
#######################################################
#                                                     #
#                        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_5-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS030_5-D2.T0386_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N     219           -
LGA    -       -      P     220           -
LGA    -       -      E     221           -
LGA    N     219      K     222          4.156
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     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          4.905
LGA    E     221      K     249          0.793
LGA    K     222      E     250          1.529
LGA    I     223      G     251          0.776
LGA    R     224      E     252          0.679
LGA    L     225      T     253          0.856
LGA    L     226      Y     254          1.868
LGA    K     227      T     255          1.563
LGA    E     228      G     256          3.193
LGA    F     229      T     257          2.482
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    M     230      V     270          1.757
LGA    -       -      K     271           -
LGA    H     231      G     272          2.681
LGA    T     232      A     273          1.914
LGA    M     233      Y     274          2.682
LGA    K     234      I     275          1.209
LGA    N     235      I     276          4.375
LGA    T     236      G     277          4.601
LGA    G     237      N     278           #
LGA    R     238      I     279          5.066
LGA    -       -      D     280           -
LGA    N     239      H     281          3.851
LGA    V     240      L     282          3.913
LGA    N     241      P     283          3.536
LGA    D     242      P     284          1.940
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    -       -      T     299           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   24   81    5.0     23    2.97     0.00     18.904     0.748

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.848880 * X  +   0.364536 * Y  +  -0.382774 * Z  +  -5.338943
  Y_new =  -0.522904 * X  +   0.685020 * Y  +  -0.507265 * Z  +  28.830442
  Z_new =   0.077291 * X  +   0.630762 * Y  +   0.772118 * Z  +  70.122734 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.684976   -2.456617  [ DEG:    39.2462   -140.7538 ]
  Theta =  -0.077369   -3.064224  [ DEG:    -4.4329   -175.5671 ]
  Phi   =  -0.552096    2.589496  [ DEG:   -31.6328    148.3672 ]
 
# 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_5-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS030_5-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   23   2.97    0.00  18.904
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS030_5-D2
PFRMAT TS
TARGET T0386
MODEL 5 
PARENT 2g03A        
ATOM   1761  N   ASN   219       9.843  56.235  77.425  1.00  1.00          
ATOM   1762  CA  ASN   219       8.884  55.151  77.586  1.00  1.00          
ATOM   1763  CB  ASN   219       7.896  55.130  76.418  1.00  1.00          
ATOM   1764  CG  ASN   219       7.219  56.490  76.279  1.00  1.00          
ATOM   1765  OD1 ASN   219       6.461  56.714  75.335  1.00  1.00          
ATOM   1766  ND2 ASN   219       7.447  57.416  77.170  1.00  1.00          
ATOM   1767  C   ASN   219       9.589  53.803  77.699  1.00  1.00          
ATOM   1768  O   ASN   219       9.385  53.061  78.659  1.00  1.00          
ATOM   1769  N   PRO   220      10.409  53.482  76.737  1.00  1.00          
ATOM   1770  CA  PRO   220      11.165  52.199  76.716  1.00  1.00          
ATOM   1771  CB  PRO   220      11.690  52.130  75.281  1.00  1.00          
ATOM   1772  CG  PRO   220      11.836  53.557  74.868  1.00  1.00          
ATOM   1773  CD  PRO   220      10.703  54.316  75.559  1.00  1.00          
ATOM   1774  C   PRO   220      12.329  52.211  77.701  1.00  1.00          
ATOM   1775  O   PRO   220      12.848  53.272  78.049  1.00  1.00          
ATOM   1776  N   GLU   221      12.734  51.027  78.146  1.00  1.00          
ATOM   1777  CA  GLU   221      13.837  50.899  79.091  1.00  1.00          
ATOM   1778  CB  GLU   221      14.686  49.671  78.761  1.00  1.00          
ATOM   1779  CG  GLU   221      13.820  48.626  78.056  1.00  1.00          
ATOM   1780  CD  GLU   221      14.206  48.532  76.583  1.00  1.00          
ATOM   1781  OE1 GLU   221      15.176  49.168  76.204  1.00  1.00          
ATOM   1782  OE2 GLU   221      13.527  47.828  75.856  1.00  1.00          
ATOM   1783  C   GLU   221      13.327  50.813  80.526  1.00  1.00          
ATOM   1784  O   GLU   221      14.036  51.160  81.470  1.00  1.00          
ATOM   1785  N   LYS   222      12.091  50.349  80.682  1.00  1.00          
ATOM   1786  CA  LYS   222      11.484  50.216  82.001  1.00  1.00          
ATOM   1787  CB  LYS   222       9.960  50.129  81.883  1.00  1.00          
ATOM   1788  CG  LYS   222       9.315  50.794  83.100  1.00  1.00          
ATOM   1789  CD  LYS   222       7.997  51.449  82.686  1.00  1.00          
ATOM   1790  CE  LYS   222       7.218  51.865  83.935  1.00  1.00          
ATOM   1791  NZ  LYS   222       7.291  53.345  84.097  1.00  1.00          
ATOM   1792  C   LYS   222      12.023  48.993  82.735  1.00  1.00          
ATOM   1793  O   LYS   222      11.992  48.931  83.964  1.00  1.00          
ATOM   1794  N   ILE   223      12.516  48.021  81.974  1.00  1.00          
ATOM   1795  CA  ILE   223      13.062  46.799  82.551  1.00  1.00          
ATOM   1796  CB  ILE   223      12.648  45.583  81.720  1.00  1.00          
ATOM   1797  CG1 ILE   223      12.210  46.040  80.327  1.00  1.00          
ATOM   1798  CG2 ILE   223      13.832  44.622  81.594  1.00  1.00          
ATOM   1799  CD1 ILE   223      10.683  46.063  80.253  1.00  1.00          
ATOM   1800  C   ILE   223      14.583  46.870  82.655  1.00  1.00          
ATOM   1801  O   ILE   223      15.153  46.640  83.720  1.00  1.00          
ATOM   1802  N   ARG   224      15.232  47.189  81.540  1.00  1.00          
ATOM   1803  CA  ARG   224      16.686  47.289  81.503  1.00  1.00          
ATOM   1804  CB  ARG   224      17.326  45.941  81.839  1.00  1.00          
ATOM   1805  CG  ARG   224      18.812  45.977  81.479  1.00  1.00          
ATOM   1806  CD  ARG   224      18.975  45.833  79.964  1.00  1.00          
ATOM   1807  NE  ARG   224      20.353  46.101  79.571  1.00  1.00          
ATOM   1808  CZ  ARG   224      20.769  47.326  79.271  1.00  1.00          
ATOM   1809  NH1 ARG   224      20.068  48.363  79.645  1.00  1.00          
ATOM   1810  NH2 ARG   224      21.877  47.495  78.603  1.00  1.00          
ATOM   1811  C   ARG   224      17.188  48.362  82.465  1.00  1.00          
ATOM   1812  O   ARG   224      16.705  49.494  82.455  1.00  1.00          
ATOM   1813  N   LEU   225      18.161  47.997  83.294  1.00  1.00          
ATOM   1814  CA  LEU   225      18.730  48.927  84.262  1.00  1.00          
ATOM   1815  CB  LEU   225      17.646  49.443  85.210  1.00  1.00          
ATOM   1816  CG  LEU   225      17.843  48.824  86.596  1.00  1.00          
ATOM   1817  CD1 LEU   225      17.803  49.926  87.657  1.00  1.00          
ATOM   1818  CD2 LEU   225      16.726  47.814  86.867  1.00  1.00          
ATOM   1819  C   LEU   225      19.417  50.096  83.565  1.00  1.00          
ATOM   1820  O   LEU   225      18.871  51.198  83.495  1.00  1.00          
ATOM   1821  N   LEU   226      20.619  49.850  83.053  1.00  1.00          
ATOM   1822  CA  LEU   226      21.382  50.882  82.362  1.00  1.00          
ATOM   1823  CB  LEU   226      22.183  50.274  81.208  1.00  1.00          
ATOM   1824  CG  LEU   226      23.537  49.786  81.727  1.00  1.00          
ATOM   1825  CD1 LEU   226      23.445  48.301  82.080  1.00  1.00          
ATOM   1826  CD2 LEU   226      24.601  49.990  80.647  1.00  1.00          
ATOM   1827  C   LEU   226      22.317  51.612  83.320  1.00  1.00          
ATOM   1828  O   LEU   226      22.887  51.006  84.227  1.00  1.00          
ATOM   1829  N   LYS   227      22.468  52.915  83.113  1.00  1.00          
ATOM   1830  CA  LYS   227      23.333  53.730  83.958  1.00  1.00          
ATOM   1831  CB  LYS   227      24.804  53.394  83.702  1.00  1.00          
ATOM   1832  CG  LYS   227      25.329  54.248  82.546  1.00  1.00          
ATOM   1833  CD  LYS   227      26.516  53.541  81.888  1.00  1.00          
ATOM   1834  CE  LYS   227      26.994  52.400  82.788  1.00  1.00          
ATOM   1835  NZ  LYS   227      26.942  51.117  82.033  1.00  1.00          
ATOM   1836  C   LYS   227      23.087  55.217  83.727  1.00  1.00          
ATOM   1837  O   LYS   227      23.051  55.680  82.587  1.00  1.00          
ATOM   1838  N   GLU   228      22.921  55.961  84.815  1.00  1.00          
ATOM   1839  CA  GLU   228      22.678  57.397  84.733  1.00  1.00          
ATOM   1840  CB  GLU   228      22.440  57.981  86.128  1.00  1.00          
ATOM   1841  CG  GLU   228      23.783  58.212  86.822  1.00  1.00          
ATOM   1842  CD  GLU   228      23.968  57.208  87.954  1.00  1.00          
ATOM   1843  OE1 GLU   228      23.372  57.407  88.999  1.00  1.00          
ATOM   1844  OE2 GLU   228      24.704  56.255  87.760  1.00  1.00          
ATOM   1845  C   GLU   228      23.841  58.114  84.057  1.00  1.00          
ATOM   1846  O   GLU   228      24.771  57.478  83.560  1.00  1.00          
ATOM   1847  N   PHE   229      23.784  59.441  84.042  1.00  1.00          
ATOM   1848  CA  PHE   229      24.831  60.247  83.427  1.00  1.00          
ATOM   1849  CB  PHE   229      24.583  61.735  83.683  1.00  1.00          
ATOM   1850  CG  PHE   229      24.332  61.959  85.154  1.00  1.00          
ATOM   1851  CD1 PHE   229      24.734  60.995  86.086  1.00  1.00          
ATOM   1852  CD2 PHE   229      23.698  63.129  85.586  1.00  1.00          
ATOM   1853  CE1 PHE   229      24.501  61.203  87.452  1.00  1.00          
ATOM   1854  CE2 PHE   229      23.465  63.337  86.951  1.00  1.00          
ATOM   1855  CZ  PHE   229      23.867  62.374  87.883  1.00  1.00          
ATOM   1856  C   PHE   229      24.922  59.981  81.928  1.00  1.00          
ATOM   1857  O   PHE   229      24.089  60.449  81.152  1.00  1.00          
ATOM   1858  N   MET   230      25.941  59.227  81.527  1.00  1.00          
ATOM   1859  CA  MET   230      26.143  58.896  80.121  1.00  1.00          
ATOM   1860  CB  MET   230      27.187  57.788  79.976  1.00  1.00          
ATOM   1861  CG  MET   230      27.159  57.244  78.545  1.00  1.00          
ATOM   1862  SD  MET   230      27.810  55.555  78.528  1.00  1.00          
ATOM   1863  CE  MET   230      29.418  55.924  79.274  1.00  1.00          
ATOM   1864  C   MET   230      26.569  60.125  79.322  1.00  1.00          
ATOM   1865  O   MET   230      27.681  60.629  79.486  1.00  1.00          
ATOM   1866  N   HIS   231      25.678  60.601  78.459  1.00  1.00          
ATOM   1867  CA  HIS   231      25.959  61.769  77.634  1.00  1.00          
ATOM   1868  CB  HIS   231      27.144  61.498  76.705  1.00  1.00          
ATOM   1869  CG  HIS   231      26.842  60.301  75.845  1.00  1.00          
ATOM   1870  ND1 HIS   231      27.613  59.151  75.882  1.00  1.00          
ATOM   1871  CD2 HIS   231      25.857  60.062  74.917  1.00  1.00          
ATOM   1872  CE1 HIS   231      27.085  58.280  75.004  1.00  1.00          
ATOM   1873  NE2 HIS   231      26.013  58.785  74.388  1.00  1.00          
ATOM   1874  C   HIS   231      24.736  62.176  76.818  1.00  1.00          
ATOM   1875  O   HIS   231      24.565  63.348  76.482  1.00  1.00          
ATOM   1876  N   THR   232      23.890  61.201  76.505  1.00  1.00          
ATOM   1877  CA  THR   232      22.682  61.455  75.729  1.00  1.00          
ATOM   1878  CB  THR   232      23.038  61.821  74.287  1.00  1.00          
ATOM   1879  OG1 THR   232      23.443  63.181  74.229  1.00  1.00          
ATOM   1880  CG2 THR   232      21.817  61.614  73.390  1.00  1.00          
ATOM   1881  C   THR   232      21.750  60.247  75.747  1.00  1.00          
ATOM   1882  O   THR   232      22.178  59.126  76.020  1.00  1.00          
ATOM   1883  N   MET   233      20.476  60.484  75.458  1.00  1.00          
ATOM   1884  CA  MET   233      19.482  59.418  75.442  1.00  1.00          
ATOM   1885  CB  MET   233      20.033  58.184  74.722  1.00  1.00          
ATOM   1886  CG  MET   233      18.887  57.440  74.034  1.00  1.00          
ATOM   1887  SD  MET   233      19.271  57.229  72.277  1.00  1.00          
ATOM   1888  CE  MET   233      18.067  55.921  71.938  1.00  1.00          
ATOM   1889  C   MET   233      19.048  59.048  76.856  1.00  1.00          
ATOM   1890  O   MET   233      19.621  58.155  77.478  1.00  1.00          
ATOM   1891  N   LYS   234      18.032  59.742  77.357  1.00  1.00          
ATOM   1892  CA  LYS   234      17.518  59.489  78.698  1.00  1.00          
ATOM   1893  CB  LYS   234      17.185  58.007  78.874  1.00  1.00          
ATOM   1894  CG  LYS   234      18.153  57.381  79.879  1.00  1.00          
ATOM   1895  CD  LYS   234      17.363  56.600  80.931  1.00  1.00          
ATOM   1896  CE  LYS   234      18.334  55.895  81.881  1.00  1.00          
ATOM   1897  NZ  LYS   234      18.328  56.587  83.201  1.00  1.00          
ATOM   1898  C   LYS   234      18.515  59.930  79.759  1.00  1.00          
ATOM   1899  O   LYS   234      19.685  59.548  79.710  1.00  1.00          
ATOM   1900  N   ASN   235      18.064  60.736  80.722  1.00  1.00          
ATOM   1901  CA  ASN   235      18.981  61.184  81.758  1.00  1.00          
ATOM   1902  CB  ASN   235      19.765  62.437  81.352  1.00  1.00          
ATOM   1903  CG  ASN   235      21.166  62.050  80.891  1.00  1.00          
ATOM   1904  OD1 ASN   235      21.748  61.094  81.405  1.00  1.00          
ATOM   1905  ND2 ASN   235      21.746  62.737  79.945  1.00  1.00          
ATOM   1906  C   ASN   235      18.409  61.308  83.182  1.00  1.00          
ATOM   1907  O   ASN   235      19.081  61.854  84.047  1.00  1.00          
ATOM   1908  N   THR   236      17.208  60.793  83.461  1.00  1.00          
ATOM   1909  CA  THR   236      16.687  60.876  84.839  1.00  1.00          
ATOM   1910  CB  THR   236      15.426  61.714  84.998  1.00  1.00          
ATOM   1911  OG1 THR   236      14.410  61.286  84.105  1.00  1.00          
ATOM   1912  CG2 THR   236      15.767  63.190  84.793  1.00  1.00          
ATOM   1913  C   THR   236      16.528  59.518  85.501  1.00  1.00          
ATOM   1914  O   THR   236      16.919  58.507  84.944  1.00  1.00          
ATOM   1915  N   GLY   237      15.956  59.506  86.703  1.00  1.00          
ATOM   1916  CA  GLY   237      15.766  58.258  87.441  1.00  1.00          
ATOM   1917  C   GLY   237      14.308  58.007  87.823  1.00  1.00          
ATOM   1918  O   GLY   237      13.496  58.918  87.822  1.00  1.00          
ATOM   1919  N   ARG   238      13.986  56.756  88.150  1.00  1.00          
ATOM   1920  CA  ARG   238      12.621  56.391  88.528  1.00  1.00          
ATOM   1921  CB  ARG   238      12.163  55.154  87.752  1.00  1.00          
ATOM   1922  CG  ARG   238      13.383  54.426  87.186  1.00  1.00          
ATOM   1923  CD  ARG   238      13.514  53.053  87.851  1.00  1.00          
ATOM   1924  NE  ARG   238      13.362  51.992  86.863  1.00  1.00          
ATOM   1925  CZ  ARG   238      12.668  52.173  85.744  1.00  1.00          
ATOM   1926  NH1 ARG   238      11.378  52.365  85.799  1.00  1.00          
ATOM   1927  NH2 ARG   238      13.276  52.158  84.589  1.00  1.00          
ATOM   1928  C   ARG   238      12.483  56.150  90.032  1.00  1.00          
ATOM   1929  O   ARG   238      11.777  55.234  90.454  1.00  1.00          
ATOM   1930  N   ASN   239      13.158  56.982  90.825  1.00  1.00          
ATOM   1931  CA  ASN   239      13.136  56.898  92.282  1.00  1.00          
ATOM   1932  CB  ASN   239      12.882  55.467  92.764  1.00  1.00          
ATOM   1933  CG  ASN   239      12.981  55.401  94.285  1.00  1.00          
ATOM   1934  OD1 ASN   239      12.582  56.340  94.974  1.00  1.00          
ATOM   1935  ND2 ASN   239      13.491  54.342  94.852  1.00  1.00          
ATOM   1936  C   ASN   239      12.119  57.858  92.889  1.00  1.00          
ATOM   1937  O   ASN   239      12.453  58.640  93.777  1.00  1.00          
ATOM   1938  N   VAL   240      10.877  57.792  92.414  1.00  1.00          
ATOM   1939  CA  VAL   240       9.821  58.655  92.932  1.00  1.00          
ATOM   1940  CB  VAL   240       9.867  60.060  92.331  1.00  1.00          
ATOM   1941  CG1 VAL   240      11.314  60.482  92.072  1.00  1.00          
ATOM   1942  CG2 VAL   240       9.056  60.095  91.035  1.00  1.00          
ATOM   1943  C   VAL   240       9.839  58.728  94.459  1.00  1.00          
ATOM   1944  O   VAL   240       9.295  59.656  95.048  1.00  1.00          
ATOM   1945  N   ASN   241      10.464  57.741  95.096  1.00  1.00          
ATOM   1946  CA  ASN   241      10.556  57.675  96.559  1.00  1.00          
ATOM   1947  CB  ASN   241       9.280  58.199  97.237  1.00  1.00          
ATOM   1948  CG  ASN   241       9.428  59.664  97.650  1.00  1.00          
ATOM   1949  OD1 ASN   241      10.295  60.003  98.457  1.00  1.00          
ATOM   1950  ND2 ASN   241       8.614  60.558  97.156  1.00  1.00          
ATOM   1951  C   ASN   241      11.797  58.383  97.103  1.00  1.00          
ATOM   1952  O   ASN   241      12.257  58.073  98.204  1.00  1.00          
ATOM   1953  N   ASP   242      12.331  59.330  96.331  1.00  1.00          
ATOM   1954  CA  ASP   242      13.523  60.091  96.720  1.00  1.00          
ATOM   1955  CB  ASP   242      14.466  59.253  97.587  1.00  1.00          
ATOM   1956  CG  ASP   242      15.901  59.743  97.428  1.00  1.00          
ATOM   1957  OD1 ASP   242      16.110  60.654  96.645  1.00  1.00          
ATOM   1958  OD2 ASP   242      16.768  59.203  98.095  1.00  1.00          
ATOM   1959  C   ASP   242      13.169  61.401  97.423  1.00  1.00          
ATOM   1960  O   ASP   242      12.270  62.123  96.992  1.00  1.00          
TER
END
