
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   25 (  196),  selected   25 , name T0316TS349_4-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316TS349_4-D2.T0316_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G     220      G     220           -
LGA    R     221      R     221           -
LGA    M     222      M     222           -
LGA    M     223      M     223           -
LGA    T     224      T     224           -
LGA    -       -      V     225           -
LGA    -       -      D     226           -
LGA    -       -      G     227           -
LGA    -       -      R     228           -
LGA    -       -      D     229           -
LGA    -       -      M     230           -
LGA    -       -      G     231           -
LGA    -       -      E     232           -
LGA    -       -      H     233           -
LGA    -       -      A     234           -
LGA    -       -      G     235           -
LGA    V     225      L     236           #
LGA    D     226      M     237          2.137
LGA    G     227      Y     238          4.249
LGA    R     228      Y     239          1.467
LGA    D     229      T     240          2.179
LGA    M     230      I     241          2.628
LGA    -       -      G     242           -
LGA    G     231      Q     243          2.721
LGA    -       -      R     244           -
LGA    -       -      G     245           -
LGA    -       -      G     246           -
LGA    -       -      L     247           -
LGA    -       -      G     248           -
LGA    -       -      I     249           -
LGA    -       -      G     250           -
LGA    -       -      G     251           -
LGA    -       -      D     256           -
LGA    -       -      N     257           -
LGA    -       -      A     258           -
LGA    -       -      P     259           -
LGA    -       -      W     260           -
LGA    -       -      F     261           -
LGA    E     232      V     262          0.650
LGA    H     233      V     263          4.787
LGA    A     234      G     264           -
LGA    -       -      K     265           -
LGA    -       -      D     266           -
LGA    -       -      L     267           -
LGA    -       -      S     268           -
LGA    -       -      K     269           -
LGA    -       -      N     270           -
LGA    -       -      I     271           -
LGA    -       -      L     272           -
LGA    -       -      Y     273           -
LGA    G     235      V     274          2.945
LGA    L     236      G     275          0.308
LGA    M     237      Q     276          2.256
LGA    Y     238      G     277          1.852
LGA    -       -      F     278           -
LGA    -       -      Y     279           -
LGA    Y     239      H     280          1.590
LGA    T     240      D     281          1.006
LGA    I     241      S     282          1.061
LGA    G     242      L     283          1.677
LGA    Q     243      -       -           -
LGA    R     244      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   25   60    5.0     16    2.40     0.00     20.573     0.641

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.719726 * X  +  -0.521695 * Y  +   0.458071 * Z  +   6.733873
  Y_new =   0.440648 * X  +   0.853132 * Y  +   0.279276 * Z  + -35.014122
  Z_new =  -0.536492 * X  +   0.000846 * Y  +   0.843905 * Z  + -26.301775 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.001002   -3.140590  [ DEG:     0.0574   -179.9426 ]
  Theta =   0.566275    2.575318  [ DEG:    32.4452    147.5548 ]
  Phi   =   0.549374   -2.592219  [ DEG:    31.4768   -148.5232 ]
 
# 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: T0316TS349_4-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS349_4-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   25   60   5.0   16   2.40    0.00  20.573
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS349_4-D2
PFRMAT TS
TARGET T0316
MODEL  4  REFINED
PARENT 1WXI_A
ATOM   1736  N   GLY   220      51.340  24.490  -8.951  1.00  0.00
ATOM   1737  CA  GLY   220      51.334  25.561  -8.040  1.00  0.00
ATOM   1738  C   GLY   220      50.417  25.103  -6.855  1.00  0.00
ATOM   1739  O   GLY   220      50.667  24.020  -6.289  1.00  0.00
ATOM   1740  N   ARG   221      49.872  26.116  -6.187  1.00  0.00
ATOM   1741  CA  ARG   221      49.071  25.867  -4.990  1.00  0.00
ATOM   1742  C   ARG   221      47.943  24.829  -5.170  1.00  0.00
ATOM   1743  O   ARG   221      47.266  24.755  -6.212  1.00  0.00
ATOM   1744  CB  ARG   221      48.401  27.163  -4.618  1.00  0.00
ATOM   1745  CG  ARG   221      49.219  28.224  -3.974  1.00  0.00
ATOM   1746  CD  ARG   221      49.106  28.135  -2.450  1.00  0.00
ATOM   1747  NE  ARG   221      48.564  29.384  -2.034  1.00  0.00
ATOM   1748  CZ  ARG   221      48.252  29.763  -0.801  1.00  0.00
ATOM   1749  NH1 ARG   221      48.413  29.078   0.315  1.00  0.00
ATOM   1750  NH2 ARG   221      47.492  30.849  -0.799  1.00  0.00
ATOM   1751  N   MET   222      47.962  23.880  -4.218  1.00  0.00
ATOM   1752  CA  MET   222      46.903  22.853  -4.143  1.00  0.00
ATOM   1753  C   MET   222      45.522  23.567  -4.054  1.00  0.00
ATOM   1754  O   MET   222      44.559  23.020  -4.628  1.00  0.00
ATOM   1755  CB  MET   222      47.120  21.938  -2.936  1.00  0.00
ATOM   1756  CG  MET   222      48.258  20.986  -3.019  1.00  0.00
ATOM   1757  SD  MET   222      48.462  20.198  -4.638  1.00  0.00
ATOM   1758  CE  MET   222      49.548  21.291  -5.502  1.00  0.00
ATOM   1759  N   MET   223      45.321  24.488  -3.082  1.00  0.00
ATOM   1760  CA  MET   223      44.101  25.281  -2.984  1.00  0.00
ATOM   1761  C   MET   223      43.699  26.042  -4.289  1.00  0.00
ATOM   1762  O   MET   223      42.507  26.358  -4.407  1.00  0.00
ATOM   1763  CB  MET   223      44.338  26.308  -1.880  1.00  0.00
ATOM   1764  CG  MET   223      43.059  26.889  -1.239  1.00  0.00
ATOM   1765  SD  MET   223      42.299  25.693  -0.121  1.00  0.00
ATOM   1766  CE  MET   223      40.615  25.728  -0.754  1.00  0.00
ATOM   1767  N   THR   224      44.558  26.183  -5.334  1.00  0.00
ATOM   1768  CA  THR   224      44.298  26.936  -6.527  1.00  0.00
ATOM   1769  C   THR   224      44.086  25.913  -7.712  1.00  0.00
ATOM   1770  O   THR   224      44.510  26.178  -8.851  1.00  0.00
ATOM   1771  CB  THR   224      45.437  27.962  -6.819  1.00  0.00
ATOM   1772  OG1 THR   224      45.585  28.961  -5.836  1.00  0.00
ATOM   1773  CG2 THR   224      45.062  28.667  -8.146  1.00  0.00
ATOM   1774  N   VAL   225      43.724  24.663  -7.457  1.00  0.00
ATOM   1775  CA  VAL   225      43.598  23.745  -8.534  1.00  0.00
ATOM   1776  C   VAL   225      42.666  24.208  -9.732  1.00  0.00
ATOM   1777  O   VAL   225      42.780  23.576 -10.795  1.00  0.00
ATOM   1778  CB  VAL   225      43.056  22.454  -7.947  1.00  0.00
ATOM   1779  CG1 VAL   225      44.025  21.357  -7.530  1.00  0.00
ATOM   1780  CG2 VAL   225      41.847  22.572  -7.069  1.00  0.00
ATOM   1781  N   ASP   226      41.720  25.170  -9.550  1.00  0.00
ATOM   1782  CA  ASP   226      40.821  25.709 -10.584  1.00  0.00
ATOM   1783  C   ASP   226      39.948  24.575 -11.209  1.00  0.00
ATOM   1784  O   ASP   226      39.466  24.788 -12.337  1.00  0.00
ATOM   1785  CB  ASP   226      41.742  26.286 -11.660  1.00  0.00
ATOM   1786  CG  ASP   226      42.404  27.576 -11.233  1.00  0.00
ATOM   1787  OD1 ASP   226      43.153  28.236 -11.992  1.00  0.00
ATOM   1788  OD2 ASP   226      42.187  27.860 -10.019  1.00  0.00
ATOM   1789  N   GLY   227      39.388  23.683 -10.335  1.00  0.00
ATOM   1790  CA  GLY   227      38.661  22.565 -10.870  1.00  0.00
ATOM   1791  C   GLY   227      37.481  22.943 -11.781  1.00  0.00
ATOM   1792  O   GLY   227      37.540  22.588 -12.964  1.00  0.00
ATOM   1793  N   ARG   228      36.459  23.642 -11.256  1.00  0.00
ATOM   1794  CA  ARG   228      35.310  23.996 -12.041  1.00  0.00
ATOM   1795  C   ARG   228      34.756  22.834 -12.932  1.00  0.00
ATOM   1796  O   ARG   228      34.472  23.020 -14.127  1.00  0.00
ATOM   1797  CB  ARG   228      35.403  25.351 -12.716  1.00  0.00
ATOM   1798  CG  ARG   228      35.318  26.521 -11.757  1.00  0.00
ATOM   1799  CD  ARG   228      35.554  27.835 -12.519  1.00  0.00
ATOM   1800  NE  ARG   228      35.622  28.850 -11.436  1.00  0.00
ATOM   1801  CZ  ARG   228      34.554  29.450 -10.889  1.00  0.00
ATOM   1802  NH1 ARG   228      33.308  28.998 -11.221  1.00  0.00
ATOM   1803  NH2 ARG   228      34.766  30.552 -10.064  1.00  0.00
ATOM   1804  N   ASP   229      34.572  21.697 -12.277  1.00  0.00
ATOM   1805  CA  ASP   229      34.001  20.505 -12.791  1.00  0.00
ATOM   1806  C   ASP   229      32.517  20.775 -13.126  1.00  0.00
ATOM   1807  O   ASP   229      32.034  20.073 -14.019  1.00  0.00
ATOM   1808  CB  ASP   229      34.193  19.329 -11.815  1.00  0.00
ATOM   1809  CG  ASP   229      33.896  17.994 -12.518  1.00  0.00
ATOM   1810  OD1 ASP   229      32.882  17.375 -12.186  1.00  0.00
ATOM   1811  OD2 ASP   229      34.643  17.538 -13.405  1.00  0.00
ATOM   1812  N   MET   230      31.684  21.340 -12.198  1.00  0.00
ATOM   1813  CA  MET   230      30.300  21.678 -12.531  1.00  0.00
ATOM   1814  C   MET   230      30.179  22.317 -13.964  1.00  0.00
ATOM   1815  O   MET   230      29.122  22.139 -14.565  1.00  0.00
ATOM   1816  CB  MET   230      29.757  22.642 -11.441  1.00  0.00
ATOM   1817  CG  MET   230      28.335  23.067 -11.804  1.00  0.00
ATOM   1818  SD  MET   230      27.587  23.887 -10.350  1.00  0.00
ATOM   1819  CE  MET   230      26.806  25.309 -11.133  1.00  0.00
ATOM   1820  N   GLY   231      31.174  23.078 -14.482  1.00  0.00
ATOM   1821  CA  GLY   231      31.113  23.632 -15.844  1.00  0.00
ATOM   1822  C   GLY   231      31.025  22.621 -17.008  1.00  0.00
ATOM   1823  O   GLY   231      30.645  23.064 -18.085  1.00  0.00
ATOM   1824  N   GLU   232      31.172  21.291 -16.798  1.00  0.00
ATOM   1825  CA  GLU   232      31.048  20.254 -17.767  1.00  0.00
ATOM   1826  C   GLU   232      29.817  20.451 -18.718  1.00  0.00
ATOM   1827  O   GLU   232      30.019  20.265 -19.914  1.00  0.00
ATOM   1828  CB  GLU   232      31.045  18.930 -17.033  1.00  0.00
ATOM   1829  CG  GLU   232      32.288  18.373 -16.380  1.00  0.00
ATOM   1830  CD  GLU   232      33.579  18.415 -17.154  1.00  0.00
ATOM   1831  OE1 GLU   232      33.693  18.543 -18.372  1.00  0.00
ATOM   1832  OE2 GLU   232      34.591  18.311 -16.389  1.00  0.00
ATOM   1833  N   HIS   233      28.565  20.592 -18.231  1.00  0.00
ATOM   1834  CA  HIS   233      27.356  20.796 -19.055  1.00  0.00
ATOM   1835  C   HIS   233      27.550  21.830 -20.245  1.00  0.00
ATOM   1836  O   HIS   233      27.019  21.530 -21.322  1.00  0.00
ATOM   1837  CB  HIS   233      26.217  21.137 -18.074  1.00  0.00
ATOM   1838  CG  HIS   233      26.283  22.578 -17.607  1.00  0.00
ATOM   1839  ND1 HIS   233      27.008  22.905 -16.483  1.00  0.00
ATOM   1840  CD2 HIS   233      25.726  23.732 -18.045  1.00  0.00
ATOM   1841  CE1 HIS   233      26.891  24.201 -16.247  1.00  0.00
ATOM   1842  NE2 HIS   233      26.119  24.726 -17.181  1.00  0.00
ATOM   1843  N   ALA   234      28.073  23.068 -20.035  1.00  0.00
ATOM   1844  CA  ALA   234      28.315  24.061 -21.090  1.00  0.00
ATOM   1845  C   ALA   234      29.129  23.460 -22.299  1.00  0.00
ATOM   1846  O   ALA   234      28.777  23.798 -23.439  1.00  0.00
ATOM   1847  CB  ALA   234      29.006  25.275 -20.467  1.00  0.00
ATOM   1848  N   GLY   235      30.229  22.702 -22.100  1.00  0.00
ATOM   1849  CA  GLY   235      31.006  22.093 -23.181  1.00  0.00
ATOM   1850  C   GLY   235      30.248  21.001 -24.009  1.00  0.00
ATOM   1851  O   GLY   235      30.632  20.796 -25.164  1.00  0.00
ATOM   1852  N   LEU   236      29.350  20.209 -23.410  1.00  0.00
ATOM   1853  CA  LEU   236      28.687  19.118 -24.061  1.00  0.00
ATOM   1854  C   LEU   236      27.191  19.427 -24.486  1.00  0.00
ATOM   1855  O   LEU   236      26.590  20.445 -24.084  1.00  0.00
ATOM   1856  CB  LEU   236      28.706  17.981 -23.040  1.00  0.00
ATOM   1857  CG  LEU   236      30.015  17.284 -22.760  1.00  0.00
ATOM   1858  CD1 LEU   236      29.853  16.257 -21.642  1.00  0.00
ATOM   1859  CD2 LEU   236      30.495  16.548 -24.030  1.00  0.00
ATOM   1860  N   MET   237      26.747  18.571 -25.446  1.00  0.00
ATOM   1861  CA  MET   237      25.430  18.566 -25.927  1.00  0.00
ATOM   1862  C   MET   237      24.562  18.215 -24.723  1.00  0.00
ATOM   1863  O   MET   237      24.927  17.274 -23.969  1.00  0.00
ATOM   1864  CB  MET   237      25.312  17.539 -26.966  1.00  0.00
ATOM   1865  CG  MET   237      25.274  17.840 -28.414  1.00  0.00
ATOM   1866  SD  MET   237      23.638  18.459 -28.865  1.00  0.00
ATOM   1867  CE  MET   237      22.524  17.463 -27.901  1.00  0.00
ATOM   1868  N   TYR   238      23.334  18.563 -24.773  1.00  0.00
ATOM   1869  CA  TYR   238      22.473  18.374 -23.660  1.00  0.00
ATOM   1870  C   TYR   238      22.190  16.897 -23.150  1.00  0.00
ATOM   1871  O   TYR   238      22.092  16.019 -24.021  1.00  0.00
ATOM   1872  CB  TYR   238      21.119  18.971 -24.105  1.00  0.00
ATOM   1873  CG  TYR   238      21.074  20.457 -24.418  1.00  0.00
ATOM   1874  CD1 TYR   238      21.241  20.800 -25.768  1.00  0.00
ATOM   1875  CD2 TYR   238      20.921  21.494 -23.497  1.00  0.00
ATOM   1876  CE1 TYR   238      21.272  22.116 -26.196  1.00  0.00
ATOM   1877  CE2 TYR   238      20.947  22.820 -23.910  1.00  0.00
ATOM   1878  CZ  TYR   238      21.122  23.126 -25.259  1.00  0.00
ATOM   1879  OH  TYR   238      21.153  24.420 -25.719  1.00  0.00
ATOM   1880  N   TYR   239      22.506  16.577 -21.856  1.00  0.00
ATOM   1881  CA  TYR   239      22.117  15.279 -21.111  1.00  0.00
ATOM   1882  C   TYR   239      22.962  13.944 -20.788  1.00  0.00
ATOM   1883  O   TYR   239      22.196  12.952 -20.642  1.00  0.00
ATOM   1884  CB  TYR   239      20.727  14.849 -21.673  1.00  0.00
ATOM   1885  CG  TYR   239      19.704  15.939 -21.860  1.00  0.00
ATOM   1886  CD1 TYR   239      19.063  16.422 -20.714  1.00  0.00
ATOM   1887  CD2 TYR   239      19.403  16.522 -23.089  1.00  0.00
ATOM   1888  CE1 TYR   239      18.133  17.442 -20.784  1.00  0.00
ATOM   1889  CE2 TYR   239      18.473  17.543 -23.168  1.00  0.00
ATOM   1890  CZ  TYR   239      17.844  18.007 -22.014  1.00  0.00
ATOM   1891  OH  TYR   239      16.905  18.991 -22.066  1.00  0.00
ATOM   1892  N   THR   240      24.306  13.748 -20.613  1.00  0.00
ATOM   1893  CA  THR   240      24.713  12.294 -20.394  1.00  0.00
ATOM   1894  C   THR   240      25.648  11.904 -19.170  1.00  0.00
ATOM   1895  O   THR   240      25.218  11.054 -18.388  1.00  0.00
ATOM   1896  CB  THR   240      25.357  11.826 -21.748  1.00  0.00
ATOM   1897  OG1 THR   240      24.646  12.342 -22.899  1.00  0.00
ATOM   1898  CG2 THR   240      25.462  10.262 -21.886  1.00  0.00
ATOM   1899  N   ILE   241      26.953  12.291 -19.118  1.00  0.00
ATOM   1900  CA  ILE   241      28.040  11.902 -18.159  1.00  0.00
ATOM   1901  C   ILE   241      27.954  12.504 -16.692  1.00  0.00
ATOM   1902  O   ILE   241      28.888  12.309 -15.911  1.00  0.00
ATOM   1903  CB  ILE   241      29.461  12.010 -18.832  1.00  0.00
ATOM   1904  CG1 ILE   241      29.453  11.096 -20.060  1.00  0.00
ATOM   1905  CG2 ILE   241      30.592  11.605 -17.792  1.00  0.00
ATOM   1906  CD1 ILE   241      29.122   9.589 -19.811  1.00  0.00
ATOM   1907  N   GLY   242      26.828  13.080 -16.240  1.00  0.00
ATOM   1908  CA  GLY   242      26.607  13.623 -14.883  1.00  0.00
ATOM   1909  C   GLY   242      26.853  12.650 -13.665  1.00  0.00
ATOM   1910  O   GLY   242      26.881  13.191 -12.546  1.00  0.00
ATOM   1911  N   GLN   243      26.843  11.300 -13.829  1.00  0.00
ATOM   1912  CA  GLN   243      27.074  10.410 -12.684  1.00  0.00
ATOM   1913  C   GLN   243      28.593  10.158 -12.393  1.00  0.00
ATOM   1914  O   GLN   243      29.132   9.087 -12.707  1.00  0.00
ATOM   1915  CB  GLN   243      26.379   9.086 -12.951  1.00  0.00
ATOM   1916  CG  GLN   243      24.898   9.261 -13.116  1.00  0.00
ATOM   1917  CD  GLN   243      24.165   7.952 -13.345  1.00  0.00
ATOM   1918  OE1 GLN   243      23.006   7.999 -13.776  1.00  0.00
ATOM   1919  NE2 GLN   243      24.820   6.851 -13.085  1.00  0.00
ATOM   1920  N   ARG   244      29.292  11.129 -11.809  1.00  0.00
ATOM   1921  CA  ARG   244      30.698  11.019 -11.401  1.00  0.00
ATOM   1922  C   ARG   244      30.725  10.954  -9.862  1.00  0.00
ATOM   1923  O   ARG   244      30.770  11.963  -9.160  1.00  0.00
ATOM   1924  CB  ARG   244      31.628  12.077 -12.024  1.00  0.00
ATOM   1925  CG  ARG   244      31.789  11.886 -13.520  1.00  0.00
ATOM   1926  CD  ARG   244      32.669  13.036 -13.962  1.00  0.00
ATOM   1927  NE  ARG   244      32.278  13.583 -15.251  1.00  0.00
ATOM   1928  CZ  ARG   244      32.149  14.874 -15.556  1.00  0.00
ATOM   1929  NH1 ARG   244      31.769  15.215 -16.803  1.00  0.00
ATOM   1930  NH2 ARG   244      32.367  15.848 -14.659  1.00  0.00
ATOM   1931  OXT ARG   244      30.723   9.786  -9.364  1.00  0.00
TER
END
