
#######################################################
#                                                     #
#                        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   24 (  200),  selected   24 , name T0386TS030_4-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS030_4-D2.T0386_D2.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    -       -      N     219           -
LGA    -       -      P     220           -
LGA    -       -      E     221           -
LGA    -       -      K     222           -
LGA    -       -      I     223           -
LGA    -       -      R     224           -
LGA    N     219      L     225           #
LGA    -       -      L     226           -
LGA    -       -      K     227           -
LGA    -       -      E     228           -
LGA    -       -      F     229           -
LGA    -       -      M     230           -
LGA    -       -      H     231           -
LGA    -       -      T     232           -
LGA    -       -      M     233           -
LGA    -       -      K     234           -
LGA    -       -      N     235           -
LGA    -       -      T     236           -
LGA    -       -      G     237           -
LGA    -       -      R     238           -
LGA    -       -      N     239           -
LGA    -       -      V     240           -
LGA    -       -      N     241           -
LGA    -       -      D     242           -
LGA    -       -      R     243           -
LGA    -       -      P     244           -
LGA    -       -      V     245           -
LGA    -       -      M     246           -
LGA    -       -      V     247           -
LGA    P     220      A     248          3.465
LGA    E     221      K     249          4.817
LGA    -       -      E     250           -
LGA    -       -      G     251           -
LGA    K     222      E     252          2.363
LGA    I     223      T     253          2.626
LGA    R     224      Y     254          4.266
LGA    L     225      T     255           #
LGA    L     226      -       -           -
LGA    K     227      -       -           -
LGA    E     228      G     256          2.343
LGA    F     229      T     257          1.033
LGA    M     230      Y     258          1.423
LGA    H     231      R     259          0.725
LGA    T     232      G     260          3.277
LGA    M     233      A     261          3.511
LGA    K     234      G     262          1.818
LGA    N     235      L     263          3.450
LGA    T     236      E     264           #
LGA    -       -      G     265           -
LGA    -       -      F     266           -
LGA    -       -      A     267           -
LGA    -       -      L     268           -
LGA    -       -      N     269           -
LGA    -       -      V     270           -
LGA    -       -      K     271           -
LGA    -       -      G     272           -
LGA    -       -      A     273           -
LGA    -       -      Y     274           -
LGA    -       -      I     275           -
LGA    -       -      I     276           -
LGA    -       -      G     277           -
LGA    -       -      N     278           -
LGA    G     237      I     279          3.990
LGA    -       -      D     280           -
LGA    -       -      H     281           -
LGA    R     238      L     282          0.479
LGA    N     239      P     283          1.484
LGA    V     240      P     284          1.983
LGA    N     241      E     285          3.978
LGA    D     242      Q     286          4.767
LGA    -       -      L     287           -
LGA    -       -      K     288           -
LGA    -       -      I     289           -
LGA    -       -      L     290           -
LGA    -       -      K     291           -
LGA    -       -      P     292           -
LGA    -       -      G     293           -
LGA    -       -      D     294           -
LGA    -       -      K     295           -
LGA    -       -      I     296           -
LGA    -       -      T     297           -
LGA    -       -      F     298           -
LGA    -       -      T     299           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   24   81    5.0     19    3.03     0.00     15.527     0.608

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.698938 * X  +  -0.553419 * Y  +  -0.453004 * Z  +  42.827278
  Y_new =  -0.063363 * X  +   0.583002 * Y  +  -0.809996 * Z  +  24.664934
  Z_new =   0.712369 * X  +   0.594841 * Y  +   0.372416 * Z  +  62.052914 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.011423   -2.130170  [ DEG:    57.9503   -122.0497 ]
  Theta =  -0.792869   -2.348724  [ DEG:   -45.4280   -134.5720 ]
  Phi   =  -0.090409    3.051184  [ DEG:    -5.1801    174.8199 ]
 
# 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: T0386TS030_4-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS030_4-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   24   81   5.0   19   3.03    0.00  15.527
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS030_4-D2
PFRMAT TS
TARGET T0386
MODEL 4 
PARENT 2g03A       
ATOM   1761  N   ASN   219      10.934  57.729  84.182  1.00  1.00          
ATOM   1762  CA  ASN   219      11.681  56.594  84.712  1.00  1.00          
ATOM   1763  CB  ASN   219      13.182  56.892  84.705  1.00  1.00          
ATOM   1764  CG  ASN   219      13.441  58.289  85.258  1.00  1.00          
ATOM   1765  OD1 ASN   219      13.070  58.589  86.392  1.00  1.00          
ATOM   1766  ND2 ASN   219      14.061  59.168  84.517  1.00  1.00          
ATOM   1767  C   ASN   219      11.396  55.327  83.913  1.00  1.00          
ATOM   1768  O   ASN   219      11.020  54.298  84.476  1.00  1.00          
ATOM   1769  N   PRO   220      11.569  55.388  82.622  1.00  1.00          
ATOM   1770  CA  PRO   220      11.326  54.227  81.721  1.00  1.00          
ATOM   1771  CB  PRO   220      11.992  54.661  80.413  1.00  1.00          
ATOM   1772  CG  PRO   220      11.889  56.150  80.418  1.00  1.00          
ATOM   1773  CD  PRO   220      12.014  56.580  81.882  1.00  1.00          
ATOM   1774  C   PRO   220      11.983  52.955  82.246  1.00  1.00          
ATOM   1775  O   PRO   220      11.494  51.850  82.011  1.00  1.00          
ATOM   1776  N   GLU   221      13.093  53.120  82.958  1.00  1.00          
ATOM   1777  CA  GLU   221      13.819  51.985  83.518  1.00  1.00          
ATOM   1778  CB  GLU   221      12.846  50.989  84.153  1.00  1.00          
ATOM   1779  CG  GLU   221      12.943  51.082  85.677  1.00  1.00          
ATOM   1780  CD  GLU   221      11.572  50.847  86.305  1.00  1.00          
ATOM   1781  OE1 GLU   221      11.068  51.760  86.937  1.00  1.00          
ATOM   1782  OE2 GLU   221      11.048  49.757  86.144  1.00  1.00          
ATOM   1783  C   GLU   221      14.661  51.290  82.455  1.00  1.00          
ATOM   1784  O   GLU   221      14.312  51.290  81.274  1.00  1.00          
ATOM   1785  N   LYS   222      15.773  50.699  82.880  1.00  1.00          
ATOM   1786  CA  LYS   222      16.668  49.999  81.966  1.00  1.00          
ATOM   1787  CB  LYS   222      16.230  48.541  81.800  1.00  1.00          
ATOM   1788  CG  LYS   222      14.963  48.291  82.620  1.00  1.00          
ATOM   1789  CD  LYS   222      13.979  47.458  81.797  1.00  1.00          
ATOM   1790  CE  LYS   222      14.361  47.531  80.317  1.00  1.00          
ATOM   1791  NZ  LYS   222      14.501  46.152  79.771  1.00  1.00          
ATOM   1792  C   LYS   222      18.111  50.062  82.452  1.00  1.00          
ATOM   1793  O   LYS   222      18.369  50.261  83.638  1.00  1.00          
ATOM   1794  N   ILE   223      19.050  49.889  81.526  1.00  1.00          
ATOM   1795  CA  ILE   223      20.469  49.926  81.858  1.00  1.00          
ATOM   1796  CB  ILE   223      20.950  48.545  82.307  1.00  1.00          
ATOM   1797  CG1 ILE   223      22.440  48.608  82.649  1.00  1.00          
ATOM   1798  CG2 ILE   223      20.727  47.535  81.179  1.00  1.00          
ATOM   1799  CD1 ILE   223      23.159  47.413  82.020  1.00  1.00          
ATOM   1800  C   ILE   223      21.300  50.411  80.675  1.00  1.00          
ATOM   1801  O   ILE   223      22.252  49.750  80.260  1.00  1.00          
ATOM   1802  N   ARG   224      20.933  51.570  80.137  1.00  1.00          
ATOM   1803  CA  ARG   224      21.644  52.145  79.002  1.00  1.00          
ATOM   1804  CB  ARG   224      21.011  53.478  78.593  1.00  1.00          
ATOM   1805  CG  ARG   224      20.090  53.259  77.392  1.00  1.00          
ATOM   1806  CD  ARG   224      20.390  54.307  76.320  1.00  1.00          
ATOM   1807  NE  ARG   224      19.157  54.932  75.856  1.00  1.00          
ATOM   1808  CZ  ARG   224      18.855  56.190  76.158  1.00  1.00          
ATOM   1809  NH1 ARG   224      17.677  56.481  76.637  1.00  1.00          
ATOM   1810  NH2 ARG   224      19.735  57.135  75.973  1.00  1.00          
ATOM   1811  C   ARG   224      23.122  52.342  79.318  1.00  1.00          
ATOM   1812  O   ARG   224      23.550  52.176  80.460  1.00  1.00          
ATOM   1813  N   LEU   225      23.899  52.698  78.300  1.00  1.00          
ATOM   1814  CA  LEU   225      25.330  52.918  78.468  1.00  1.00          
ATOM   1815  CB  LEU   225      26.127  51.838  77.734  1.00  1.00          
ATOM   1816  CG  LEU   225      26.538  50.746  78.725  1.00  1.00          
ATOM   1817  CD1 LEU   225      26.401  51.274  80.153  1.00  1.00          
ATOM   1818  CD2 LEU   225      25.634  49.524  78.541  1.00  1.00          
ATOM   1819  C   LEU   225      25.737  54.300  77.968  1.00  1.00          
ATOM   1820  O   LEU   225      24.906  55.202  77.862  1.00  1.00          
ATOM   1821  N   LEU   226      27.020  54.459  77.663  1.00  1.00          
ATOM   1822  CA  LEU   226      27.540  55.731  77.173  1.00  1.00          
ATOM   1823  CB  LEU   226      28.660  55.497  76.157  1.00  1.00          
ATOM   1824  CG  LEU   226      29.914  55.007  76.883  1.00  1.00          
ATOM   1825  CD1 LEU   226      29.966  53.478  76.837  1.00  1.00          
ATOM   1826  CD2 LEU   226      31.156  55.581  76.199  1.00  1.00          
ATOM   1827  C   LEU   226      28.047  56.597  78.321  1.00  1.00          
ATOM   1828  O   LEU   226      28.806  56.135  79.173  1.00  1.00          
ATOM   1829  N   LYS   227      27.622  57.856  78.337  1.00  1.00          
ATOM   1830  CA  LYS   227      28.032  58.790  79.380  1.00  1.00          
ATOM   1831  CB  LYS   227      27.579  60.210  79.036  1.00  1.00          
ATOM   1832  CG  LYS   227      26.906  60.213  77.662  1.00  1.00          
ATOM   1833  CD  LYS   227      27.418  61.400  76.844  1.00  1.00          
ATOM   1834  CE  LYS   227      26.868  61.314  75.420  1.00  1.00          
ATOM   1835  NZ  LYS   227      25.559  62.022  75.348  1.00  1.00          
ATOM   1836  C   LYS   227      27.477  58.377  80.739  1.00  1.00          
ATOM   1837  O   LYS   227      26.760  57.383  80.852  1.00  1.00          
ATOM   1838  N   GLU   228      27.812  59.148  81.768  1.00  1.00          
ATOM   1839  CA  GLU   228      27.349  58.865  83.121  1.00  1.00          
ATOM   1840  CB  GLU   228      27.969  57.565  83.639  1.00  1.00          
ATOM   1841  CG  GLU   228      29.483  57.738  83.770  1.00  1.00          
ATOM   1842  CD  GLU   228      30.064  56.628  84.639  1.00  1.00          
ATOM   1843  OE1 GLU   228      31.246  56.356  84.506  1.00  1.00          
ATOM   1844  OE2 GLU   228      29.319  56.068  85.426  1.00  1.00          
ATOM   1845  C   GLU   228      27.675  60.014  84.068  1.00  1.00          
ATOM   1846  O   GLU   228      28.831  60.420  84.192  1.00  1.00          
ATOM   1847  N   PHE   229      26.650  60.536  84.734  1.00  1.00          
ATOM   1848  CA  PHE   229      26.826  61.639  85.670  1.00  1.00          
ATOM   1849  CB  PHE   229      27.549  62.805  84.993  1.00  1.00          
ATOM   1850  CG  PHE   229      28.380  63.545  86.015  1.00  1.00          
ATOM   1851  CD1 PHE   229      29.741  63.247  86.158  1.00  1.00          
ATOM   1852  CD2 PHE   229      27.791  64.528  86.819  1.00  1.00          
ATOM   1853  CE1 PHE   229      30.511  63.931  87.105  1.00  1.00          
ATOM   1854  CE2 PHE   229      28.562  65.213  87.765  1.00  1.00          
ATOM   1855  CZ  PHE   229      29.922  64.915  87.909  1.00  1.00          
ATOM   1856  C   PHE   229      25.487  62.106  86.231  1.00  1.00          
ATOM   1857  O   PHE   229      24.911  61.462  87.106  1.00  1.00          
ATOM   1858  N   MET   230      24.998  63.232  85.721  1.00  1.00          
ATOM   1859  CA  MET   230      23.727  63.788  86.168  1.00  1.00          
ATOM   1860  CB  MET   230      23.961  64.945  87.140  1.00  1.00          
ATOM   1861  CG  MET   230      22.930  64.881  88.269  1.00  1.00          
ATOM   1862  SD  MET   230      21.800  63.498  87.976  1.00  1.00          
ATOM   1863  CE  MET   230      21.562  63.029  89.708  1.00  1.00          
ATOM   1864  C   MET   230      22.883  64.257  84.988  1.00  1.00          
ATOM   1865  O   MET   230      22.892  63.641  83.922  1.00  1.00          
ATOM   1866  N   HIS   231      22.155  65.351  85.186  1.00  1.00          
ATOM   1867  CA  HIS   231      21.305  65.906  84.139  1.00  1.00          
ATOM   1868  CB  HIS   231      21.656  67.373  83.885  1.00  1.00          
ATOM   1869  CG  HIS   231      22.551  67.474  82.680  1.00  1.00          
ATOM   1870  ND1 HIS   231      23.616  68.358  82.623  1.00  1.00          
ATOM   1871  CD2 HIS   231      22.552  66.808  81.479  1.00  1.00          
ATOM   1872  CE1 HIS   231      24.208  68.203  81.427  1.00  1.00          
ATOM   1873  NE2 HIS   231      23.599  67.271  80.689  1.00  1.00          
ATOM   1874  C   HIS   231      19.829  65.774  84.501  1.00  1.00          
ATOM   1875  O   HIS   231      19.034  66.676  84.240  1.00  1.00          
ATOM   1876  N   THR   232      19.471  64.645  85.103  1.00  1.00          
ATOM   1877  CA  THR   232      18.091  64.393  85.502  1.00  1.00          
ATOM   1878  CB  THR   232      17.881  62.906  85.793  1.00  1.00          
ATOM   1879  OG1 THR   232      18.384  62.135  84.712  1.00  1.00          
ATOM   1880  CG2 THR   232      18.621  62.527  87.078  1.00  1.00          
ATOM   1881  C   THR   232      17.113  64.860  84.429  1.00  1.00          
ATOM   1882  O   THR   232      17.036  64.276  83.349  1.00  1.00          
ATOM   1883  N   MET   233      16.367  65.917  84.736  1.00  1.00          
ATOM   1884  CA  MET   233      15.392  66.464  83.800  1.00  1.00          
ATOM   1885  CB  MET   233      16.070  67.428  82.824  1.00  1.00          
ATOM   1886  CG  MET   233      15.668  67.069  81.391  1.00  1.00          
ATOM   1887  SD  MET   233      15.498  68.583  80.414  1.00  1.00          
ATOM   1888  CE  MET   233      16.400  68.013  78.953  1.00  1.00          
ATOM   1889  C   MET   233      14.260  67.172  84.536  1.00  1.00          
ATOM   1890  O   MET   233      14.491  67.877  85.519  1.00  1.00          
ATOM   1891  N   LYS   234      13.037  66.982  84.053  1.00  1.00          
ATOM   1892  CA  LYS   234      11.867  67.602  84.665  1.00  1.00          
ATOM   1893  CB  LYS   234      11.926  69.124  84.511  1.00  1.00          
ATOM   1894  CG  LYS   234      12.000  69.484  83.026  1.00  1.00          
ATOM   1895  CD  LYS   234      12.060  71.005  82.872  1.00  1.00          
ATOM   1896  CE  LYS   234      12.489  71.359  81.446  1.00  1.00          
ATOM   1897  NZ  LYS   234      13.597  72.353  81.493  1.00  1.00          
ATOM   1898  C   LYS   234      11.753  67.228  86.139  1.00  1.00          
ATOM   1899  O   LYS   234      12.495  67.752  86.970  1.00  1.00          
ATOM   1900  N   ASN   235      10.817  66.322  86.451  1.00  1.00          
ATOM   1901  CA  ASN   235      10.586  65.870  87.824  1.00  1.00          
ATOM   1902  CB  ASN   235      10.987  66.927  88.854  1.00  1.00          
ATOM   1903  CG  ASN   235      12.340  66.576  89.465  1.00  1.00          
ATOM   1904  OD1 ASN   235      12.451  65.601  90.209  1.00  1.00          
ATOM   1905  ND2 ASN   235      13.380  67.315  89.195  1.00  1.00          
ATOM   1906  C   ASN   235      11.247  64.531  88.128  1.00  1.00          
ATOM   1907  O   ASN   235      10.626  63.649  88.709  1.00  1.00          
ATOM   1908  N   THR   236      12.505  64.377  87.733  1.00  1.00          
ATOM   1909  CA  THR   236      13.216  63.124  87.967  1.00  1.00          
ATOM   1910  CB  THR   236      14.522  63.095  87.170  1.00  1.00          
ATOM   1911  OG1 THR   236      15.565  63.664  87.949  1.00  1.00          
ATOM   1912  CG2 THR   236      14.354  63.898  85.879  1.00  1.00          
ATOM   1913  C   THR   236      13.503  62.873  89.443  1.00  1.00          
ATOM   1914  O   THR   236      14.147  63.682  90.112  1.00  1.00          
ATOM   1915  N   GLY   237      13.035  61.730  89.934  1.00  1.00          
ATOM   1916  CA  GLY   237      13.244  61.330  91.320  1.00  1.00          
ATOM   1917  C   GLY   237      12.760  59.894  91.543  1.00  1.00          
ATOM   1918  O   GLY   237      11.581  59.602  91.342  1.00  1.00          
ATOM   1919  N   ARG   238      13.672  59.002  91.942  1.00  1.00          
ATOM   1920  CA  ARG   238      13.345  57.586  92.171  1.00  1.00          
ATOM   1921  CB  ARG   238      12.162  57.119  91.318  1.00  1.00          
ATOM   1922  CG  ARG   238      12.562  57.127  89.842  1.00  1.00          
ATOM   1923  CD  ARG   238      14.053  56.807  89.713  1.00  1.00          
ATOM   1924  NE  ARG   238      14.264  55.738  88.745  1.00  1.00          
ATOM   1925  CZ  ARG   238      13.821  54.503  88.961  1.00  1.00          
ATOM   1926  NH1 ARG   238      14.586  53.480  88.695  1.00  1.00          
ATOM   1927  NH2 ARG   238      12.622  54.314  89.438  1.00  1.00          
ATOM   1928  C   ARG   238      13.148  57.197  93.641  1.00  1.00          
ATOM   1929  O   ARG   238      12.532  56.170  93.926  1.00  1.00          
ATOM   1930  N   ASN   239      13.693  57.992  94.564  1.00  1.00          
ATOM   1931  CA  ASN   239      13.601  57.697  96.002  1.00  1.00          
ATOM   1932  CB  ASN   239      13.601  56.191  96.270  1.00  1.00          
ATOM   1933  CG  ASN   239      13.188  55.913  97.712  1.00  1.00          
ATOM   1934  OD1 ASN   239      12.034  55.577  97.975  1.00  1.00          
ATOM   1935  ND2 ASN   239      14.069  56.033  98.667  1.00  1.00          
ATOM   1936  C   ASN   239      12.424  58.371  96.708  1.00  1.00          
ATOM   1937  O   ASN   239      12.607  59.372  97.400  1.00  1.00          
ATOM   1938  N   VAL   240      11.221  57.822  96.550  1.00  1.00          
ATOM   1939  CA  VAL   240      10.064  58.404  97.212  1.00  1.00          
ATOM   1940  CB  VAL   240       8.844  57.492  97.059  1.00  1.00          
ATOM   1941  CG1 VAL   240       8.052  57.903  95.816  1.00  1.00          
ATOM   1942  CG2 VAL   240       7.954  57.616  98.297  1.00  1.00          
ATOM   1943  C   VAL   240      10.363  58.637  98.697  1.00  1.00          
ATOM   1944  O   VAL   240       9.835  59.559  99.311  1.00  1.00          
ATOM   1945  N   ASN   241      11.223  57.789  99.260  1.00  1.00          
ATOM   1946  CA  ASN   241      11.616  57.870 100.671  1.00  1.00          
ATOM   1947  CB  ASN   241      10.439  58.280 101.570  1.00  1.00          
ATOM   1948  CG  ASN   241      10.443  59.785 101.843  1.00  1.00          
ATOM   1949  OD1 ASN   241       9.520  60.491 101.437  1.00  1.00          
ATOM   1950  ND2 ASN   241      11.421  60.317 102.524  1.00  1.00          
ATOM   1951  C   ASN   241      12.826  58.779 100.890  1.00  1.00          
ATOM   1952  O   ASN   241      13.557  58.626 101.868  1.00  1.00          
ATOM   1953  N   ASP   242      13.034  59.722  99.980  1.00  1.00          
ATOM   1954  CA  ASP   242      14.157  60.649 100.081  1.00  1.00          
ATOM   1955  CB  ASP   242      14.674  61.016  98.688  1.00  1.00          
ATOM   1956  CG  ASP   242      15.788  62.053  98.797  1.00  1.00          
ATOM   1957  OD1 ASP   242      16.683  61.849  99.598  1.00  1.00          
ATOM   1958  OD2 ASP   242      15.727  63.035  98.074  1.00  1.00          
ATOM   1959  C   ASP   242      13.770  61.910 100.846  1.00  1.00          
ATOM   1960  O   ASP   242      12.598  62.271 100.912  1.00  1.00             
TER         
END
