
#######################################################
#                                                     #
#                        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   23 (  193),  selected   23 , name T0386TS338_5_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS338_5_1-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    -       -      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     219      N     239          0.395
LGA    P     220      V     240          0.973
LGA    E     221      N     241          2.462
LGA    K     222      D     242          3.539
LGA    I     223      R     243          2.184
LGA    R     224      -       -           -
LGA    L     225      P     244          3.816
LGA    L     226      V     245          2.156
LGA    K     227      -       -           -
LGA    E     228      M     246           #
LGA    F     229      V     247          4.714
LGA    M     230      A     248          5.270
LGA    -       -      K     249           -
LGA    -       -      E     250           -
LGA    -       -      G     251           -
LGA    -       -      E     252           -
LGA    -       -      T     253           -
LGA    -       -      Y     254           -
LGA    -       -      T     255           -
LGA    -       -      G     256           -
LGA    -       -      T     257           -
LGA    -       -      Y     258           -
LGA    -       -      R     259           -
LGA    -       -      G     260           -
LGA    -       -      A     261           -
LGA    -       -      G     262           -
LGA    -       -      L     263           -
LGA    -       -      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    H     231      Y     274          4.403
LGA    T     232      I     275          5.015
LGA    M     233      I     276          2.962
LGA    K     234      G     277          3.043
LGA    N     235      -       -           -
LGA    T     236      N     278          1.008
LGA    G     237      I     279           #
LGA    R     238      -       -           -
LGA    N     239      D     280          2.161
LGA    V     240      H     281          2.972
LGA    -       -      L     282           -
LGA    -       -      P     283           -
LGA    -       -      P     284           -
LGA    -       -      E     285           -
LGA    -       -      Q     286           -
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    N     241      T     299           #

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   23   81    5.0     16    3.27     6.25     12.151     0.475

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.696956 * X  +   0.182156 * Y  +  -0.693593 * Z  +  -7.871688
  Y_new =  -0.577890 * X  +  -0.715357 * Y  +   0.392820 * Z  +  84.437866
  Z_new =  -0.424612 * X  +   0.674599 * Y  +   0.603839 * Z  +  35.037350 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.840691   -2.300902  [ DEG:    48.1680   -131.8320 ]
  Theta =   0.438533    2.703059  [ DEG:    25.1261    154.8739 ]
  Phi   =  -2.449321    0.692272  [ DEG:  -140.3358     39.6642 ]
 
# 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: T0386TS338_5_1-D2                             
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS338_5_1-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   23   81   5.0   16   3.27    6.25  12.151
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS338_5_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0386
PARENT 2g03_A 2f6s_A
ATOM   1761  N   ASN   219      22.124  71.776  70.586  1.00  0.02
ATOM   1762  CA  ASN   219      21.413  71.258  69.445  1.00  0.02
ATOM   1763  CB  ASN   219      21.788  71.964  68.131  1.00  0.02
ATOM   1764  CG  ASN   219      21.371  73.430  68.219  1.00  0.02
ATOM   1765  OD1 ASN   219      20.240  73.764  68.565  1.00  0.02
ATOM   1766  ND2 ASN   219      22.322  74.343  67.889  1.00  0.02
ATOM   1767  C   ASN   219      21.795  69.808  69.300  1.00  0.02
ATOM   1768  O   ASN   219      22.948  69.485  69.018  1.00  0.02
ATOM   1769  N   PRO   220      20.841  68.935  69.520  1.00  0.03
ATOM   1770  CA  PRO   220      21.121  67.517  69.495  1.00  0.03
ATOM   1771  CD  PRO   220      19.836  69.263  70.515  1.00  0.03
ATOM   1772  CB  PRO   220      20.045  66.853  70.355  1.00  0.03
ATOM   1773  CG  PRO   220      19.590  67.970  71.307  1.00  0.03
ATOM   1774  C   PRO   220      21.258  66.834  68.184  1.00  0.03
ATOM   1775  O   PRO   220      20.321  66.905  67.387  1.00  0.03
ATOM   1776  N   GLU   221      22.394  66.150  67.906  1.00  0.01
ATOM   1777  CA  GLU   221      22.270  65.295  66.768  1.00  0.01
ATOM   1778  CB  GLU   221      23.594  64.688  66.282  1.00  0.01
ATOM   1779  CG  GLU   221      24.564  65.686  65.656  1.00  0.01
ATOM   1780  CD  GLU   221      25.800  64.905  65.234  1.00  0.01
ATOM   1781  OE1 GLU   221      25.624  63.759  64.742  1.00  0.01
ATOM   1782  OE2 GLU   221      26.932  65.433  65.393  1.00  0.01
ATOM   1783  C   GLU   221      21.431  64.124  67.218  1.00  0.01
ATOM   1784  O   GLU   221      20.713  64.172  68.215  1.00  0.01
ATOM   1785  N   LYS   222      21.668  62.969  66.571  1.00  0.01
ATOM   1786  CA  LYS   222      20.985  61.739  66.847  1.00  0.01
ATOM   1787  CB  LYS   222      21.450  60.653  65.869  1.00  0.01
ATOM   1788  CG  LYS   222      21.334  61.064  64.402  1.00  0.01
ATOM   1789  CD  LYS   222      22.284  60.299  63.476  1.00  0.01
ATOM   1790  CE  LYS   222      23.659  60.966  63.353  1.00  0.01
ATOM   1791  NZ  LYS   222      24.483  60.294  62.321  1.00  0.01
ATOM   1792  C   LYS   222      21.387  61.260  68.188  1.00  0.01
ATOM   1793  O   LYS   222      20.549  60.867  68.992  1.00  0.01
ATOM   1794  N   ILE   223      22.708  61.302  68.441  1.00  0.01
ATOM   1795  CA  ILE   223      23.298  60.793  69.638  1.00  0.01
ATOM   1796  CB  ILE   223      24.803  60.848  69.611  1.00  0.01
ATOM   1797  CG2 ILE   223      25.320  60.514  71.018  1.00  0.01
ATOM   1798  CG1 ILE   223      25.358  59.920  68.511  1.00  0.01
ATOM   1799  CD1 ILE   223      26.876  59.997  68.330  1.00  0.01
ATOM   1800  C   ILE   223      22.818  61.587  70.794  1.00  0.01
ATOM   1801  O   ILE   223      22.474  61.035  71.835  1.00  0.01
ATOM   1802  N   ARG   224      22.783  62.917  70.642  1.00  0.01
ATOM   1803  CA  ARG   224      22.387  63.757  71.729  1.00  0.01
ATOM   1804  CB  ARG   224      22.599  65.250  71.420  1.00  0.01
ATOM   1805  CG  ARG   224      24.093  65.585  71.340  1.00  0.01
ATOM   1806  CD  ARG   224      24.432  67.064  71.148  1.00  0.01
ATOM   1807  NE  ARG   224      25.920  67.170  71.185  1.00  0.01
ATOM   1808  CZ  ARG   224      26.512  68.298  71.677  1.00  0.01
ATOM   1809  NH1 ARG   224      25.741  69.350  72.077  1.00  0.01
ATOM   1810  NH2 ARG   224      27.871  68.372  71.785  1.00  0.01
ATOM   1811  C   ARG   224      20.966  63.498  72.094  1.00  0.01
ATOM   1812  O   ARG   224      20.626  63.463  73.278  1.00  0.01
ATOM   1813  N   LEU   225      20.095  63.313  71.083  1.00  0.01
ATOM   1814  CA  LEU   225      18.702  63.114  71.361  1.00  0.01
ATOM   1815  CB  LEU   225      17.823  63.091  70.097  1.00  0.01
ATOM   1816  CG  LEU   225      16.303  63.174  70.369  1.00  0.01
ATOM   1817  CD1 LEU   225      15.755  61.933  71.086  1.00  0.01
ATOM   1818  CD2 LEU   225      15.942  64.473  71.105  1.00  0.01
ATOM   1819  C   LEU   225      18.511  61.831  72.097  1.00  0.01
ATOM   1820  O   LEU   225      17.696  61.773  73.017  1.00  0.01
ATOM   1821  N   LEU   226      19.238  60.767  71.700  1.00  0.01
ATOM   1822  CA  LEU   226      19.074  59.503  72.360  1.00  0.01
ATOM   1823  CB  LEU   226      19.828  58.334  71.706  1.00  0.01
ATOM   1824  CG  LEU   226      19.107  57.723  70.491  1.00  0.01
ATOM   1825  CD1 LEU   226      18.859  58.749  69.375  1.00  0.01
ATOM   1826  CD2 LEU   226      19.857  56.474  70.004  1.00  0.01
ATOM   1827  C   LEU   226      19.494  59.602  73.794  1.00  0.01
ATOM   1828  O   LEU   226      18.841  59.019  74.656  1.00  0.01
ATOM   1829  N   LYS   227      20.596  60.319  74.102  1.00  0.01
ATOM   1830  CA  LYS   227      21.034  60.397  75.473  1.00  0.01
ATOM   1831  CB  LYS   227      22.335  61.192  75.664  1.00  0.01
ATOM   1832  CG  LYS   227      23.559  60.580  74.980  1.00  0.01
ATOM   1833  CD  LYS   227      23.844  59.130  75.381  1.00  0.01
ATOM   1834  CE  LYS   227      23.723  58.852  76.880  1.00  0.01
ATOM   1835  NZ  LYS   227      22.475  58.103  77.152  1.00  0.01
ATOM   1836  C   LYS   227      19.999  61.090  76.304  1.00  0.01
ATOM   1837  O   LYS   227      19.742  60.706  77.445  1.00  0.01
ATOM   1838  N   GLU   228      19.395  62.164  75.755  1.00  0.01
ATOM   1839  CA  GLU   228      18.438  62.890  76.543  1.00  0.01
ATOM   1840  CB  GLU   228      18.010  64.233  75.916  1.00  0.01
ATOM   1841  CG  GLU   228      17.464  64.152  74.491  1.00  0.01
ATOM   1842  CD  GLU   228      17.434  65.580  73.956  1.00  0.01
ATOM   1843  OE1 GLU   228      16.810  66.450  74.619  1.00  0.01
ATOM   1844  OE2 GLU   228      18.054  65.824  72.886  1.00  0.01
ATOM   1845  C   GLU   228      17.238  62.050  76.846  1.00  0.01
ATOM   1846  O   GLU   228      16.705  62.105  77.955  1.00  0.01
ATOM   1847  N   PHE   229      16.791  61.243  75.864  1.00  0.01
ATOM   1848  CA  PHE   229      15.620  60.449  76.076  1.00  0.01
ATOM   1849  CB  PHE   229      15.089  59.701  74.847  1.00  0.01
ATOM   1850  CG  PHE   229      13.748  59.243  75.311  1.00  0.01
ATOM   1851  CD1 PHE   229      12.666  60.090  75.242  1.00  0.01
ATOM   1852  CD2 PHE   229      13.568  57.987  75.841  1.00  0.01
ATOM   1853  CE1 PHE   229      11.425  59.686  75.677  1.00  0.01
ATOM   1854  CE2 PHE   229      12.330  57.577  76.279  1.00  0.01
ATOM   1855  CZ  PHE   229      11.252  58.427  76.202  1.00  0.01
ATOM   1856  C   PHE   229      15.883  59.436  77.138  1.00  0.01
ATOM   1857  O   PHE   229      14.995  59.159  77.936  1.00  0.01
ATOM   1858  N   MET   230      17.088  58.831  77.154  1.00  0.01
ATOM   1859  CA  MET   230      17.437  57.811  78.098  1.00  0.01
ATOM   1860  CB  MET   230      18.840  57.247  77.829  1.00  0.01
ATOM   1861  CG  MET   230      19.236  56.060  78.705  1.00  0.01
ATOM   1862  SD  MET   230      20.870  55.387  78.279  1.00  0.01
ATOM   1863  CE  MET   230      20.756  53.913  79.330  1.00  0.01
ATOM   1864  C   MET   230      17.402  58.393  79.476  1.00  0.01
ATOM   1865  O   MET   230      16.941  57.733  80.397  1.00  0.01
ATOM   1866  N   HIS   231      17.890  59.635  79.663  1.00  0.01
ATOM   1867  CA  HIS   231      17.933  60.249  80.965  1.00  0.01
ATOM   1868  ND1 HIS   231      18.276  62.134  83.443  1.00  0.01
ATOM   1869  CG  HIS   231      19.093  61.996  82.345  1.00  0.01
ATOM   1870  CB  HIS   231      18.620  61.620  80.972  1.00  0.01
ATOM   1871  NE2 HIS   231      20.349  62.549  84.136  1.00  0.01
ATOM   1872  CD2 HIS   231      20.356  62.252  82.785  1.00  0.01
ATOM   1873  CE1 HIS   231      19.080  62.466  84.488  1.00  0.01
ATOM   1874  C   HIS   231      16.534  60.467  81.468  1.00  0.01
ATOM   1875  O   HIS   231      16.245  60.259  82.646  1.00  0.01
ATOM   1876  N   THR   232      15.624  60.915  80.577  1.00  0.01
ATOM   1877  CA  THR   232      14.284  61.212  80.997  1.00  0.01
ATOM   1878  CB  THR   232      13.440  61.807  79.909  1.00  0.01
ATOM   1879  OG1 THR   232      13.295  60.891  78.835  1.00  0.01
ATOM   1880  CG2 THR   232      14.110  63.105  79.428  1.00  0.01
ATOM   1881  C   THR   232      13.611  59.965  81.470  1.00  0.01
ATOM   1882  O   THR   232      12.880  59.976  82.457  1.00  0.01
ATOM   1883  N   MET   233      13.839  58.862  80.748  1.00  0.01
ATOM   1884  CA  MET   233      13.252  57.587  81.039  1.00  0.01
ATOM   1885  CB  MET   233      13.667  56.551  79.982  1.00  0.01
ATOM   1886  CG  MET   233      13.263  55.105  80.275  1.00  0.01
ATOM   1887  SD  MET   233      14.353  54.245  81.450  1.00  0.01
ATOM   1888  CE  MET   233      13.860  52.575  80.941  1.00  0.01
ATOM   1889  C   MET   233      13.738  57.110  82.365  1.00  0.01
ATOM   1890  O   MET   233      12.961  56.521  83.109  1.00  0.01
ATOM   1891  N   LYS   234      15.035  57.308  82.683  1.00  0.01
ATOM   1892  CA  LYS   234      15.562  56.818  83.922  1.00  0.01
ATOM   1893  CB  LYS   234      17.074  57.004  84.103  1.00  0.01
ATOM   1894  CG  LYS   234      17.525  56.424  85.444  1.00  0.01
ATOM   1895  CD  LYS   234      19.028  56.184  85.586  1.00  0.01
ATOM   1896  CE  LYS   234      19.382  55.578  86.944  1.00  0.01
ATOM   1897  NZ  LYS   234      20.847  55.462  87.092  1.00  0.01
ATOM   1898  C   LYS   234      14.908  57.530  85.035  1.00  0.01
ATOM   1899  O   LYS   234      14.581  56.901  86.034  1.00  0.01
ATOM   1900  N   ASN   235      14.700  58.857  84.892  1.00  0.01
ATOM   1901  CA  ASN   235      14.119  59.598  85.973  1.00  0.01
ATOM   1902  CB  ASN   235      14.022  61.112  85.695  1.00  0.01
ATOM   1903  CG  ASN   235      13.475  61.820  86.934  1.00  0.01
ATOM   1904  OD1 ASN   235      14.122  61.915  87.977  1.00  0.01
ATOM   1905  ND2 ASN   235      12.231  62.355  86.808  1.00  0.01
ATOM   1906  C   ASN   235      12.742  59.107  86.246  1.00  0.01
ATOM   1907  O   ASN   235      12.365  58.935  87.406  1.00  0.01
ATOM   1908  N   THR   236      11.955  58.872  85.182  1.00  0.01
ATOM   1909  CA  THR   236      10.591  58.473  85.372  1.00  0.01
ATOM   1910  CB  THR   236       9.791  58.429  84.103  1.00  0.01
ATOM   1911  OG1 THR   236       8.424  58.188  84.400  1.00  0.01
ATOM   1912  CG2 THR   236      10.332  57.302  83.210  1.00  0.01
ATOM   1913  C   THR   236      10.478  57.119  86.012  1.00  0.01
ATOM   1914  O   THR   236       9.607  56.910  86.854  1.00  0.01
ATOM   1915  N   GLY   237      11.314  56.148  85.590  1.00  0.01
ATOM   1916  CA  GLY   237      11.233  54.809  86.107  1.00  0.01
ATOM   1917  C   GLY   237      11.571  54.800  87.526  1.00  0.01
ATOM   1918  O   GLY   237      10.978  54.112  88.357  1.00  0.01
ATOM   1919  N   ARG   238      12.598  55.571  87.828  1.00  0.01
ATOM   1920  CA  ARG   238      12.984  55.564  89.189  1.00  0.01
ATOM   1921  CB  ARG   238      14.272  56.369  89.424  1.00  0.01
ATOM   1922  CG  ARG   238      14.723  56.391  90.885  1.00  0.01
ATOM   1923  CD  ARG   238      16.148  56.906  91.077  1.00  0.01
ATOM   1924  NE  ARG   238      17.057  55.875  90.509  1.00  0.01
ATOM   1925  CZ  ARG   238      18.405  56.046  90.602  1.00  0.01
ATOM   1926  NH1 ARG   238      18.911  57.190  91.150  1.00  0.01
ATOM   1927  NH2 ARG   238      19.253  55.071  90.158  1.00  0.01
ATOM   1928  C   ARG   238      11.898  56.144  90.028  1.00  0.01
ATOM   1929  O   ARG   238      11.685  55.644  91.119  1.00  0.01
ATOM   1930  N   ASN   239      11.194  57.211  89.590  1.00  0.01
ATOM   1931  CA  ASN   239      10.170  57.792  90.443  1.00  0.01
ATOM   1932  CB  ASN   239       9.562  59.083  89.866  1.00  0.01
ATOM   1933  CG  ASN   239       8.682  59.717  90.935  1.00  0.01
ATOM   1934  OD1 ASN   239       7.480  59.880  90.731  1.00  0.01
ATOM   1935  ND2 ASN   239       9.282  60.080  92.102  1.00  0.01
ATOM   1936  C   ASN   239       9.058  56.815  90.649  1.00  0.01
ATOM   1937  O   ASN   239       8.481  56.748  91.730  1.00  0.01
ATOM   1938  N   VAL   240       8.691  56.055  89.602  1.00  0.02
ATOM   1939  CA  VAL   240       7.612  55.128  89.779  1.00  0.02
ATOM   1940  CB  VAL   240       7.141  54.478  88.505  1.00  0.02
ATOM   1941  CG1 VAL   240       6.474  55.563  87.645  1.00  0.02
ATOM   1942  CG2 VAL   240       8.321  53.792  87.803  1.00  0.02
ATOM   1943  C   VAL   240       7.985  54.075  90.786  1.00  0.02
ATOM   1944  O   VAL   240       7.144  53.664  91.587  1.00  0.02
ATOM   1945  N   ASN   241       9.252  53.596  90.782  1.00  0.01
ATOM   1946  CA  ASN   241       9.555  52.542  91.715  1.00  0.01
ATOM   1947  CB  ASN   241      10.737  51.622  91.327  1.00  0.01
ATOM   1948  CG  ASN   241      12.056  52.373  91.376  1.00  0.01
ATOM   1949  OD1 ASN   241      12.315  53.259  90.563  1.00  0.01
ATOM   1950  ND2 ASN   241      12.926  52.002  92.353  1.00  0.01
ATOM   1951  C   ASN   241       9.811  53.079  93.130  1.00  0.01
ATOM   1952  O   ASN   241       9.354  52.437  94.125  1.00  0.01
ATOM   1953  OXT ASN   241      10.479  54.140  93.231  1.00  0.01
TER
END
