
#######################################################
#                                                     #
#                        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   25 (  211),  selected   25 , name T0386TS046_3-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS046_3-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          1.782
LGA    P     220      E     221          1.225
LGA    E     221      K     222          0.693
LGA    K     222      I     223          1.664
LGA    I     223      R     224          0.617
LGA    R     224      L     225          1.432
LGA    L     225      L     226          2.322
LGA    L     226      K     227          2.082
LGA    K     227      E     228          3.206
LGA    -       -      F     229           -
LGA    -       -      M     230           -
LGA    E     228      H     231          2.717
LGA    F     229      T     232          3.057
LGA    -       -      M     233           -
LGA    M     230      K     234          1.813
LGA    H     231      N     235          2.421
LGA    T     232      T     236          2.239
LGA    M     233      G     237          3.702
LGA    K     234      R     238          2.534
LGA    N     235      N     239          5.360
LGA    T     236      V     240          2.818
LGA    G     237      N     241          4.389
LGA    R     238      -       -           -
LGA    N     239      -       -           -
LGA    V     240      D     242          3.463
LGA    N     241      R     243          1.476
LGA    D     242      P     244          0.412
LGA    R     243      V     245          5.412
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    -       -      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    -       -      I     279           -
LGA    -       -      D     280           -
LGA    -       -      H     281           -
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    -       -      T     299           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   25   81    5.0     23    2.80    13.04     19.385     0.792

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.146817 * X  +   0.828256 * Y  +  -0.540775 * Z  + -29.350348
  Y_new =  -0.011750 * X  +  -0.548121 * Y  +  -0.836317 * Z  +  90.471741
  Z_new =  -0.989094 * X  +  -0.116432 * Y  +   0.090206 * Z  +  54.682610 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.911643    2.229950  [ DEG:   -52.2333    127.7667 ]
  Theta =   1.422972    1.718621  [ DEG:    81.5303     98.4697 ]
  Phi   =  -3.061733    0.079860  [ DEG:  -175.4244      4.5756 ]
 
# 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: T0386TS046_3-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS046_3-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   25   81   5.0   23   2.80   13.04  19.385
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS046_3-D2
PFRMAT TS
TARGET T0386
MODEL 3
PARENT 2F6S_A
ATOM   1693  N   ASN   219       3.308  58.340  73.807  1.00  8.70
ATOM   1694  CA  ASN   219       2.530  59.158  74.683  1.00  8.70
ATOM   1695  C   ASN   219       3.237  59.352  75.994  1.00  8.70
ATOM   1696  O   ASN   219       4.106  60.219  76.060  1.00  8.70
ATOM   1697  CB  ASN   219       1.173  58.507  74.959  1.00  8.70
ATOM   1698  CG  ASN   219       0.233  58.594  73.773  1.00  8.70
ATOM   1699  OD1 ASN   219       0.432  59.406  72.869  1.00  8.70
ATOM   1700  ND2 ASN   219      -0.795  57.755  73.772  1.00  8.70
ATOM   1701  N   PRO   220       2.913  58.621  77.041  1.00 14.88
ATOM   1702  CA  PRO   220       3.457  58.907  78.339  1.00 14.88
ATOM   1703  C   PRO   220       4.948  58.946  78.329  1.00 14.88
ATOM   1704  O   PRO   220       5.517  59.724  79.091  1.00 14.88
ATOM   1705  CB  PRO   220       2.945  57.761  79.215  1.00 14.88
ATOM   1706  CG  PRO   220       1.650  57.364  78.590  1.00 14.88
ATOM   1707  CD  PRO   220       1.860  57.447  77.105  1.00 14.88
ATOM   1708  N   GLU   221       5.619  58.102  77.527  1.00 13.85
ATOM   1709  CA  GLU   221       7.045  58.175  77.607  1.00 13.85
ATOM   1710  C   GLU   221       7.490  59.495  77.056  1.00 13.85
ATOM   1711  O   GLU   221       8.389  60.127  77.608  1.00 13.85
ATOM   1712  CB  GLU   221       7.686  57.047  76.797  1.00 13.85
ATOM   1713  CG  GLU   221       7.502  55.665  77.404  1.00 13.85
ATOM   1714  CD  GLU   221       8.071  55.565  78.806  1.00 13.85
ATOM   1715  OE1 GLU   221       9.253  55.922  78.994  1.00 13.85
ATOM   1716  OE2 GLU   221       7.334  55.129  79.715  1.00 13.85
ATOM   1717  N   LYS   222       6.862  59.955  75.954  1.00 15.00
ATOM   1718  CA  LYS   222       7.240  61.194  75.334  1.00 15.00
ATOM   1719  C   LYS   222       6.883  62.338  76.233  1.00 15.00
ATOM   1720  O   LYS   222       7.640  63.297  76.361  1.00 15.00
ATOM   1721  CB  LYS   222       6.513  61.370  73.999  1.00 15.00
ATOM   1722  CG  LYS   222       6.894  62.634  73.246  1.00 15.00
ATOM   1723  CD  LYS   222       8.368  62.633  72.875  1.00 15.00
ATOM   1724  CE  LYS   222       8.670  63.672  71.808  1.00 15.00
ATOM   1725  NZ  LYS   222       8.533  65.060  72.331  1.00 15.00
ATOM   1726  N   ILE   223       5.720  62.255  76.904  1.00 15.00
ATOM   1727  CA  ILE   223       5.215  63.357  77.676  1.00 15.00
ATOM   1728  C   ILE   223       6.158  63.719  78.783  1.00 15.00
ATOM   1729  O   ILE   223       6.334  64.896  79.090  1.00 15.00
ATOM   1730  CB  ILE   223       3.855  63.021  78.317  1.00 15.00
ATOM   1731  CG1 ILE   223       2.778  62.878  77.239  1.00 15.00
ATOM   1732  CG2 ILE   223       3.433  64.122  79.277  1.00 15.00
ATOM   1733  CD1 ILE   223       1.479  62.293  77.747  1.00 15.00
ATOM   1734  N   ARG   224       6.767  62.719  79.439  1.00 15.00
ATOM   1735  CA  ARG   224       7.625  62.979  80.564  1.00 15.00
ATOM   1736  C   ARG   224       8.867  63.726  80.158  1.00 15.00
ATOM   1737  O   ARG   224       9.375  64.553  80.912  1.00 15.00
ATOM   1738  CB  ARG   224       8.062  61.667  81.220  1.00 15.00
ATOM   1739  CG  ARG   224       6.953  60.948  81.969  1.00 15.00
ATOM   1740  CD  ARG   224       7.435  59.619  82.526  1.00 15.00
ATOM   1741  NE  ARG   224       6.378  58.912  83.246  1.00 15.00
ATOM   1742  CZ  ARG   224       6.512  57.695  83.764  1.00 15.00
ATOM   1743  NH1 ARG   224       5.495  57.130  84.402  1.00 15.00
ATOM   1744  NH2 ARG   224       7.661  57.045  83.641  1.00 15.00
ATOM   1745  N   LEU   225       9.391  63.408  78.961  1.00 15.00
ATOM   1746  CA  LEU   225      10.639  63.836  78.379  1.00 15.00
ATOM   1747  C   LEU   225      10.696  65.270  77.925  1.00 15.00
ATOM   1748  O   LEU   225      11.783  65.788  77.676  1.00 15.00
ATOM   1749  CB  LEU   225      10.968  63.001  77.140  1.00 15.00
ATOM   1750  CG  LEU   225      11.266  61.519  77.381  1.00 15.00
ATOM   1751  CD1 LEU   225      11.456  60.787  76.061  1.00 15.00
ATOM   1752  CD2 LEU   225      12.534  61.353  78.204  1.00 15.00
ATOM   1753  N   LEU   226       9.545  65.921  77.718  1.00 13.53
ATOM   1754  CA  LEU   226       9.441  67.213  77.095  1.00 13.53
ATOM   1755  C   LEU   226      10.114  68.315  77.885  1.00 13.53
ATOM   1756  O   LEU   226      10.138  68.292  79.115  1.00 13.53
ATOM   1757  CB  LEU   226       7.973  67.614  76.933  1.00 13.53
ATOM   1758  CG  LEU   226       7.148  66.783  75.948  1.00 13.53
ATOM   1759  CD1 LEU   226       5.686  67.201  75.985  1.00 13.53
ATOM   1760  CD2 LEU   226       7.660  66.969  74.528  1.00 13.53
ATOM   1761  N   LYS   227      10.716  69.305  77.168  1.00 10.20
ATOM   1762  CA  LYS   227      11.391  70.424  77.782  1.00 10.20
ATOM   1763  C   LYS   227      11.076  71.700  77.056  1.00 10.20
ATOM   1764  O   LYS   227      10.826  71.717  75.851  1.00 10.20
ATOM   1765  CB  LYS   227      12.906  70.217  77.752  1.00 10.20
ATOM   1766  CG  LYS   227      13.373  68.945  78.440  1.00 10.20
ATOM   1767  CD  LYS   227      13.233  69.050  79.950  1.00 10.20
ATOM   1768  CE  LYS   227      13.725  67.787  80.639  1.00 10.20
ATOM   1769  NZ  LYS   227      13.483  67.826  82.108  1.00 10.20
ATOM   1770  N   GLU   228      11.051  72.805  77.831  1.00 11.78
ATOM   1771  CA  GLU   228      10.795  74.146  77.389  1.00 11.78
ATOM   1772  C   GLU   228      11.955  74.697  76.614  1.00 11.78
ATOM   1773  O   GLU   228      11.756  75.496  75.700  1.00 11.78
ATOM   1774  CB  GLU   228      10.547  75.067  78.586  1.00 11.78
ATOM   1775  CG  GLU   228       9.233  74.809  79.305  1.00 11.78
ATOM   1776  CD  GLU   228       9.063  75.676  80.538  1.00 11.78
ATOM   1777  OE1 GLU   228      10.002  76.433  80.865  1.00 11.78
ATOM   1778  OE2 GLU   228       7.993  75.598  81.177  1.00 11.78
ATOM   1779  N   PHE   229      13.202  74.318  76.964  1.00 14.07
ATOM   1780  CA  PHE   229      14.325  74.951  76.323  1.00 14.07
ATOM   1781  C   PHE   229      14.499  74.404  74.944  1.00 14.07
ATOM   1782  O   PHE   229      15.369  73.572  74.688  1.00 14.07
ATOM   1783  CB  PHE   229      15.608  74.698  77.117  1.00 14.07
ATOM   1784  CG  PHE   229      15.616  75.338  78.475  1.00 14.07
ATOM   1785  CD1 PHE   229      15.410  74.581  79.616  1.00 14.07
ATOM   1786  CD2 PHE   229      15.828  76.700  78.613  1.00 14.07
ATOM   1787  CE1 PHE   229      15.418  75.170  80.865  1.00 14.07
ATOM   1788  CE2 PHE   229      15.836  77.289  79.864  1.00 14.07
ATOM   1789  CZ  PHE   229      15.631  76.531  80.986  1.00 14.07
ATOM   1790  N   MET   230      13.677  74.910  74.012  1.00 12.73
ATOM   1791  CA  MET   230      13.673  74.511  72.638  1.00 12.73
ATOM   1792  C   MET   230      14.894  74.984  71.907  1.00 12.73
ATOM   1793  O   MET   230      15.328  74.336  70.957  1.00 12.73
ATOM   1794  CB  MET   230      12.452  75.085  71.917  1.00 12.73
ATOM   1795  CG  MET   230      11.130  74.470  72.348  1.00 12.73
ATOM   1796  SD  MET   230       9.750  74.994  71.314  1.00 12.73
ATOM   1797  CE  MET   230       9.499  76.667  71.905  1.00 12.73
ATOM   1798  N   HIS   231      15.410  76.173  72.275  1.00 10.13
ATOM   1799  CA  HIS   231      16.512  76.835  71.622  1.00 10.13
ATOM   1800  C   HIS   231      17.875  76.255  71.883  1.00 10.13
ATOM   1801  O   HIS   231      18.704  76.235  70.974  1.00 10.13
ATOM   1802  CB  HIS   231      16.597  78.297  72.064  1.00 10.13
ATOM   1803  CG  HIS   231      17.700  79.065  71.404  1.00 10.13
ATOM   1804  ND1 HIS   231      17.677  79.398  70.067  1.00 10.13
ATOM   1805  CD2 HIS   231      18.965  79.640  71.833  1.00 10.13
ATOM   1806  CE1 HIS   231      18.796  80.082  69.768  1.00 10.13
ATOM   1807  NE2 HIS   231      19.574  80.230  70.823  1.00 10.13
ATOM   1808  N   THR   232      18.160  75.770  73.110  1.00 11.84
ATOM   1809  CA  THR   232      19.504  75.381  73.463  1.00 11.84
ATOM   1810  C   THR   232      20.071  74.397  72.484  1.00 11.84
ATOM   1811  O   THR   232      19.532  73.316  72.259  1.00 11.84
ATOM   1812  CB  THR   232      19.555  74.723  74.854  1.00 11.84
ATOM   1813  OG1 THR   232      19.028  75.627  75.833  1.00 11.84
ATOM   1814  CG2 THR   232      20.987  74.374  75.226  1.00 11.84
ATOM   1815  N   MET   233      21.209  74.785  71.871  1.00 14.98
ATOM   1816  CA  MET   233      21.910  73.999  70.895  1.00 14.98
ATOM   1817  C   MET   233      22.488  72.774  71.533  1.00 14.98
ATOM   1818  O   MET   233      22.491  71.697  70.938  1.00 14.98
ATOM   1819  CB  MET   233      23.050  74.808  70.273  1.00 14.98
ATOM   1820  CG  MET   233      22.587  75.938  69.368  1.00 14.98
ATOM   1821  SD  MET   233      23.945  76.702  68.461  1.00 14.98
ATOM   1822  CE  MET   233      24.716  77.669  69.756  1.00 14.98
ATOM   1823  N   LYS   234      23.013  72.905  72.764  1.00 11.52
ATOM   1824  CA  LYS   234      23.635  71.781  73.403  1.00 11.52
ATOM   1825  C   LYS   234      22.610  70.712  73.607  1.00 11.52
ATOM   1826  O   LYS   234      22.853  69.539  73.326  1.00 11.52
ATOM   1827  CB  LYS   234      24.217  72.188  74.759  1.00 11.52
ATOM   1828  CG  LYS   234      25.435  73.092  74.665  1.00 11.52
ATOM   1829  CD  LYS   234      25.960  73.455  76.044  1.00 11.52
ATOM   1830  CE  LYS   234      27.164  74.379  75.951  1.00 11.52
ATOM   1831  NZ  LYS   234      27.669  74.770  77.296  1.00 11.52
ATOM   1832  N   ASN   235      21.416  71.103  74.085  1.00 10.99
ATOM   1833  CA  ASN   235      20.374  70.162  74.359  1.00 10.99
ATOM   1834  C   ASN   235      19.965  69.508  73.079  1.00 10.99
ATOM   1835  O   ASN   235      19.729  68.303  73.046  1.00 10.99
ATOM   1836  CB  ASN   235      19.164  70.866  74.977  1.00 10.99
ATOM   1837  CG  ASN   235      19.407  71.291  76.412  1.00 10.99
ATOM   1838  OD1 ASN   235      20.299  70.771  77.081  1.00 10.99
ATOM   1839  ND2 ASN   235      18.610  72.240  76.889  1.00 10.99
ATOM   1840  N   THR   236      19.874  70.295  71.987  1.00 12.97
ATOM   1841  CA  THR   236      19.425  69.778  70.726  1.00 12.97
ATOM   1842  C   THR   236      20.402  68.771  70.203  1.00 12.97
ATOM   1843  O   THR   236      20.005  67.731  69.683  1.00 12.97
ATOM   1844  CB  THR   236      19.284  70.896  69.676  1.00 12.97
ATOM   1845  OG1 THR   236      18.305  71.846  70.115  1.00 12.97
ATOM   1846  CG2 THR   236      18.845  70.319  68.338  1.00 12.97
ATOM   1847  N   GLY   237      21.712  69.057  70.323  1.00 12.49
ATOM   1848  CA  GLY   237      22.713  68.160  69.818  1.00 12.49
ATOM   1849  C   GLY   237      22.625  66.875  70.574  1.00 12.49
ATOM   1850  O   GLY   237      22.767  65.791  70.012  1.00 12.49
ATOM   1851  N   ARG   238      22.395  66.965  71.890  1.00 14.08
ATOM   1852  CA  ARG   238      22.339  65.787  72.697  1.00 14.08
ATOM   1853  C   ARG   238      21.214  64.940  72.192  1.00 14.08
ATOM   1854  O   ARG   238      21.341  63.721  72.074  1.00 14.08
ATOM   1855  CB  ARG   238      22.096  66.152  74.163  1.00 14.08
ATOM   1856  CG  ARG   238      23.283  66.814  74.843  1.00 14.08
ATOM   1857  CD  ARG   238      22.949  67.215  76.270  1.00 14.08
ATOM   1858  NE  ARG   238      24.072  67.879  76.929  1.00 14.08
ATOM   1859  CZ  ARG   238      24.021  68.393  78.153  1.00 14.08
ATOM   1860  NH1 ARG   238      25.092  68.979  78.672  1.00 14.08
ATOM   1861  NH2 ARG   238      22.899  68.323  78.856  1.00 14.08
ATOM   1862  N   ASN   239      20.079  65.583  71.868  1.00 13.71
ATOM   1863  CA  ASN   239      18.907  64.893  71.421  1.00 13.71
ATOM   1864  C   ASN   239      19.191  64.186  70.131  1.00 13.71
ATOM   1865  O   ASN   239      18.862  63.011  69.974  1.00 13.71
ATOM   1866  CB  ASN   239      17.758  65.879  71.196  1.00 13.71
ATOM   1867  CG  ASN   239      17.178  66.401  72.496  1.00 13.71
ATOM   1868  OD1 ASN   239      17.360  65.801  73.554  1.00 13.71
ATOM   1869  ND2 ASN   239      16.476  67.526  72.418  1.00 13.71
ATOM   1870  N   VAL   240      19.823  64.888  69.173  1.00 15.00
ATOM   1871  CA  VAL   240      20.066  64.334  67.870  1.00 15.00
ATOM   1872  C   VAL   240      21.004  63.177  67.992  1.00 15.00
ATOM   1873  O   VAL   240      20.836  62.159  67.321  1.00 15.00
ATOM   1874  CB  VAL   240      20.693  65.374  66.923  1.00 15.00
ATOM   1875  CG1 VAL   240      21.124  64.717  65.621  1.00 15.00
ATOM   1876  CG2 VAL   240      19.690  66.471  66.599  1.00 15.00
ATOM   1877  N   ASN   241      22.018  63.301  68.866  1.00 15.00
ATOM   1878  CA  ASN   241      22.984  62.252  68.978  1.00 15.00
ATOM   1879  C   ASN   241      22.260  61.012  69.385  1.00 15.00
ATOM   1880  O   ASN   241      22.472  59.943  68.816  1.00 15.00
ATOM   1881  CB  ASN   241      24.040  62.606  70.028  1.00 15.00
ATOM   1882  CG  ASN   241      24.994  63.685  69.554  1.00 15.00
ATOM   1883  OD1 ASN   241      25.119  63.932  68.354  1.00 15.00
ATOM   1884  ND2 ASN   241      25.670  64.331  70.496  1.00 15.00
ATOM   1885  N   ASP   242      21.362  61.132  70.379  1.00 15.00
ATOM   1886  CA  ASP   242      20.687  59.974  70.872  1.00 15.00
ATOM   1887  C   ASP   242      19.840  59.376  69.801  1.00 15.00
ATOM   1888  O   ASP   242      19.921  58.171  69.565  1.00 15.00
ATOM   1889  CB  ASP   242      19.788  60.341  72.056  1.00 15.00
ATOM   1890  CG  ASP   242      19.102  59.133  72.661  1.00 15.00
ATOM   1891  OD1 ASP   242      19.812  58.227  73.146  1.00 15.00
ATOM   1892  OD2 ASP   242      17.853  59.093  72.652  1.00 15.00
ATOM   1893  N   ARG   243      19.062  60.210  69.081  1.00 15.00
ATOM   1894  CA  ARG   243      18.123  59.695  68.126  1.00 15.00
ATOM   1895  C   ARG   243      17.322  58.647  68.899  1.00 15.00
ATOM   1896  O   ARG   243      16.670  59.017  69.912  1.00 15.00
ATOM   1897  CB  ARG   243      18.857  59.072  66.937  1.00 15.00
ATOM   1898  CG  ARG   243      19.757  60.040  66.186  1.00 15.00
ATOM   1899  CD  ARG   243      20.376  59.384  64.963  1.00 15.00
ATOM   1900  NE  ARG   243      21.229  58.253  65.322  1.00 15.00
ATOM   1901  CZ  ARG   243      22.451  58.372  65.833  1.00 15.00
ATOM   1902  NH1 ARG   243      23.153  57.287  66.130  1.00 15.00
ATOM   1903  NH2 ARG   243      22.965  59.575  66.048  1.00 15.00
TER
END
