
#######################################################
#                                                     #
#                        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   21 (  177),  selected   21 , name T0386TS338_3_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS338_3_1-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    N     219      P     220          1.627
LGA    P     220      E     221          3.485
LGA    -       -      K     222           -
LGA    E     221      I     223          1.031
LGA    -       -      R     224           -
LGA    -       -      L     225           -
LGA    K     222      L     226          2.045
LGA    I     223      K     227          3.987
LGA    R     224      E     228           #
LGA    L     225      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    -       -      A     248           -
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    L     226      E     264          5.187
LGA    K     227      G     265          2.306
LGA    E     228      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    F     229      N     278          1.576
LGA    M     230      I     279          1.820
LGA    H     231      D     280          2.447
LGA    T     232      H     281          1.704
LGA    M     233      L     282          0.955
LGA    K     234      -       -           -
LGA    N     235      P     283          3.480
LGA    T     236      P     284          4.122
LGA    G     237      E     285          1.723
LGA    R     238      Q     286          1.490
LGA    N     239      L     287          2.299
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)   21   81    5.0     17    2.69     0.00     14.376     0.609

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.936119 * X  +   0.351641 * Y  +   0.005383 * Z  +  10.749698
  Y_new =  -0.232745 * X  +   0.630931 * Y  +  -0.740105 * Z  +  22.709440
  Z_new =  -0.263648 * X  +   0.691574 * Y  +   0.672469 * Z  +  45.718945 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.799403   -2.342189  [ DEG:    45.8024   -134.1976 ]
  Theta =   0.266802    2.874791  [ DEG:    15.2866    164.7134 ]
  Phi   =  -0.243686    2.897906  [ DEG:   -13.9622    166.0378 ]
 
# 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_3_1-D2                             
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS338_3_1-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   21   81   5.0   17   2.69    0.00  14.376
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS338_3_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0386
PARENT 2g03_A 2f6s_A
ATOM   1761  N   ASN   219      -0.268  59.216  78.579  1.00  0.02
ATOM   1762  CA  ASN   219       0.312  59.038  77.267  1.00  0.02
ATOM   1763  CB  ASN   219      -0.058  60.171  76.291  1.00  0.02
ATOM   1764  CG  ASN   219      -1.565  60.148  76.077  1.00  0.02
ATOM   1765  OD1 ASN   219      -2.134  59.233  75.484  1.00  0.02
ATOM   1766  ND2 ASN   219      -2.241  61.210  76.595  1.00  0.02
ATOM   1767  C   ASN   219       1.825  59.005  77.343  1.00  0.02
ATOM   1768  O   ASN   219       2.445  59.235  78.379  1.00  0.02
ATOM   1769  N   PRO   220       2.380  58.654  76.202  1.00  0.04
ATOM   1770  CA  PRO   220       3.803  58.453  75.974  1.00  0.04
ATOM   1771  CD  PRO   220       1.582  57.819  75.316  1.00  0.04
ATOM   1772  CB  PRO   220       3.907  57.635  74.689  1.00  0.04
ATOM   1773  CG  PRO   220       2.568  56.888  74.603  1.00  0.04
ATOM   1774  C   PRO   220       4.740  59.627  75.929  1.00  0.04
ATOM   1775  O   PRO   220       5.938  59.375  75.806  1.00  0.04
ATOM   1776  N   GLU   221       4.266  60.887  76.003  1.00  0.01
ATOM   1777  CA  GLU   221       5.137  62.021  75.812  1.00  0.01
ATOM   1778  CB  GLU   221       4.428  63.369  76.043  1.00  0.01
ATOM   1779  CG  GLU   221       5.211  64.573  75.523  1.00  0.01
ATOM   1780  CD  GLU   221       4.252  65.752  75.426  1.00  0.01
ATOM   1781  OE1 GLU   221       3.074  65.600  75.846  1.00  0.01
ATOM   1782  OE2 GLU   221       4.687  66.821  74.919  1.00  0.01
ATOM   1783  C   GLU   221       6.352  61.926  76.696  1.00  0.01
ATOM   1784  O   GLU   221       6.292  61.444  77.826  1.00  0.01
ATOM   1785  N   LYS   222       7.506  62.371  76.146  1.00  0.01
ATOM   1786  CA  LYS   222       8.805  62.319  76.762  1.00  0.01
ATOM   1787  CB  LYS   222       9.913  62.880  75.850  1.00  0.01
ATOM   1788  CG  LYS   222       9.727  64.366  75.531  1.00  0.01
ATOM   1789  CD  LYS   222      10.953  65.042  74.908  1.00  0.01
ATOM   1790  CE  LYS   222      10.938  65.070  73.377  1.00  0.01
ATOM   1791  NZ  LYS   222      12.019  65.952  72.881  1.00  0.01
ATOM   1792  C   LYS   222       8.817  63.144  78.012  1.00  0.01
ATOM   1793  O   LYS   222       9.402  62.738  79.015  1.00  0.01
ATOM   1794  N   ILE   223       8.175  64.329  77.981  1.00  0.01
ATOM   1795  CA  ILE   223       8.166  65.214  79.112  1.00  0.01
ATOM   1796  CB  ILE   223       7.478  66.524  78.800  1.00  0.01
ATOM   1797  CG2 ILE   223       6.020  66.220  78.415  1.00  0.01
ATOM   1798  CG1 ILE   223       7.639  67.561  79.930  1.00  0.01
ATOM   1799  CD1 ILE   223       6.880  67.242  81.220  1.00  0.01
ATOM   1800  C   ILE   223       7.472  64.531  80.247  1.00  0.01
ATOM   1801  O   ILE   223       7.950  64.548  81.382  1.00  0.01
ATOM   1802  N   ARG   224       6.330  63.886  79.965  1.00  0.01
ATOM   1803  CA  ARG   224       5.596  63.227  80.999  1.00  0.01
ATOM   1804  CB  ARG   224       4.335  62.525  80.466  1.00  0.01
ATOM   1805  CG  ARG   224       3.428  61.911  81.536  1.00  0.01
ATOM   1806  CD  ARG   224       2.325  61.035  80.936  1.00  0.01
ATOM   1807  NE  ARG   224       2.542  59.629  81.383  1.00  0.01
ATOM   1808  CZ  ARG   224       3.567  58.882  80.879  1.00  0.01
ATOM   1809  NH1 ARG   224       4.498  59.459  80.064  1.00  0.01
ATOM   1810  NH2 ARG   224       3.668  57.561  81.206  1.00  0.01
ATOM   1811  C   ARG   224       6.489  62.168  81.535  1.00  0.01
ATOM   1812  O   ARG   224       6.550  61.942  82.742  1.00  0.01
ATOM   1813  N   LEU   225       7.218  61.489  80.633  1.00  0.01
ATOM   1814  CA  LEU   225       8.029  60.401  81.071  1.00  0.01
ATOM   1815  CB  LEU   225       8.586  59.527  79.947  1.00  0.01
ATOM   1816  CG  LEU   225       9.177  58.234  80.521  1.00  0.01
ATOM   1817  CD1 LEU   225       8.133  57.486  81.367  1.00  0.01
ATOM   1818  CD2 LEU   225       9.732  57.348  79.402  1.00  0.01
ATOM   1819  C   LEU   225       9.150  60.891  81.931  1.00  0.01
ATOM   1820  O   LEU   225       9.508  60.232  82.904  1.00  0.01
ATOM   1821  N   LEU   226       9.740  62.058  81.601  1.00  0.01
ATOM   1822  CA  LEU   226      10.828  62.570  82.388  1.00  0.01
ATOM   1823  CB  LEU   226      11.354  63.927  81.886  1.00  0.01
ATOM   1824  CG  LEU   226      11.912  63.913  80.452  1.00  0.01
ATOM   1825  CD1 LEU   226      12.502  65.285  80.085  1.00  0.01
ATOM   1826  CD2 LEU   226      12.896  62.755  80.231  1.00  0.01
ATOM   1827  C   LEU   226      10.300  62.823  83.765  1.00  0.01
ATOM   1828  O   LEU   226      10.945  62.491  84.757  1.00  0.01
ATOM   1829  N   LYS   227       9.086  63.406  83.841  1.00  0.01
ATOM   1830  CA  LYS   227       8.447  63.753  85.080  1.00  0.01
ATOM   1831  CB  LYS   227       7.020  64.295  84.860  1.00  0.01
ATOM   1832  CG  LYS   227       6.926  65.643  84.138  1.00  0.01
ATOM   1833  CD  LYS   227       7.482  66.813  84.947  1.00  0.01
ATOM   1834  CE  LYS   227       6.723  67.053  86.253  1.00  0.01
ATOM   1835  NZ  LYS   227       7.333  68.181  86.987  1.00  0.01
ATOM   1836  C   LYS   227       8.279  62.490  85.859  1.00  0.01
ATOM   1837  O   LYS   227       8.525  62.445  87.063  1.00  0.01
ATOM   1838  N   GLU   228       7.851  61.425  85.161  1.00  0.01
ATOM   1839  CA  GLU   228       7.601  60.142  85.743  1.00  0.01
ATOM   1840  CB  GLU   228       7.119  59.130  84.692  1.00  0.01
ATOM   1841  CG  GLU   228       7.217  57.674  85.147  1.00  0.01
ATOM   1842  CD  GLU   228       6.636  56.806  84.039  1.00  0.01
ATOM   1843  OE1 GLU   228       5.712  57.301  83.340  1.00  0.01
ATOM   1844  OE2 GLU   228       7.100  55.646  83.872  1.00  0.01
ATOM   1845  C   GLU   228       8.854  59.568  86.311  1.00  0.01
ATOM   1846  O   GLU   228       8.868  59.096  87.446  1.00  0.01
ATOM   1847  N   PHE   229       9.950  59.603  85.534  1.00  0.01
ATOM   1848  CA  PHE   229      11.175  59.001  85.966  1.00  0.01
ATOM   1849  CB  PHE   229      12.284  59.023  84.901  1.00  0.01
ATOM   1850  CG  PHE   229      13.510  58.519  85.581  1.00  0.01
ATOM   1851  CD1 PHE   229      13.647  57.184  85.887  1.00  0.01
ATOM   1852  CD2 PHE   229      14.531  59.382  85.914  1.00  0.01
ATOM   1853  CE1 PHE   229      14.777  56.722  86.519  1.00  0.01
ATOM   1854  CE2 PHE   229      15.663  58.923  86.545  1.00  0.01
ATOM   1855  CZ  PHE   229      15.788  57.590  86.853  1.00  0.01
ATOM   1856  C   PHE   229      11.690  59.706  87.173  1.00  0.01
ATOM   1857  O   PHE   229      12.179  59.071  88.105  1.00  0.01
ATOM   1858  N   MET   230      11.606  61.047  87.186  1.00  0.01
ATOM   1859  CA  MET   230      12.128  61.779  88.298  1.00  0.01
ATOM   1860  CB  MET   230      12.115  63.305  88.074  1.00  0.01
ATOM   1861  CG  MET   230      10.737  63.926  87.845  1.00  0.01
ATOM   1862  SD  MET   230      10.806  65.626  87.200  1.00  0.01
ATOM   1863  CE  MET   230      11.701  66.314  88.624  1.00  0.01
ATOM   1864  C   MET   230      11.366  61.415  89.535  1.00  0.01
ATOM   1865  O   MET   230      11.958  61.264  90.603  1.00  0.01
ATOM   1866  N   HIS   231      10.033  61.258  89.439  1.00  0.01
ATOM   1867  CA  HIS   231       9.292  60.889  90.612  1.00  0.01
ATOM   1868  ND1 HIS   231       6.975  63.393  89.809  1.00  0.01
ATOM   1869  CG  HIS   231       7.401  62.498  90.765  1.00  0.01
ATOM   1870  CB  HIS   231       7.770  61.068  90.501  1.00  0.01
ATOM   1871  NE2 HIS   231       7.065  64.510  91.731  1.00  0.01
ATOM   1872  CD2 HIS   231       7.449  63.196  91.932  1.00  0.01
ATOM   1873  CE1 HIS   231       6.789  64.581  90.443  1.00  0.01
ATOM   1874  C   HIS   231       9.614  59.489  91.039  1.00  0.01
ATOM   1875  O   HIS   231       9.696  59.218  92.234  1.00  0.01
ATOM   1876  N   THR   232       9.819  58.558  90.085  1.00  0.01
ATOM   1877  CA  THR   232      10.095  57.196  90.457  1.00  0.01
ATOM   1878  CB  THR   232      10.237  56.273  89.285  1.00  0.01
ATOM   1879  OG1 THR   232      11.343  56.657  88.483  1.00  0.01
ATOM   1880  CG2 THR   232       8.938  56.327  88.463  1.00  0.01
ATOM   1881  C   THR   232      11.370  57.174  91.242  1.00  0.01
ATOM   1882  O   THR   232      11.502  56.430  92.213  1.00  0.01
ATOM   1883  N   MET   233      12.346  57.998  90.826  1.00  0.01
ATOM   1884  CA  MET   233      13.610  58.132  91.491  1.00  0.01
ATOM   1885  CB  MET   233      14.531  59.130  90.771  1.00  0.01
ATOM   1886  CG  MET   233      15.889  59.312  91.448  1.00  0.01
ATOM   1887  SD  MET   233      16.986  60.493  90.612  1.00  0.01
ATOM   1888  CE  MET   233      15.936  61.930  90.975  1.00  0.01
ATOM   1889  C   MET   233      13.339  58.699  92.850  1.00  0.01
ATOM   1890  O   MET   233      14.002  58.363  93.828  1.00  0.01
ATOM   1891  N   LYS   234      12.340  59.596  92.933  1.00  0.01
ATOM   1892  CA  LYS   234      11.971  60.279  94.140  1.00  0.01
ATOM   1893  CB  LYS   234      10.806  61.258  93.886  1.00  0.01
ATOM   1894  CG  LYS   234      10.382  62.120  95.076  1.00  0.01
ATOM   1895  CD  LYS   234       9.493  63.298  94.656  1.00  0.01
ATOM   1896  CE  LYS   234       8.835  64.037  95.821  1.00  0.01
ATOM   1897  NZ  LYS   234       7.787  63.187  96.430  1.00  0.01
ATOM   1898  C   LYS   234      11.529  59.279  95.164  1.00  0.01
ATOM   1899  O   LYS   234      11.815  59.430  96.350  1.00  0.01
ATOM   1900  N   ASN   235      10.823  58.220  94.733  1.00  0.01
ATOM   1901  CA  ASN   235      10.287  57.263  95.655  1.00  0.01
ATOM   1902  CB  ASN   235       9.466  56.167  94.959  1.00  0.01
ATOM   1903  CG  ASN   235       8.221  56.820  94.371  1.00  0.01
ATOM   1904  OD1 ASN   235       7.923  56.671  93.187  1.00  0.01
ATOM   1905  ND2 ASN   235       7.467  57.564  95.224  1.00  0.01
ATOM   1906  C   ASN   235      11.399  56.602  96.407  1.00  0.01
ATOM   1907  O   ASN   235      11.288  56.378  97.612  1.00  0.01
ATOM   1908  N   THR   236      12.501  56.251  95.716  1.00  0.01
ATOM   1909  CA  THR   236      13.578  55.591  96.391  1.00  0.01
ATOM   1910  CB  THR   236      14.642  55.054  95.474  1.00  0.01
ATOM   1911  OG1 THR   236      15.553  54.256  96.215  1.00  0.01
ATOM   1912  CG2 THR   236      15.388  56.211  94.795  1.00  0.01
ATOM   1913  C   THR   236      14.193  56.534  97.370  1.00  0.01
ATOM   1914  O   THR   236      14.543  56.138  98.480  1.00  0.01
ATOM   1915  N   GLY   237      14.365  57.813  96.991  1.00  0.01
ATOM   1916  CA  GLY   237      14.873  58.716  97.977  1.00  0.01
ATOM   1917  C   GLY   237      15.760  59.731  97.336  1.00  0.01
ATOM   1918  O   GLY   237      16.717  60.191  97.957  1.00  0.01
ATOM   1919  N   ARG   238      15.469  60.132  96.084  1.00  0.01
ATOM   1920  CA  ARG   238      16.304  61.137  95.499  1.00  0.01
ATOM   1921  CB  ARG   238      16.709  60.844  94.044  1.00  0.01
ATOM   1922  CG  ARG   238      17.893  61.693  93.584  1.00  0.01
ATOM   1923  CD  ARG   238      17.509  63.132  93.269  1.00  0.01
ATOM   1924  NE  ARG   238      18.770  63.918  93.203  1.00  0.01
ATOM   1925  CZ  ARG   238      19.302  64.407  94.360  1.00  0.01
ATOM   1926  NH1 ARG   238      18.698  64.131  95.553  1.00  0.01
ATOM   1927  NH2 ARG   238      20.429  65.177  94.329  1.00  0.01
ATOM   1928  C   ARG   238      15.511  62.403  95.523  1.00  0.01
ATOM   1929  O   ARG   238      14.396  62.462  95.008  1.00  0.01
ATOM   1930  N   ASN   239      16.083  63.454  96.137  1.00  0.01
ATOM   1931  CA  ASN   239      15.399  64.702  96.305  1.00  0.01
ATOM   1932  CB  ASN   239      16.076  65.621  97.337  1.00  0.01
ATOM   1933  CG  ASN   239      15.224  66.865  97.549  1.00  0.01
ATOM   1934  OD1 ASN   239      14.018  66.791  97.774  1.00  0.01
ATOM   1935  ND2 ASN   239      15.879  68.056  97.478  1.00  0.01
ATOM   1936  C   ASN   239      15.351  65.425  95.000  1.00  0.01
ATOM   1937  O   ASN   239      16.290  65.389  94.208  1.00  0.01
TER
END
