
#######################################################
#                                                     #
#                        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   22 (  178),  selected   22 , name T0316TS389_5-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316TS389_5-D3.T0316_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M     284           -
LGA    -       -      S     285           -
LGA    -       -      T     286           -
LGA    -       -      S     287           -
LGA    -       -      L     288           -
LGA    -       -      E     289           -
LGA    -       -      A     290           -
LGA    -       -      S     291           -
LGA    -       -      Q     292           -
LGA    -       -      V     293           -
LGA    -       -      H     294           -
LGA    -       -      F     295           -
LGA    M     284      T     296           #
LGA    S     285      R     297           -
LGA    T     286      E     298           -
LGA    S     287      M     299           -
LGA    -       -      P     300           -
LGA    -       -      E     301           -
LGA    -       -      E     302           -
LGA    -       -      F     303           -
LGA    -       -      T     304           -
LGA    -       -      L     305           -
LGA    -       -      E     306           -
LGA    -       -      C     307           -
LGA    -       -      T     308           -
LGA    -       -      A     309           -
LGA    -       -      K     310           -
LGA    -       -      F     311           -
LGA    -       -      R     312           -
LGA    -       -      Y     313           -
LGA    -       -      R     314           -
LGA    -       -      Q     315           -
LGA    -       -      P     316           -
LGA    -       -      D     317           -
LGA    -       -      S     318           -
LGA    -       -      K     319           -
LGA    -       -      V     320           -
LGA    -       -      T     321           -
LGA    -       -      V     322           -
LGA    -       -      H     323           -
LGA    -       -      V     324           -
LGA    -       -      K     325           -
LGA    -       -      G     326           -
LGA    -       -      E     327           -
LGA    -       -      K     328           -
LGA    -       -      T     329           -
LGA    -       -      E     330           -
LGA    -       -      V     331           -
LGA    -       -      I     332           -
LGA    -       -      F     333           -
LGA    -       -      A     334           -
LGA    -       -      E     335           -
LGA    -       -      P     336           -
LGA    -       -      Q     337           -
LGA    -       -      R     338           -
LGA    -       -      A     339           -
LGA    -       -      I     340           -
LGA    -       -      T     341           -
LGA    -       -      P     342           -
LGA    -       -      G     343           -
LGA    -       -      Q     344           -
LGA    -       -      A     345           -
LGA    -       -      V     346           -
LGA    -       -      V     347           -
LGA    L     288      F     348           #
LGA    -       -      Y     349           -
LGA    -       -      D     350           -
LGA    -       -      G     351           -
LGA    -       -      E     352           -
LGA    E     289      E     353          2.052
LGA    A     290      C     354          1.269
LGA    S     291      L     355          1.519
LGA    Q     292      G     356          1.007
LGA    V     293      G     357          0.740
LGA    H     294      G     358          1.300
LGA    F     295      L     359          1.404
LGA    T     296      I     360          1.581
LGA    R     297      D     361          1.375
LGA    E     298      N     362          2.194
LGA    M     299      A     363           #
LGA    P     300      Y     364           -
LGA    E     301      R     365           -
LGA    -       -      D     366           -
LGA    -       -      G     367           -
LGA    E     302      Q     368          3.967
LGA    F     303      V     369          1.756
LGA    T     304      C     370          2.166
LGA    -       -      Q     371           -
LGA    L     305      Y     372          4.361
LGA    -       -      I     373           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   22   90    5.0     14    2.16     7.14     13.178     0.621

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.281400 * X  +  -0.699302 * Y  +   0.657108 * Z  +   4.881843
  Y_new =   0.539986 * X  +   0.450671 * Y  +   0.710852 * Z  +  11.794228
  Z_new =  -0.793240 * X  +   0.554863 * Y  +   0.250794 * Z  + -11.090114 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.146286   -1.995307  [ DEG:    65.6774   -114.3226 ]
  Theta =   0.916111    2.225482  [ DEG:    52.4893    127.5107 ]
  Phi   =   2.051201   -1.090392  [ DEG:   117.5251    -62.4749 ]
 
# 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: T0316TS389_5-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS389_5-D3.T0316_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   22   90   5.0   14   2.16    7.14  13.178
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS389_5-D3
PFRMAT TS
TARGET T0316
MODEL  5
PARENT N/A
ATOM   1723  N   MET   284      25.222  19.308   9.822  1.00  0.00
ATOM   1724  CA  MET   284      24.488  18.527  10.811  1.00  0.00
ATOM   1725  CB  MET   284      25.410  17.506  11.480  1.00  0.00
ATOM   1726  CG  MET   284      25.844  16.370  10.567  1.00  0.00
ATOM   1727  SD  MET   284      26.716  15.063  11.450  1.00  0.00
ATOM   1728  CE  MET   284      28.308  15.840  11.721  1.00  0.00
ATOM   1729  O   MET   284      22.766  19.155  12.356  1.00  0.00
ATOM   1730  C   MET   284      23.889  19.397  11.916  1.00  0.00
ATOM   1731  N   SER   285      24.622  20.427  12.336  1.00  0.00
ATOM   1732  CA  SER   285      24.157  21.309  13.402  1.00  0.00
ATOM   1733  CB  SER   285      25.331  22.071  14.018  1.00  0.00
ATOM   1734  OG  SER   285      25.921  22.950  13.075  1.00  0.00
ATOM   1735  O   SER   285      22.282  22.779  13.751  1.00  0.00
ATOM   1736  C   SER   285      23.143  22.371  12.964  1.00  0.00
ATOM   1737  N   THR   286      23.236  22.813  11.713  1.00  0.00
ATOM   1738  CA  THR   286      22.360  23.863  11.206  1.00  0.00
ATOM   1739  CB  THR   286      23.099  24.786  10.218  1.00  0.00
ATOM   1740  CG2 THR   286      24.288  25.451  10.897  1.00  0.00
ATOM   1741  OG1 THR   286      23.571  24.019   9.104  1.00  0.00
ATOM   1742  O   THR   286      20.090  24.150  10.499  1.00  0.00
ATOM   1743  C   THR   286      21.113  23.448  10.449  1.00  0.00
ATOM   1744  N   SER   287      21.186  22.338   9.725  1.00  0.00
ATOM   1745  CA  SER   287      20.037  21.881   8.953  1.00  0.00
ATOM   1746  CB  SER   287      20.490  21.285   7.620  1.00  0.00
ATOM   1747  OG  SER   287      21.131  22.260   6.817  1.00  0.00
ATOM   1748  O   SER   287      19.680  19.664   9.772  1.00  0.00
ATOM   1749  C   SER   287      19.268  20.819   9.717  1.00  0.00
ATOM   1750  N   LEU   288      18.146  21.216  10.303  1.00  0.00
ATOM   1751  CA  LEU   288      17.307  20.295  11.066  1.00  0.00
ATOM   1752  CB  LEU   288      16.167  21.053  11.750  1.00  0.00
ATOM   1753  CG  LEU   288      15.240  20.222  12.641  1.00  0.00
ATOM   1754  CD1 LEU   288      15.996  19.676  13.842  1.00  0.00
ATOM   1755  CD2 LEU   288      14.083  21.069  13.152  1.00  0.00
ATOM   1756  O   LEU   288      15.974  19.622   9.207  1.00  0.00
ATOM   1757  C   LEU   288      16.728  19.268  10.109  1.00  0.00
ATOM   1758  N   GLU   289      17.102  18.006  10.287  1.00  0.00
ATOM   1759  CA  GLU   289      16.610  16.958   9.412  1.00  0.00
ATOM   1760  CB  GLU   289      15.807  17.558   8.256  1.00  0.00
ATOM   1761  CG  GLU   289      16.644  18.359   7.270  1.00  0.00
ATOM   1762  CD  GLU   289      16.903  19.775   7.741  1.00  0.00
ATOM   1763  OE1 GLU   289      16.497  20.107   8.876  1.00  0.00
ATOM   1764  OE2 GLU   289      17.510  20.555   6.979  1.00  0.00
ATOM   1765  O   GLU   289      17.500  15.115   8.160  1.00  0.00
ATOM   1766  C   GLU   289      17.739  16.138   8.811  1.00  0.00
ATOM   1767  N   ALA   290      18.972  16.613   8.990  1.00  0.00
ATOM   1768  CA  ALA   290      20.160  15.928   8.477  1.00  0.00
ATOM   1769  CB  ALA   290      20.896  16.814   7.485  1.00  0.00
ATOM   1770  O   ALA   290      21.477  16.503  10.410  1.00  0.00
ATOM   1771  C   ALA   290      21.081  15.606   9.659  1.00  0.00
ATOM   1772  N   SER   291      21.393  14.326   9.835  1.00  0.00
ATOM   1773  CA  SER   291      22.245  13.891  10.939  1.00  0.00
ATOM   1774  CB  SER   291      21.561  12.781  11.739  1.00  0.00
ATOM   1775  OG  SER   291      21.331  11.639  10.933  1.00  0.00
ATOM   1776  O   SER   291      24.463  13.070  11.375  1.00  0.00
ATOM   1777  C   SER   291      23.607  13.335  10.519  1.00  0.00
ATOM   1778  N   GLN   292      23.823  13.167   9.216  1.00  0.00
ATOM   1779  CA  GLN   292      25.094  12.638   8.736  1.00  0.00
ATOM   1780  CB  GLN   292      25.026  11.116   8.604  1.00  0.00
ATOM   1781  CG  GLN   292      24.955  10.380   9.932  1.00  0.00
ATOM   1782  CD  GLN   292      24.960   8.873   9.766  1.00  0.00
ATOM   1783  OE1 GLN   292      25.140   8.363   8.659  1.00  0.00
ATOM   1784  NE2 GLN   292      24.766   8.157  10.866  1.00  0.00
ATOM   1785  O   GLN   292      24.628  13.404   6.514  1.00  0.00
ATOM   1786  C   GLN   292      25.482  13.192   7.377  1.00  0.00
ATOM   1787  N   VAL   293      26.777  13.424   7.197  1.00  0.00
ATOM   1788  CA  VAL   293      27.298  13.934   5.942  1.00  0.00
ATOM   1789  CB  VAL   293      27.842  15.366   6.099  1.00  0.00
ATOM   1790  CG1 VAL   293      28.426  15.861   4.784  1.00  0.00
ATOM   1791  CG2 VAL   293      26.730  16.316   6.518  1.00  0.00
ATOM   1792  O   VAL   293      29.231  12.590   6.344  1.00  0.00
ATOM   1793  C   VAL   293      28.419  13.006   5.511  1.00  0.00
ATOM   1794  N   HIS   294      28.424  12.649   4.228  1.00  0.00
ATOM   1795  CA  HIS   294      29.451  11.768   3.659  1.00  0.00
ATOM   1796  CB  HIS   294      28.826  10.452   3.191  1.00  0.00
ATOM   1797  CG  HIS   294      28.167   9.673   4.286  1.00  0.00
ATOM   1798  CD2 HIS   294      26.796   9.438   4.712  1.00  0.00
ATOM   1799  ND1 HIS   294      28.879   8.937   5.208  1.00  0.00
ATOM   1800  CE1 HIS   294      28.018   8.352   6.059  1.00  0.00
ATOM   1801  NE2 HIS   294      26.766   8.648   5.767  1.00  0.00
ATOM   1802  O   HIS   294      29.576  13.443   1.943  1.00  0.00
ATOM   1803  C   HIS   294      30.106  12.463   2.466  1.00  0.00
ATOM   1804  N   PHE   295      31.246  11.949   2.029  1.00  0.00
ATOM   1805  CA  PHE   295      31.945  12.549   0.908  1.00  0.00
ATOM   1806  CB  PHE   295      33.312  13.079   1.351  1.00  0.00
ATOM   1807  CG  PHE   295      33.232  14.199   2.349  1.00  0.00
ATOM   1808  CD1 PHE   295      33.252  13.936   3.708  1.00  0.00
ATOM   1809  CD2 PHE   295      33.139  15.513   1.930  1.00  0.00
ATOM   1810  CE1 PHE   295      33.179  14.965   4.627  1.00  0.00
ATOM   1811  CE2 PHE   295      33.066  16.543   2.849  1.00  0.00
ATOM   1812  CZ  PHE   295      33.086  16.275   4.191  1.00  0.00
ATOM   1813  O   PHE   295      32.598  10.414   0.058  1.00  0.00
ATOM   1814  C   PHE   295      32.171  11.535  -0.206  1.00  0.00
ATOM   1815  N   THR   296      31.866  11.925  -1.447  1.00  0.00
ATOM   1816  CA  THR   296      32.039  11.035  -2.591  1.00  0.00
ATOM   1817  CB  THR   296      31.286  11.554  -3.830  1.00  0.00
ATOM   1818  CG2 THR   296      31.478  10.609  -5.005  1.00  0.00
ATOM   1819  OG1 THR   296      29.886  11.649  -3.536  1.00  0.00
ATOM   1820  O   THR   296      34.170  11.902  -3.300  1.00  0.00
ATOM   1821  C   THR   296      33.512  10.909  -2.964  1.00  0.00
ATOM   1822  N   ARG   297      34.030   9.689  -2.890  1.00  0.00
ATOM   1823  CA  ARG   297      35.426   9.446  -3.205  1.00  0.00
ATOM   1824  CB  ARG   297      36.134   8.778  -2.025  1.00  0.00
ATOM   1825  CG  ARG   297      36.189   9.634  -0.769  1.00  0.00
ATOM   1826  CD  ARG   297      37.096   9.016   0.282  1.00  0.00
ATOM   1827  NE  ARG   297      37.195   9.847   1.478  1.00  0.00
ATOM   1828  CZ  ARG   297      37.952   9.557   2.530  1.00  0.00
ATOM   1829  NH1 ARG   297      37.979  10.374   3.575  1.00  0.00
ATOM   1830  NH2 ARG   297      38.685   8.451   2.534  1.00  0.00
ATOM   1831  O   ARG   297      36.500   7.776  -4.545  1.00  0.00
ATOM   1832  C   ARG   297      35.544   8.538  -4.412  1.00  0.00
ATOM   1833  N   GLU   298      34.556   8.626  -5.292  1.00  0.00
ATOM   1834  CA  GLU   298      34.534   7.832  -6.512  1.00  0.00
ATOM   1835  CB  GLU   298      33.146   7.226  -6.733  1.00  0.00
ATOM   1836  CG  GLU   298      32.742   6.203  -5.685  1.00  0.00
ATOM   1837  CD  GLU   298      31.381   5.593  -5.961  1.00  0.00
ATOM   1838  OE1 GLU   298      30.754   5.973  -6.971  1.00  0.00
ATOM   1839  OE2 GLU   298      30.941   4.738  -5.164  1.00  0.00
ATOM   1840  O   GLU   298      34.291   9.833  -7.811  1.00  0.00
ATOM   1841  C   GLU   298      34.888   8.763  -7.664  1.00  0.00
ATOM   1842  N   MET   299      35.875   8.379  -8.458  1.00  0.00
ATOM   1843  CA  MET   299      36.287   9.200  -9.577  1.00  0.00
ATOM   1844  CB  MET   299      37.789   9.057  -9.822  1.00  0.00
ATOM   1845  CG  MET   299      38.652   9.931  -8.925  1.00  0.00
ATOM   1846  SD  MET   299      38.523   9.479  -7.183  1.00  0.00
ATOM   1847  CE  MET   299      39.373   7.903  -7.178  1.00  0.00
ATOM   1848  O   MET   299      34.713   7.963 -10.900  1.00  0.00
ATOM   1849  C   MET   299      35.587   8.834 -10.868  1.00  0.00
ATOM   1850  N   PRO   300      35.951   9.530 -11.932  1.00  0.00
ATOM   1851  CA  PRO   300      35.395   9.266 -13.248  1.00  0.00
ATOM   1852  CB  PRO   300      34.636  10.548 -13.591  1.00  0.00
ATOM   1853  CG  PRO   300      35.345  11.619 -12.833  1.00  0.00
ATOM   1854  CD  PRO   300      35.814  10.982 -11.554  1.00  0.00
ATOM   1855  O   PRO   300      37.391   9.863 -14.442  1.00  0.00
ATOM   1856  C   PRO   300      36.547   8.990 -14.205  1.00  0.00
ATOM   1857  N   GLU   301      36.683   7.734 -14.644  1.00  0.00
ATOM   1858  CA  GLU   301      35.814   6.617 -14.266  1.00  0.00
ATOM   1859  CB  GLU   301      35.853   5.523 -15.335  1.00  0.00
ATOM   1860  CG  GLU   301      35.289   5.948 -16.680  1.00  0.00
ATOM   1861  CD  GLU   301      35.185   4.793 -17.660  1.00  0.00
ATOM   1862  OE1 GLU   301      36.161   4.024 -17.774  1.00  0.00
ATOM   1863  OE2 GLU   301      34.129   4.661 -18.312  1.00  0.00
ATOM   1864  O   GLU   301      37.252   6.565 -12.332  1.00  0.00
ATOM   1865  C   GLU   301      36.304   6.041 -12.928  1.00  0.00
ATOM   1866  N   GLU   302      35.676   4.961 -12.435  1.00  0.00
ATOM   1867  CA  GLU   302      34.551   4.212 -12.994  1.00  0.00
ATOM   1868  CB  GLU   302      34.551   2.775 -12.470  1.00  0.00
ATOM   1869  CG  GLU   302      35.720   1.935 -12.961  1.00  0.00
ATOM   1870  CD  GLU   302      35.756   0.559 -12.324  1.00  0.00
ATOM   1871  OE1 GLU   302      34.889   0.277 -11.471  1.00  0.00
ATOM   1872  OE2 GLU   302      36.652  -0.235 -12.679  1.00  0.00
ATOM   1873  O   GLU   302      32.158   4.204 -13.109  1.00  0.00
ATOM   1874  C   GLU   302      33.167   4.768 -12.676  1.00  0.00
ATOM   1875  N   PHE   303      33.102   5.854 -11.915  1.00  0.00
ATOM   1876  CA  PHE   303      31.808   6.442 -11.590  1.00  0.00
ATOM   1877  CB  PHE   303      31.741   6.800 -10.103  1.00  0.00
ATOM   1878  CG  PHE   303      31.754   5.607  -9.191  1.00  0.00
ATOM   1879  CD1 PHE   303      32.920   5.213  -8.559  1.00  0.00
ATOM   1880  CD2 PHE   303      30.598   4.879  -8.965  1.00  0.00
ATOM   1881  CE1 PHE   303      32.933   4.115  -7.720  1.00  0.00
ATOM   1882  CE2 PHE   303      30.611   3.781  -8.126  1.00  0.00
ATOM   1883  CZ  PHE   303      31.770   3.398  -7.505  1.00  0.00
ATOM   1884  O   PHE   303      32.543   8.167 -13.079  1.00  0.00
ATOM   1885  C   PHE   303      31.615   7.706 -12.419  1.00  0.00
ATOM   1886  N   THR   304      30.391   8.223 -12.437  1.00  0.00
ATOM   1887  CA  THR   304      30.079   9.452 -13.156  1.00  0.00
ATOM   1888  CB  THR   304      28.686   9.384 -13.810  1.00  0.00
ATOM   1889  CG2 THR   304      28.580   8.165 -14.713  1.00  0.00
ATOM   1890  OG1 THR   304      27.680   9.296 -12.793  1.00  0.00
ATOM   1891  O   THR   304      30.181  10.344 -10.919  1.00  0.00
ATOM   1892  C   THR   304      30.113  10.588 -12.141  1.00  0.00
ATOM   1893  N   LEU   305      30.096  11.827 -12.637  1.00  0.00
ATOM   1894  CA  LEU   305      30.113  13.005 -11.766  1.00  0.00
ATOM   1895  CB  LEU   305      30.299  14.279 -12.592  1.00  0.00
ATOM   1896  CG  LEU   305      31.577  14.366 -13.430  1.00  0.00
ATOM   1897  CD1 LEU   305      31.582  15.629 -14.274  1.00  0.00
ATOM   1898  CD2 LEU   305      32.806  14.387 -12.534  1.00  0.00
ATOM   1899  O   LEU   305      28.806  13.221  -9.773  1.00  0.00
ATOM   1900  C   LEU   305      28.801  13.104 -11.001  1.00  0.00
TER
END
