.494 15.455 10.303 - LGA C 2 P 3 3.077 2 0.401 0.422 5.375 26.364 15.065 - LGA P 3 Q 4 3.286 4 0.455 0.458 4.542 25.455 11.515 - LGA R 4 G 5 2.858 0 0.045 0.045 5.569 15.000 15.000 - LGA - - R 6 - - - - - - - - LGA - - G 7 - - - - - - - - LGA - - D 8 - - - - - - - - LGA I 5 W 9 2.690 9 0.316 0.368 3.820 20.909 6.753 - LGA L 6 A 10 2.951 0 0.153 0.201 3.320 22.727 25.818 - LGA - - P 11 - - - - - - - - LGA I 7 T 12 0.201 2 0.076 0.071 0.806 90.909 66.234 - LGA R 8 S 13 0.506 1 0.000 0.008 0.655 86.364 71.212 - LGA C 9 C 14 0.627 0 0.008 0.058 0.678 81.818 84.848 0.451 LGA K 10 S 15 0.393 1 0.223 0.224 0.981 90.909 77.273 - LGA Q 11 Q 16 0.489 0 0.033 0.988 2.318 86.364 78.182 2.318 LGA D 12 D 17 0.461 1 0.027 0.596 1.730 90.909 74.545 1.730 LGA S 13 S 18 0.781 1 0.012 0.027 0.953 81.818 68.182 - LGA D 14 D 19 0.801 2 0.040 0.362 0.967 81.818 61.364 - LGA C 15 C 20 0.454 0 0.064 0.111 0.569 95.455 96.970 0.272 LGA L 16 L 21 0.522 0 0.027 0.381 1.679 81.818 75.909 1.291 LGA A 17 A 22 1.200 0 0.051 0.078 1.386 69.545 68.727 - LGA G 18 G 23 1.639 0 0.036 0.036 1.639 58.182 58.182 - LGA C 19 C 24 0.854 0 0.044 0.151 1.087 77.727 79.091 0.913 LGA V 20 V 25 0.398 0 0.053 0.096 0.537 95.455 94.805 0.457 LGA C 21 C 26 0.277 0 0.043 0.082 0.633 95.455 96.970 0.221 LGA T 22 G 27 0.749 0 0.028 0.028 0.749 90.909 90.909 - LGA N 23 P 28 0.705 2 0.053 0.065 0.895 81.818 61.039 - LGA N 24 N 29 0.891 3 0.076 0.074 1.243 90.909 53.636 - LGA K 25 G 30 0.317 0 0.042 0.042 0.609 95.455 95.455 - LGA F 26 F 31 0.525 2 0.024 0.802 4.471 95.455 52.066 2.782 LGA C 27 C 32 0.411 0 0.058 0.111 0.563 90.909 93.939 0.422 LGA G 28 G 33 1.129 0 0.194 0.194 2.556 60.000 60.000 - LGA S 29 - - - - - - - - - - LGA P 30 - - - - - - - - - - # RMSD_GDC results: CA MC common percent ALL common percent GDC_mc GDC_all GDC_at NUMBER_OF_ATOMS_AA: 28 112 112 100.00 177 155 87.57 32 10 SUMMARY(RMSD_GDC): 1.528 1.673 1.710 62.372 54.500 76.364 #CA N1 N2 DIST N RMSD Seq_Id LGA_S LGA_Q SUMMARY(LGA) 30 32 4.0 28 1.53 57.14 82.908 1.719 Unitary ROTATION matrix and the SHIFT vector superimpose molecules (1=>2) X_new = -0.570037 * X + 0.785817 * Y + 0.239896 * Z + -56.838669 Y_new = -0.668312 * X + -0.613310 * Y + 0.420962 * Z + 97.109596 Z_new = 0.477930 * X + 0.079638 * Y + 0.874781 * Z + -30.589777 Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ: Phi Theta Psi [DEG: Phi Theta Psi ] XYZ: -2.277000 -0.498296 0.090787 [DEG: -130.4625 -28.5503 5.2017 ] ZXZ: 2.623617 0.505814 1.405682 [DEG: 150.3222 28.9810 80.5397 ] # END of job REMARK ---------------------------------------------------------- REMARK Citing LGA: REMARK Zemla A., LGA - a Method for Finding 3D Similarities in REMARK Protein Structures, Nucleic Acids Research, 2003, V. 31, REMARK No. 13, pp. 3370-3374. REMARK ---------------------------------------------------------- REMARK Superimposed MOLECULES (1=>2) Output: 1 molecule REMARK 1: pdb1h9iI REMARK 2: T0711.pdb REMARK Structure alignment analysis REMARK Search for Atom-Atom correspondence REMARK LGA parameters: -4 -ie -o1 -sia -d:4 -swap -gdc_sc 1h9iI.T0711.pdb REMARK #CA N1 N2 DIST N RMSD Seq_Id LGA_S REMARK SUMMARY: 30 32 4.0 28 1.53 57.14 82.908 REMARK ---------------------------------------------------------- MOLECULE pdb1h9iI ATOM 1686 N GLY 1 0.716 2.436 -5.408 1.00 68.28 N ATOM 1687 CA GLY 1 -0.563 2.917 -4.903 1.00 48.29 C ATOM 1688 C GLY 1 -1.664 1.878 -4.893 1.00 43.78 C ATOM 1689 O GLY 1 -2.084 1.405 -5.952 1.00 55.42 O ATOM 1690 N CYS 2 -2.166 1.507 -3.714 1.00 28.85 N ATOM 1691 CA CYS 2 -3.251 0.534 -3.652 1.00 26.81 C ATOM 1692 C CYS 2 -4.453 1.129 -2.920 1.00 24.37 C ATOM 1693 O CYS 2 -4.315 1.553 -1.779 1.00 25.36 O ATOM 1694 CB CYS 2 -2.727 -0.724 -2.969 1.00 29.58 C ATOM 1695 SG CYS 2 -3.973 -1.973 -2.633 1.00 31.04 S ATOM 1696 N PRO 3 -5.608 1.173 -3.555 1.00 24.47 N ATOM 1697 CA PRO 3 -6.828 1.644 -2.878 1.00 25.22 C ATOM 1698 C PRO 3 -7.163 0.839 -1.632 1.00 22.41 C ATOM 1699 O PRO 3 -6.842 -0.346 -1.499 1.00 23.51 O ATOM 1700 CB PRO 3 -7.922 1.485 -3.933 1.00 29.62 C ATOM 1701 CG PRO 3 -7.215 1.294 -5.222 1.00 39.43 C ATOM 1702 CD PRO 3 -5.832 0.800 -4.953 1.00 29.25 C ATOM 1703 N ARG 4 -7.831 1.494 -0.660 1.00 21.75 N ATOM 1704 CA ARG 4 -7.994 0.874 0.665 1.00 19.28 C ATOM 1705 C ARG 4 -9.334 0.188 0.867 1.00 23.67 C ATOM 1706 O ARG 4 -9.963 0.160 1.918 1.00 20.85 O ATOM 1707 CB ARG 4 -7.677 1.971 1.695 1.00 18.92 C ATOM 1708 CG ARG 4 -6.141 2.098 1.736 1.00 24.80 C ATOM 1709 CD ARG 4 -5.668 3.357 2.420 1.00 22.53 C ATOM 1710 NE ARG 4 -4.225 3.299 2.657 1.00 22.85 N ATOM 1711 CZ ARG 4 -3.543 4.183 3.368 1.00 24.74 C ATOM 1712 NH1 ARG 4 -4.099 5.240 3.944 1.00 24.42 N ATOM 1713 NH2 ARG 4 -2.241 3.993 3.503 1.00 26.49 N ATOM 1714 N ILE 5 -9.803 -0.393 -0.245 1.00 21.61 N ATOM 1715 CA ILE 5 -10.970 -1.251 -0.246 1.00 21.07 C ATOM 1716 C ILE 5 -10.578 -2.639 0.264 1.00 28.27 C ATOM 1717 O ILE 5 -9.469 -3.129 0.096 1.00 28.38 O ATOM 1718 CB ILE 5 -11.619 -1.408 -1.626 1.00 24.98 C ATOM 1719 CG1 ILE 5 -12.822 -2.356 -1.652 1.00 23.42 C ATOM 1720 CG2 ILE 5 -10.628 -1.891 -2.670 1.00 26.33 C ATOM 1721 CD1 ILE 5 -13.653 -2.227 -2.911 1.00 27.76 C ATOM 1722 N LEU 6 -11.524 -3.302 0.917 1.00 25.11 N ATOM 1723 CA LEU 6 -11.306 -4.642 1.433 1.00 23.27 C ATOM 1724 C LEU 6 -11.790 -5.624 0.377 1.00 32.86 C ATOM 1725 O LEU 6 -12.991 -5.678 0.085 1.00 28.44 O ATOM 1726 CB LEU 6 -12.065 -4.849 2.722 1.00 26.94 C ATOM 1727 CG LEU 6 -11.635 -5.860 3.774 1.00 46.48 C ATOM 1728 CD1 LEU 6 -12.733 -6.006 4.839 1.00 37.75 C ATOM 1729 CD2 LEU 6 -11.308 -7.230 3.211 1.00 67.25 C ATOM 1730 N ILE 7 -10.850 -6.373 -0.187 1.00 27.60 N ATOM 1731 CA ILE 7 -11.321 -7.374 -1.155 1.00 26.52 C ATOM 1732 C ILE 7 -10.685 -8.715 -0.812 1.00 37.30 C ATOM 1733 O ILE 7 -9.465 -8.782 -0.681 1.00 34.47 O ATOM 1734 CB ILE 7 -10.979 -6.979 -2.585 1.00 32.96 C ATOM 1735 CG1 ILE 7 -11.797 -5.819 -3.165 1.00 32.57 C ATOM 1736 CG2 ILE 7 -11.098 -8.184 -3.515 1.00 37.71 C ATOM 1737 CD1 ILE 7 -11.195 -5.285 -4.443 1.00 31.31 C ATOM 1738 N ARG 8 -11.445 -9.783 -0.637 1.00 38.64 N ATOM 1739 CA ARG 8 -10.834 -11.087 -0.353 1.00 45.28 C ATOM 1740 C ARG 8 -10.335 -11.650 -1.668 1.00 47.85 C ATOM 1741 O ARG 8 -11.014 -11.535 -2.695 1.00 40.64 O ATOM 1742 CB ARG 8 -11.810 -12.062 0.300 1.00 45.81 C ATOM 1743 CG ARG 8 -11.791 -11.972 1.820 1.00 55.19 C ATOM 1744 CD ARG 8 -13.201 -11.862 2.379 1.00 75.14 C ATOM 1745 N CYS 9 -9.143 -12.242 -1.709 1.00 45.55 N ATOM 1746 CA CYS 9 -8.713 -12.624 -3.058 1.00 37.08 C ATOM 1747 C CYS 9 -8.054 -14.004 -3.061 1.00 51.23 C ATOM 1748 O CYS 9 -7.752 -14.521 -1.983 1.00 42.69 O ATOM 1749 CB CYS 9 -7.743 -11.564 -3.583 1.00 28.61 C ATOM 1750 SG CYS 9 -6.367 -11.388 -2.434 1.00 35.70 S ATOM 1751 N LYS 10 -7.857 -14.528 -4.257 1.00 56.18 N ATOM 1752 CA LYS 10 -7.143 -15.739 -4.622 1.00 60.95 C ATOM 1753 C LYS 10 -5.976 -15.474 -5.572 1.00 53.95 C ATOM 1754 O LYS 10 -4.924 -16.109 -5.461 1.00 65.46 O ATOM 1755 CB LYS 10 -8.085 -16.754 -5.285 1.00 74.08 C ATOM 1756 N GLN 11 -6.155 -14.550 -6.507 1.00 46.18 N ATOM 1757 CA GLN 11 -5.113 -14.182 -7.460 1.00 43.53 C ATOM 1758 C GLN 11 -5.069 -12.662 -7.579 1.00 49.12 C ATOM 1759 O GLN 11 -6.032 -11.970 -7.234 1.00 41.58 O ATOM 1760 CB GLN 11 -5.348 -14.882 -8.798 0.50 37.39 C ATOM 1761 CG GLN 11 -6.598 -14.544 -9.575 0.50 36.73 C ATOM 1762 CD GLN 11 -6.993 -15.540 -10.645 0.50 42.66 C ATOM 1763 OE1 GLN 11 -7.993 -16.249 -10.523 0.50 43.24 O ATOM 1764 NE2 GLN 11 -6.243 -15.621 -11.738 0.50 37.02 N ATOM 1765 N ASP 12 -3.947 -12.156 -8.066 1.00 41.40 N ATOM 1766 CA ASP 12 -3.719 -10.735 -8.230 1.00 45.57 C ATOM 1767 C ASP 12 -4.821 -10.078 -9.052 1.00 56.41 C ATOM 1768 O ASP 12 -5.141 -8.910 -8.812 1.00 49.63 O ATOM 1769 CB ASP 12 -2.357 -10.481 -8.884 1.00 40.90 C ATOM 1770 CG ASP 12 -1.223 -10.810 -7.921 1.00 51.61 C ATOM 1771 OD1 ASP 12 -1.524 -11.108 -6.741 1.00 38.53 O ATOM 1772 OD2 ASP 12 -0.039 -10.772 -8.329 1.00 60.76 O ATOM 1773 N SER 13 -5.387 -10.820 -9.995 1.00 52.67 N ATOM 1774 CA SER 13 -6.403 -10.296 -10.905 1.00 54.78 C ATOM 1775 C SER 13 -7.711 -9.939 -10.203 1.00 41.69 C ATOM 1776 O SER 13 -8.503 -9.181 -10.775 1.00 45.89 O ATOM 1777 CB SER 13 -6.668 -11.309 -12.031 1.00 65.64 C ATOM 1778 OG SER 13 -7.605 -12.303 -11.641 1.00 82.92 O ATOM 1779 N ASP 14 -7.928 -10.473 -9.001 1.00 33.45 N ATOM 1780 CA ASP 14 -9.109 -10.157 -8.208 1.00 37.05 C ATOM 1781 C ASP 14 -9.036 -8.767 -7.575 1.00 40.75 C ATOM 1782 O ASP 14 -10.030 -8.233 -7.093 1.00 44.52 O ATOM 1783 CB ASP 14 -9.320 -11.185 -7.097 1.00 45.08 C ATOM 1784 CG ASP 14 -9.545 -12.586 -7.649 1.00 55.28 C ATOM 1785 OD1 ASP 14 -9.965 -12.738 -8.815 1.00 61.70 O ATOM 1786 OD2 ASP 14 -9.291 -13.547 -6.894 1.00 50.59 O ATOM 1787 N CYS 15 -7.843 -8.201 -7.580 1.00 33.11 N ATOM 1788 CA CYS 15 -7.518 -6.941 -6.960 1.00 31.13 C ATOM 1789 C CYS 15 -7.508 -5.815 -7.984 1.00 40.73 C ATOM 1790 O CYS 15 -7.408 -6.082 -9.179 1.00 51.07 O ATOM 1791 CB CYS 15 -6.142 -7.015 -6.282 1.00 30.02 C ATOM 1792 SG CYS 15 -6.040 -8.323 -5.041 1.00 32.83 S ATOM 1793 N LEU 16 -7.621 -4.603 -7.448 1.00 37.25 N ATOM 1794 CA LEU 16 -7.532 -3.424 -8.289 1.00 35.87 C ATOM 1795 C LEU 16 -6.068 -3.149 -8.629 1.00 42.25 C ATOM 1796 O LEU 16 -5.178 -3.673 -7.967 1.00 43.23 O ATOM 1797 CB LEU 16 -8.122 -2.189 -7.623 1.00 36.28 C ATOM 1798 CG LEU 16 -9.595 -2.249 -7.235 1.00 37.71 C ATOM 1799 CD1 LEU 16 -10.126 -0.834 -7.063 1.00 54.10 C ATOM 1800 CD2 LEU 16 -10.406 -3.019 -8.260 1.00 47.73 C ATOM 1801 N ALA 17 -5.898 -2.330 -9.652 1.00 46.53 N ATOM 1802 CA ALA 17 -4.595 -1.833 -10.054 1.00 48.87 C ATOM 1803 C ALA 17 -3.845 -1.268 -8.849 1.00 50.49 C ATOM 1804 O ALA 17 -4.382 -0.409 -8.143 1.00 47.23 O ATOM 1805 CB ALA 17 -4.766 -0.769 -11.132 1.00 60.85 C ATOM 1806 N GLY 18 -2.632 -1.745 -8.616 1.00 47.02 N ATOM 1807 CA GLY 18 -1.751 -1.257 -7.576 1.00 42.91 C ATOM 1808 C GLY 18 -1.618 -2.225 -6.420 1.00 46.97 C ATOM 1809 O GLY 18 -0.681 -2.168 -5.627 1.00 41.70 O ATOM 1810 N CYS 19 -2.595 -3.126 -6.336 1.00 38.14 N ATOM 1811 CA CYS 19 -2.620 -4.100 -5.268 1.00 33.02 C ATOM 1812 C CYS 19 -2.264 -5.483 -5.801 1.00 36.41 C ATOM 1813 O CYS 19 -2.411 -5.743 -6.992 1.00 40.88 O ATOM 1814 CB CYS 19 -4.017 -4.174 -4.659 1.00 29.48 C ATOM 1815 SG CYS 19 -4.723 -2.534 -4.396 1.00 36.96 S ATOM 1816 N VAL 20 -1.840 -6.314 -4.874 1.00 31.97 N ATOM 1817 CA VAL 20 -1.581 -7.718 -5.128 1.00 36.36 C ATOM 1818 C VAL 20 -2.382 -8.529 -4.128 1.00 39.52 C ATOM 1819 O VAL 20 -2.755 -8.010 -3.073 1.00 34.60 O ATOM 1820 CB VAL 20 -0.086 -8.072 -4.987 1.00 45.92 C ATOM 1821 CG1 VAL 20 0.705 -7.395 -6.090 1.00 44.23 C ATOM 1822 CG2 VAL 20 0.429 -7.657 -3.620 1.00 44.28 C ATOM 1823 N CYS 21 -2.643 -9.782 -4.453 1.00 36.91 N ATOM 1824 CA CYS 21 -3.269 -10.662 -3.472 1.00 39.11 C ATOM 1825 C CYS 21 -2.181 -11.140 -2.519 1.00 46.70 C ATOM 1826 O CYS 21 -1.248 -11.842 -2.914 1.00 41.10 O ATOM 1827 CB CYS 21 -3.985 -11.802 -4.202 1.00 37.42 C ATOM 1828 SG CYS 21 -4.996 -12.763 -3.061 1.00 38.66 S ATOM 1829 N THR 22 -2.233 -10.752 -1.251 1.00 55.06 N ATOM 1830 CA THR 22 -1.156 -11.107 -0.331 1.00 63.34 C ATOM 1831 C THR 22 -1.436 -12.441 0.372 1.00 65.34 C ATOM 1832 O THR 22 -2.495 -13.048 0.201 1.00 45.07 O ATOM 1833 CB THR 22 -0.876 -10.012 0.723 1.00 71.11 C ATOM 1834 OG1 THR 22 -2.040 -9.772 1.524 1.00 86.81 O ATOM 1835 CG2 THR 22 -0.494 -8.681 0.073 1.00 59.16 C ATOM 1836 N ASN 23 -0.458 -12.875 1.147 1.00 65.61 N ATOM 1837 CA ASN 23 -0.372 -14.077 1.937 1.00 60.59 C ATOM 1838 C ASN 23 -1.637 -14.385 2.723 1.00 55.80 C ATOM 1839 O ASN 23 -1.886 -15.555 3.028 1.00 84.20 O ATOM 1840 CB ASN 23 0.798 -13.962 2.939 1.00 62.60 C ATOM 1841 N ASN 24 -2.431 -13.380 3.074 1.00 51.64 N ATOM 1842 CA ASN 24 -3.617 -13.652 3.901 1.00 49.24 C ATOM 1843 C ASN 24 -4.891 -13.611 3.064 1.00 41.10 C ATOM 1844 O ASN 24 -6.019 -13.693 3.553 1.00 48.64 O ATOM 1845 CB ASN 24 -3.652 -12.684 5.079 1.00 50.99 C ATOM 1846 N LYS 25 -4.724 -13.507 1.749 1.00 40.73 N ATOM 1847 CA LYS 25 -5.862 -13.621 0.830 1.00 42.44 C ATOM 1848 C LYS 25 -6.751 -12.384 0.884 1.00 42.86 C ATOM 1849 O LYS 25 -7.951 -12.389 0.612 1.00 37.65 O ATOM 1850 CB LYS 25 -6.663 -14.893 1.110 1.00 48.73 C ATOM 1851 N PHE 26 -6.099 -11.282 1.242 1.00 33.34 N ATOM 1852 CA PHE 26 -6.673 -9.953 1.049 1.00 34.68 C ATOM 1853 C PHE 26 -5.853 -9.138 0.055 1.00 36.74 C ATOM 1854 O PHE 26 -4.624 -9.229 0.001 1.00 37.44 O ATOM 1855 CB PHE 26 -6.730 -9.235 2.392 1.00 37.35 C ATOM 1856 CG PHE 26 -7.731 -9.811 3.379 1.00 48.21 C ATOM 1857 CD1 PHE 26 -7.266 -10.396 4.551 1.00 56.36 C ATOM 1858 CD2 PHE 26 -9.095 -9.751 3.131 1.00 51.47 C ATOM 1859 CE1 PHE 26 -8.154 -10.913 5.480 1.00 49.11 C ATOM 1860 CE2 PHE 26 -9.990 -10.256 4.063 1.00 52.06 C ATOM 1861 CZ PHE 26 -9.507 -10.818 5.228 1.00 47.98 C ATOM 1862 N CYS 27 -6.479 -8.302 -0.764 1.00 29.32 N ATOM 1863 CA CYS 27 -5.730 -7.376 -1.592 1.00 28.18 C ATOM 1864 C CYS 27 -5.025 -6.367 -0.690 1.00 30.19 C ATOM 1865 O CYS 27 -5.582 -5.939 0.319 1.00 29.04 O ATOM 1866 CB CYS 27 -6.649 -6.665 -2.592 1.00 31.27 C ATOM 1867 SG CYS 27 -7.492 -7.820 -3.718 1.00 32.77 S ATOM 1868 N GLY 28 -3.812 -5.990 -1.058 1.00 35.03 N ATOM 1869 CA GLY 28 -3.008 -4.981 -0.393 1.00 36.59 C ATOM 1870 C GLY 28 -1.858 -4.525 -1.278 1.00 39.28 C ATOM 1871 O GLY 28 -1.672 -5.006 -2.399 1.00 32.15 O ATOM 1872 N SER 29 -1.085 -3.585 -0.745 1.00 33.90 N ATOM 1873 CA SER 29 0.145 -3.171 -1.407 1.00 33.92 C ATOM 1874 C SER 29 1.157 -4.306 -1.336 1.00 33.70 C ATOM 1875 O SER 29 1.177 -5.071 -0.377 1.00 30.60 O ATOM 1876 CB SER 29 0.733 -1.928 -0.734 1.00 33.10 C ATOM 1877 OG SER 29 0.048 -0.771 -1.182 1.00 34.07 O ATOM 1878 N PRO 30 2.011 -4.467 -2.328 1.00 42.23 N ATOM 1879 CA PRO 30 3.035 -5.521 -2.259 1.00 53.90 C ATOM 1880 C PRO 30 3.895 -5.439 -1.004 1.00 61.88 C ATOM 1881 O PRO 30 4.020 -4.385 -0.379 1.00 73.35 O ATOM 1882 CB PRO 30 3.872 -5.233 -3.508 1.00 48.74 C ATOM 1883 CG PRO 30 2.909 -4.594 -4.462 1.00 51.82 C ATOM 1884 CD PRO 30 2.057 -3.709 -3.588 1.00 51.35 C END