
#######################################################
#                                                     #
#                        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_1_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS338_1_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          2.302
LGA    P     220      E     221          3.007
LGA    -       -      K     222           -
LGA    E     221      I     223          1.956
LGA    -       -      R     224           -
LGA    K     222      L     225          2.065
LGA    -       -      L     226           -
LGA    -       -      K     227           -
LGA    I     223      E     228          3.264
LGA    R     224      F     229           -
LGA    L     225      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          4.933
LGA    K     227      G     265          2.320
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          1.821
LGA    M     230      I     279          1.821
LGA    H     231      D     280          2.113
LGA    T     232      H     281          1.408
LGA    M     233      L     282          0.664
LGA    K     234      P     283          3.567
LGA    N     235      P     284          3.290
LGA    T     236      -       -           -
LGA    G     237      E     285          2.236
LGA    R     238      Q     286          0.668
LGA    N     239      L     287          2.453
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    2.56     0.00     14.969     0.639

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.913990 * X  +   0.405707 * Y  +  -0.004828 * Z  +   7.615127
  Y_new =  -0.263992 * X  +   0.585610 * Y  +  -0.766400 * Z  +  24.187483
  Z_new =  -0.308107 * X  +   0.701757 * Y  +   0.642345 * Z  +  44.072788 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.829571   -2.312022  [ DEG:    47.5309   -132.4691 ]
  Theta =   0.313203    2.828390  [ DEG:    17.9452    162.0548 ]
  Phi   =  -0.281182    2.860410  [ DEG:   -16.1105    163.8895 ]
 
# 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_1_1-D2                             
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS338_1_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   2.56    0.00  14.969
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS338_1_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0386
PARENT 2g03_A 2f6s_A
ATOM   1761  N   ASN   219      -0.540  59.482  79.184  1.00  0.02
ATOM   1762  CA  ASN   219      -0.014  59.338  77.848  1.00  0.02
ATOM   1763  CB  ASN   219      -0.449  60.496  76.933  1.00  0.02
ATOM   1764  CG  ASN   219      -1.972  60.459  76.846  1.00  0.02
ATOM   1765  OD1 ASN   219      -2.620  59.577  77.409  1.00  0.02
ATOM   1766  ND2 ASN   219      -2.565  61.445  76.121  1.00  0.02
ATOM   1767  C   ASN   219       1.501  59.287  77.865  1.00  0.02
ATOM   1768  O   ASN   219       2.151  59.400  78.902  1.00  0.02
ATOM   1769  N   PRO   220       2.032  59.045  76.686  1.00  0.04
ATOM   1770  CA  PRO   220       3.455  58.862  76.436  1.00  0.04
ATOM   1771  CD  PRO   220       1.231  58.275  75.747  1.00  0.04
ATOM   1772  CB  PRO   220       3.555  58.138  75.094  1.00  0.04
ATOM   1773  CG  PRO   220       2.217  57.400  74.963  1.00  0.04
ATOM   1774  C   PRO   220       4.391  60.038  76.480  1.00  0.04
ATOM   1775  O   PRO   220       5.585  59.798  76.300  1.00  0.04
ATOM   1776  N   GLU   221       3.920  61.286  76.688  1.00  0.01
ATOM   1777  CA  GLU   221       4.780  62.442  76.583  1.00  0.01
ATOM   1778  CB  GLU   221       4.117  63.759  77.025  1.00  0.01
ATOM   1779  CG  GLU   221       4.941  64.999  76.660  1.00  0.01
ATOM   1780  CD  GLU   221       4.195  66.232  77.155  1.00  0.01
ATOM   1781  OE1 GLU   221       3.373  66.079  78.097  1.00  0.01
ATOM   1782  OE2 GLU   221       4.443  67.342  76.612  1.00  0.01
ATOM   1783  C   GLU   221       6.035  62.261  77.388  1.00  0.01
ATOM   1784  O   GLU   221       6.024  61.712  78.489  1.00  0.01
ATOM   1785  N   LYS   222       7.168  62.717  76.807  1.00  0.01
ATOM   1786  CA  LYS   222       8.484  62.581  77.373  1.00  0.01
ATOM   1787  CB  LYS   222       9.611  63.072  76.441  1.00  0.01
ATOM   1788  CG  LYS   222       9.504  64.548  76.047  1.00  0.01
ATOM   1789  CD  LYS   222       8.301  64.863  75.153  1.00  0.01
ATOM   1790  CE  LYS   222       8.651  65.027  73.669  1.00  0.01
ATOM   1791  NZ  LYS   222       9.309  66.335  73.443  1.00  0.01
ATOM   1792  C   LYS   222       8.588  63.350  78.654  1.00  0.01
ATOM   1793  O   LYS   222       9.233  62.894  79.596  1.00  0.01
ATOM   1794  N   ILE   223       7.968  64.544  78.717  1.00  0.01
ATOM   1795  CA  ILE   223       8.043  65.367  79.893  1.00  0.01
ATOM   1796  CB  ILE   223       7.364  66.689  79.712  1.00  0.01
ATOM   1797  CG2 ILE   223       7.282  67.370  81.088  1.00  0.01
ATOM   1798  CG1 ILE   223       8.104  67.511  78.644  1.00  0.01
ATOM   1799  CD1 ILE   223       7.320  68.723  78.148  1.00  0.01
ATOM   1800  C   ILE   223       7.383  64.651  81.026  1.00  0.01
ATOM   1801  O   ILE   223       7.889  64.635  82.148  1.00  0.01
ATOM   1802  N   ARG   224       6.225  64.027  80.759  1.00  0.01
ATOM   1803  CA  ARG   224       5.545  63.306  81.789  1.00  0.01
ATOM   1804  CB  ARG   224       4.212  62.695  81.311  1.00  0.01
ATOM   1805  CG  ARG   224       3.168  63.736  80.887  1.00  0.01
ATOM   1806  CD  ARG   224       1.843  63.115  80.426  1.00  0.01
ATOM   1807  NE  ARG   224       0.926  64.216  80.011  1.00  0.01
ATOM   1808  CZ  ARG   224      -0.319  63.921  79.534  1.00  0.01
ATOM   1809  NH1 ARG   224      -0.727  62.619  79.459  1.00  0.01
ATOM   1810  NH2 ARG   224      -1.159  64.923  79.140  1.00  0.01
ATOM   1811  C   ARG   224       6.468  62.202  82.188  1.00  0.01
ATOM   1812  O   ARG   224       6.533  61.813  83.353  1.00  0.01
ATOM   1813  N   LEU   225       7.209  61.670  81.204  1.00  0.01
ATOM   1814  CA  LEU   225       8.127  60.597  81.429  1.00  0.01
ATOM   1815  CB  LEU   225       8.765  60.128  80.107  1.00  0.01
ATOM   1816  CG  LEU   225       9.800  58.995  80.235  1.00  0.01
ATOM   1817  CD1 LEU   225      11.151  59.500  80.778  1.00  0.01
ATOM   1818  CD2 LEU   225       9.231  57.815  81.042  1.00  0.01
ATOM   1819  C   LEU   225       9.218  61.021  82.370  1.00  0.01
ATOM   1820  O   LEU   225       9.543  60.298  83.309  1.00  0.01
ATOM   1821  N   LEU   226       9.829  62.199  82.154  1.00  0.01
ATOM   1822  CA  LEU   226      10.924  62.568  83.006  1.00  0.01
ATOM   1823  CB  LEU   226      11.715  63.797  82.519  1.00  0.01
ATOM   1824  CG  LEU   226      12.499  63.511  81.223  1.00  0.01
ATOM   1825  CD1 LEU   226      13.420  64.680  80.834  1.00  0.01
ATOM   1826  CD2 LEU   226      13.239  62.164  81.312  1.00  0.01
ATOM   1827  C   LEU   226      10.415  62.806  84.388  1.00  0.01
ATOM   1828  O   LEU   226      11.059  62.433  85.366  1.00  0.01
ATOM   1829  N   LYS   227       9.226  63.427  84.502  1.00  0.01
ATOM   1830  CA  LYS   227       8.663  63.713  85.790  1.00  0.01
ATOM   1831  CB  LYS   227       7.269  64.364  85.709  1.00  0.01
ATOM   1832  CG  LYS   227       7.238  65.778  85.126  1.00  0.01
ATOM   1833  CD  LYS   227       7.946  66.827  85.984  1.00  0.01
ATOM   1834  CE  LYS   227       7.863  68.240  85.401  1.00  0.01
ATOM   1835  NZ  LYS   227       8.427  69.212  86.363  1.00  0.01
ATOM   1836  C   LYS   227       8.451  62.413  86.496  1.00  0.01
ATOM   1837  O   LYS   227       8.731  62.290  87.686  1.00  0.01
ATOM   1838  N   GLU   228       7.932  61.405  85.772  1.00  0.01
ATOM   1839  CA  GLU   228       7.645  60.143  86.383  1.00  0.01
ATOM   1840  CB  GLU   228       6.786  59.215  85.502  1.00  0.01
ATOM   1841  CG  GLU   228       7.393  58.835  84.155  1.00  0.01
ATOM   1842  CD  GLU   228       6.274  58.245  83.317  1.00  0.01
ATOM   1843  OE1 GLU   228       5.110  58.249  83.800  1.00  0.01
ATOM   1844  OE2 GLU   228       6.563  57.791  82.179  1.00  0.01
ATOM   1845  C   GLU   228       8.902  59.450  86.805  1.00  0.01
ATOM   1846  O   GLU   228       8.937  58.833  87.866  1.00  0.01
ATOM   1847  N   PHE   229       9.980  59.530  86.005  1.00  0.01
ATOM   1848  CA  PHE   229      11.184  58.849  86.395  1.00  0.01
ATOM   1849  CB  PHE   229      12.292  58.832  85.333  1.00  0.01
ATOM   1850  CG  PHE   229      13.399  58.069  85.972  1.00  0.01
ATOM   1851  CD1 PHE   229      13.314  56.701  86.094  1.00  0.01
ATOM   1852  CD2 PHE   229      14.515  58.713  86.452  1.00  0.01
ATOM   1853  CE1 PHE   229      14.328  55.988  86.686  1.00  0.01
ATOM   1854  CE2 PHE   229      15.534  58.005  87.043  1.00  0.01
ATOM   1855  CZ  PHE   229      15.442  56.640  87.164  1.00  0.01
ATOM   1856  C   PHE   229      11.745  59.489  87.624  1.00  0.01
ATOM   1857  O   PHE   229      12.287  58.809  88.494  1.00  0.01
ATOM   1858  N   MET   230      11.646  60.827  87.721  1.00  0.01
ATOM   1859  CA  MET   230      12.188  61.529  88.849  1.00  0.01
ATOM   1860  CB  MET   230      11.974  63.054  88.750  1.00  0.01
ATOM   1861  CG  MET   230      12.693  63.881  89.817  1.00  0.01
ATOM   1862  SD  MET   230      12.446  65.676  89.683  1.00  0.01
ATOM   1863  CE  MET   230      13.331  65.841  88.103  1.00  0.01
ATOM   1864  C   MET   230      11.484  61.031  90.072  1.00  0.01
ATOM   1865  O   MET   230      12.103  60.815  91.114  1.00  0.01
ATOM   1866  N   HIS   231      10.158  60.827  89.975  1.00  0.01
ATOM   1867  CA  HIS   231       9.400  60.356  91.098  1.00  0.01
ATOM   1868  ND1 HIS   231       7.274  60.522  93.303  1.00  0.01
ATOM   1869  CG  HIS   231       7.209  59.821  92.121  1.00  0.01
ATOM   1870  CB  HIS   231       7.885  60.285  90.868  1.00  0.01
ATOM   1871  NE2 HIS   231       6.091  58.686  93.718  1.00  0.01
ATOM   1872  CD2 HIS   231       6.481  58.701  92.391  1.00  0.01
ATOM   1873  CE1 HIS   231       6.590  59.799  94.225  1.00  0.01
ATOM   1874  C   HIS   231       9.823  58.968  91.452  1.00  0.01
ATOM   1875  O   HIS   231       9.912  58.622  92.628  1.00  0.01
ATOM   1876  N   THR   232      10.094  58.134  90.432  1.00  0.01
ATOM   1877  CA  THR   232      10.415  56.757  90.660  1.00  0.01
ATOM   1878  CB  THR   232      10.695  56.029  89.380  1.00  0.01
ATOM   1879  OG1 THR   232       9.583  56.141  88.503  1.00  0.01
ATOM   1880  CG2 THR   232      10.958  54.550  89.704  1.00  0.01
ATOM   1881  C   THR   232      11.648  56.695  91.508  1.00  0.01
ATOM   1882  O   THR   232      11.722  55.898  92.441  1.00  0.01
ATOM   1883  N   MET   233      12.649  57.541  91.199  1.00  0.01
ATOM   1884  CA  MET   233      13.881  57.590  91.933  1.00  0.01
ATOM   1885  CB  MET   233      14.924  58.528  91.301  1.00  0.01
ATOM   1886  CG  MET   233      16.273  58.508  92.025  1.00  0.01
ATOM   1887  SD  MET   233      17.591  59.455  91.204  1.00  0.01
ATOM   1888  CE  MET   233      17.890  58.230  89.896  1.00  0.01
ATOM   1889  C   MET   233      13.606  58.089  93.317  1.00  0.01
ATOM   1890  O   MET   233      14.272  57.695  94.271  1.00  0.01
ATOM   1891  N   LYS   234      12.632  59.004  93.464  1.00  0.01
ATOM   1892  CA  LYS   234      12.341  59.564  94.753  1.00  0.01
ATOM   1893  CB  LYS   234      11.258  60.655  94.708  1.00  0.01
ATOM   1894  CG  LYS   234      11.733  61.943  94.035  1.00  0.01
ATOM   1895  CD  LYS   234      10.603  62.919  93.712  1.00  0.01
ATOM   1896  CE  LYS   234      11.107  64.258  93.175  1.00  0.01
ATOM   1897  NZ  LYS   234       9.969  65.168  92.935  1.00  0.01
ATOM   1898  C   LYS   234      11.867  58.485  95.669  1.00  0.01
ATOM   1899  O   LYS   234      12.188  58.493  96.857  1.00  0.01
ATOM   1900  N   ASN   235      11.099  57.517  95.138  1.00  0.01
ATOM   1901  CA  ASN   235      10.539  56.507  95.983  1.00  0.01
ATOM   1902  CB  ASN   235       9.691  55.481  95.214  1.00  0.01
ATOM   1903  CG  ASN   235       8.881  54.667  96.219  1.00  0.01
ATOM   1904  OD1 ASN   235       9.254  54.538  97.383  1.00  0.01
ATOM   1905  ND2 ASN   235       7.736  54.097  95.758  1.00  0.01
ATOM   1906  C   ASN   235      11.651  55.776  96.663  1.00  0.01
ATOM   1907  O   ASN   235      11.561  55.489  97.856  1.00  0.01
ATOM   1908  N   THR   236      12.728  55.444  95.923  1.00  0.01
ATOM   1909  CA  THR   236      13.807  54.730  96.539  1.00  0.01
ATOM   1910  CB  THR   236      14.857  54.246  95.567  1.00  0.01
ATOM   1911  OG1 THR   236      15.745  53.352  96.220  1.00  0.01
ATOM   1912  CG2 THR   236      15.644  55.432  94.981  1.00  0.01
ATOM   1913  C   THR   236      14.435  55.611  97.564  1.00  0.01
ATOM   1914  O   THR   236      14.678  55.183  98.689  1.00  0.01
ATOM   1915  N   GLY   237      14.705  56.880  97.213  1.00  0.00
ATOM   1916  CA  GLY   237      15.249  57.755  98.203  1.00  0.00
ATOM   1917  C   GLY   237      16.209  58.702  97.565  1.00  0.00
ATOM   1918  O   GLY   237      17.395  58.697  97.890  1.00  0.00
ATOM   1919  N   ARG   238      15.727  59.543  96.633  1.00  0.01
ATOM   1920  CA  ARG   238      16.583  60.574  96.129  1.00  0.01
ATOM   1921  CB  ARG   238      17.074  60.399  94.688  1.00  0.01
ATOM   1922  CG  ARG   238      18.096  61.476  94.311  1.00  0.01
ATOM   1923  CD  ARG   238      17.846  62.049  92.925  1.00  0.01
ATOM   1924  NE  ARG   238      16.370  62.200  92.827  1.00  0.01
ATOM   1925  CZ  ARG   238      15.779  62.331  91.609  1.00  0.01
ATOM   1926  NH1 ARG   238      16.555  62.430  90.492  1.00  0.01
ATOM   1927  NH2 ARG   238      14.419  62.360  91.513  1.00  0.01
ATOM   1928  C   ARG   238      15.746  61.807  96.169  1.00  0.01
ATOM   1929  O   ARG   238      14.577  61.772  95.791  1.00  0.01
ATOM   1930  N   ASN   239      16.327  62.938  96.615  1.00  0.01
ATOM   1931  CA  ASN   239      15.519  64.108  96.810  1.00  0.01
ATOM   1932  CB  ASN   239      15.740  64.807  98.162  1.00  0.01
ATOM   1933  CG  ASN   239      14.993  64.038  99.238  1.00  0.01
ATOM   1934  OD1 ASN   239      13.770  63.919  99.187  1.00  0.01
ATOM   1935  ND2 ASN   239      15.745  63.511 100.242  1.00  0.01
ATOM   1936  C   ASN   239      15.801  65.138  95.773  1.00  0.01
ATOM   1937  O   ASN   239      16.777  65.063  95.028  1.00  0.01
TER
END
