
#######################################################
#                                                     #
#                        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 (  181),  selected   24 , name T0386TS490_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS490_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          4.338
LGA    V     240      E     221          3.340
LGA    -       -      K     222           -
LGA    N     241      I     223          1.334
LGA    D     242      R     224          2.063
LGA    -       -      L     225           -
LGA    -       -      L     226           -
LGA    R     243      K     227          2.662
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    -       -      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    P     244      G     262           #
LGA    V     245      -       -           -
LGA    M     246      -       -           -
LGA    V     247      L     263          5.440
LGA    A     248      E     264          1.325
LGA    K     249      G     265          3.523
LGA    E     250      F     266          3.664
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    G     251      I     279          3.001
LGA    E     252      D     280          2.976
LGA    T     253      H     281          2.759
LGA    Y     254      L     282          3.129
LGA    T     255      P     283          4.459
LGA    G     256      P     284          2.002
LGA    T     257      E     285          3.772
LGA    Y     258      -       -           -
LGA    R     259      -       -           -
LGA    G     260      Q     286          1.965
LGA    A     261      L     287          2.080
LGA    G     262      K     288          1.709
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     19    3.12     0.00     14.865     0.590

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.839621 * X  +   0.398095 * Y  +   0.369536 * Z  +   2.521652
  Y_new =   0.072291 * X  +   0.592378 * Y  +  -0.802410 * Z  +  29.680620
  Z_new =  -0.538341 * X  +   0.700434 * Y  +   0.468595 * Z  +  38.003624 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.981176   -2.160417  [ DEG:    56.2172   -123.7828 ]
  Theta =   0.568467    2.573126  [ DEG:    32.5708    147.4292 ]
  Phi   =   0.085887   -3.055705  [ DEG:     4.9210   -175.0790 ]
 
# 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: T0386TS490_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS490_1-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   19   3.12    0.00  14.865
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS490_1-D2
PFRMAT     TS
TARGET     T0386
MODEL      1
PARENT     2f6sA
ATOM   1495  N   ASN   219      -1.311  56.325  78.880  1.00 50.00
ATOM   1496  CA  ASN   219      -1.225  55.898  77.488  1.00 50.00
ATOM   1497  C   ASN   219      -2.257  54.832  77.151  1.00 50.00
ATOM   1498  O   ASN   219      -2.445  53.896  77.929  1.00 50.00
ATOM   1499  CB  ASN   219      -0.057  55.110  77.473  1.00 50.00
ATOM   1500  CG  ASN   219       0.460  54.035  78.092  1.00 50.00
ATOM   1501  OD1 ASN   219      -0.236  53.074  77.947  1.00 50.00
ATOM   1502  ND2 ASN   219       1.483  54.156  78.904  1.00 50.00
ATOM   1672  N   VAL   240       2.275  60.275  76.289  1.00 50.00
ATOM   1673  CA  VAL   240       3.541  59.563  76.288  1.00 50.00
ATOM   1674  C   VAL   240       4.623  60.478  75.775  1.00 50.00
ATOM   1675  O   VAL   240       5.795  60.184  75.811  1.00 50.00
ATOM   1676  CB  VAL   240       3.684  58.376  75.394  1.00 50.00
ATOM   1677  CG1 VAL   240       3.247  58.746  73.936  1.00 50.00
ATOM   1678  CG2 VAL   240       4.676  57.443  75.465  1.00 50.00
ATOM   1679  N   ASN   241       4.257  61.631  75.244  1.00 50.00
ATOM   1680  CA  ASN   241       5.252  62.489  74.583  1.00 50.00
ATOM   1681  C   ASN   241       5.449  63.842  75.254  1.00 50.00
ATOM   1682  O   ASN   241       6.337  64.591  74.930  1.00 50.00
ATOM   1683  CB  ASN   241       4.898  62.668  73.104  1.00 50.00
ATOM   1684  CG  ASN   241       5.057  61.376  72.339  1.00 50.00
ATOM   1685  OD1 ASN   241       5.551  60.465  72.909  1.00 50.00
ATOM   1686  ND2 ASN   241       4.694  61.437  71.083  1.00 50.00
ATOM   1687  N   ASP   242       4.547  64.211  76.154  1.00 50.00
ATOM   1688  CA  ASP   242       4.657  65.490  76.865  1.00 50.00
ATOM   1689  C   ASP   242       5.914  65.490  77.733  1.00 50.00
ATOM   1690  O   ASP   242       6.073  64.794  78.673  1.00 50.00
ATOM   1691  CB  ASP   242       3.408  65.736  77.709  1.00 50.00
ATOM   1692  CG  ASP   242       3.473  67.093  78.406  1.00 50.00
ATOM   1693  OD1 ASP   242       4.154  67.962  77.848  1.00 50.00
ATOM   1694  OD2 ASP   242       2.804  67.255  79.437  1.00 50.00
ATOM   1695  N   ARG   243       6.906  66.255  77.340  1.00 50.00
ATOM   1696  CA  ARG   243       8.191  66.326  78.070  1.00 50.00
ATOM   1697  C   ARG   243       8.050  66.754  79.524  1.00 50.00
ATOM   1698  O   ARG   243       8.812  66.304  80.373  1.00 50.00
ATOM   1699  CB  ARG   243       9.179  67.212  77.315  1.00 50.00
ATOM   1700  CG  ARG   243       9.519  66.641  75.938  1.00 50.00
ATOM   1701  CD  ARG   243      10.351  65.412  76.006  1.00 50.00
ATOM   1702  NE  ARG   243      10.549  64.726  74.745  1.00 50.00
ATOM   1703  CZ  ARG   243       9.696  64.062  73.958  1.00 50.00
ATOM   1704  NH1 ARG   243       8.478  63.823  74.322  1.00 50.00
ATOM   1705  NH2 ARG   243      10.086  63.625  72.766  1.00 50.00
ATOM   1706  N   PRO   244       7.102  67.645  79.810  1.00 50.00
ATOM   1707  CA  PRO   244       6.811  68.083  81.182  1.00 50.00
ATOM   1708  C   PRO   244       6.414  66.876  82.035  1.00 50.00
ATOM   1709  O   PRO   244       6.934  66.649  83.118  1.00 50.00
ATOM   1710  CB  PRO   244       5.637  69.045  81.029  1.00 50.00
ATOM   1711  CG  PRO   244       5.875  69.656  79.651  1.00 50.00
ATOM   1712  CD  PRO   244       6.427  68.505  78.842  1.00 50.00
ATOM   1713  N   VAL   245       5.493  66.093  81.509  1.00 50.00
ATOM   1714  CA  VAL   245       5.029  64.881  82.176  1.00 50.00
ATOM   1715  C   VAL   245       6.181  63.887  82.372  1.00 50.00
ATOM   1716  O   VAL   245       6.316  63.260  83.411  1.00 50.00
ATOM   1717  CB  VAL   245       3.991  64.378  81.205  1.00 50.00
ATOM   1718  CG1 VAL   245       2.836  65.233  81.066  1.00 50.00
ATOM   1719  CG2 VAL   245       4.372  63.731  80.022  1.00 50.00
ATOM   1720  N   MET   246       7.029  63.800  81.352  1.00 50.00
ATOM   1721  CA  MET   246       8.173  62.879  81.368  1.00 50.00
ATOM   1722  C   MET   246       9.205  63.299  82.415  1.00 50.00
ATOM   1723  O   MET   246       9.735  62.464  83.145  1.00 50.00
ATOM   1724  CB  MET   246       8.825  62.821  79.989  1.00 50.00
ATOM   1725  CG  MET   246       7.890  62.166  78.971  1.00 50.00
ATOM   1726  SD  MET   246       8.607  62.046  77.302  1.00 50.00
ATOM   1727  CE  MET   246       8.464  63.631  76.951  1.00 50.00
ATOM   1728  N   VAL   247       9.464  64.598  82.487  1.00 50.00
ATOM   1729  CA  VAL   247      10.441  65.141  83.443  1.00 50.00
ATOM   1730  C   VAL   247       9.954  64.934  84.880  1.00 50.00
ATOM   1731  O   VAL   247      10.721  64.546  85.756  1.00 50.00
ATOM   1732  CB  VAL   247      10.682  66.628  83.178  1.00 50.00
ATOM   1733  CG1 VAL   247      11.277  66.832  81.784  1.00 50.00
ATOM   1734  CG2 VAL   247       9.405  67.435  83.333  1.00 50.00
ATOM   1735  N   ALA   248       8.661  65.174  85.090  1.00 50.00
ATOM   1736  CA  ALA   248       8.050  64.980  86.410  1.00 50.00
ATOM   1737  C   ALA   248       8.179  63.508  86.808  1.00 50.00
ATOM   1738  O   ALA   248       8.445  63.183  87.963  1.00 50.00
ATOM   1739  CB  ALA   248       6.571  65.366  86.356  1.00 50.00
ATOM   1740  N   LYS   249       8.024  62.642  85.808  1.00 50.00
ATOM   1741  CA  LYS   249       8.127  61.192  86.001  1.00 50.00
ATOM   1742  C   LYS   249       9.545  60.800  86.426  1.00 50.00
ATOM   1743  O   LYS   249       9.728  60.051  87.382  1.00 50.00
ATOM   1744  CB  LYS   249       7.784  60.474  84.694  1.00 50.00
ATOM   1745  CG  LYS   249       7.854  58.955  84.850  1.00 50.00
ATOM   1746  CD  LYS   249       6.793  58.439  85.822  1.00 50.00
ATOM   1747  CE  LYS   249       6.851  56.919  85.956  1.00 50.00
ATOM   1748  NZ  LYS   249       8.119  56.479  86.555  1.00 50.00
ATOM   1749  N   GLU   250      10.532  61.333  85.711  1.00 50.00
ATOM   1750  CA  GLU   250      11.934  60.965  85.953  1.00 50.00
ATOM   1751  C   GLU   250      12.426  61.549  87.279  1.00 50.00
ATOM   1752  O   GLU   250      13.241  60.986  87.979  1.00 50.00
ATOM   1753  CB  GLU   250      12.832  61.417  84.801  1.00 50.00
ATOM   1754  CG  GLU   250      12.826  62.933  84.600  1.00 50.00
ATOM   1755  CD  GLU   250      13.750  63.327  83.455  1.00 50.00
ATOM   1756  OE1 GLU   250      13.478  62.873  82.324  1.00 50.00
ATOM   1757  OE2 GLU   250      14.718  64.052  83.741  1.00 50.00
ATOM   1758  N   GLY   251      11.906  62.727  87.615  1.00 50.00
ATOM   1759  CA  GLY   251      12.247  63.387  88.881  1.00 50.00
ATOM   1760  C   GLY   251      11.803  62.505  90.050  1.00 50.00
ATOM   1761  O   GLY   251      12.510  62.371  91.044  1.00 50.00
ATOM   1762  N   GLU   252      10.638  61.885  89.875  1.00 50.00
ATOM   1763  CA  GLU   252      10.057  61.006  90.885  1.00 50.00
ATOM   1764  C   GLU   252      10.867  59.711  90.989  1.00 50.00
ATOM   1765  O   GLU   252      11.117  59.188  92.061  1.00 50.00
ATOM   1766  CB  GLU   252       8.602  60.703  90.566  1.00 50.00
ATOM   1767  CG  GLU   252       7.917  59.870  91.658  1.00 50.00
ATOM   1768  CD  GLU   252       7.885  60.600  93.004  1.00 50.00
ATOM   1769  OE1 GLU   252       8.137  61.828  93.000  1.00 50.00
ATOM   1770  OE2 GLU   252       7.632  59.914  94.017  1.00 50.00
ATOM   1771  N   THR   253      11.283  59.221  89.833  1.00 50.00
ATOM   1772  CA  THR   253      12.092  57.995  89.761  1.00 50.00
ATOM   1773  C   THR   253      13.379  58.176  90.572  1.00 50.00
ATOM   1774  O   THR   253      13.762  57.297  91.342  1.00 50.00
ATOM   1775  CB  THR   253      12.440  57.668  88.308  1.00 50.00
ATOM   1776  OG1 THR   253      13.213  58.695  87.745  1.00 50.00
ATOM   1777  CG2 THR   253      11.176  57.427  87.482  1.00 50.00
ATOM   1778  N   TYR   254      14.013  59.334  90.402  1.00 50.00
ATOM   1779  CA  TYR   254      15.226  59.670  91.160  1.00 50.00
ATOM   1780  C   TYR   254      14.916  59.885  92.642  1.00 50.00
ATOM   1781  O   TYR   254      15.753  59.616  93.503  1.00 50.00
ATOM   1782  CB  TYR   254      15.913  60.905  90.576  1.00 50.00
ATOM   1783  CG  TYR   254      16.820  60.526  89.402  1.00 50.00
ATOM   1784  CD1 TYR   254      16.288  59.966  88.247  1.00 50.00
ATOM   1785  CD2 TYR   254      18.193  60.714  89.513  1.00 50.00
ATOM   1786  CE1 TYR   254      17.130  59.588  87.207  1.00 50.00
ATOM   1787  CE2 TYR   254      19.034  60.346  88.470  1.00 50.00
ATOM   1788  CZ  TYR   254      18.501  59.782  87.318  1.00 50.00
ATOM   1789  OH  TYR   254      19.320  59.411  86.301  1.00 50.00
ATOM   1790  N   THR   255      13.723  60.394  92.919  1.00 99.99
ATOM   1791  CA  THR   255      13.285  60.607  94.307  1.00 99.99
ATOM   1792  C   THR   255      12.664  59.315  94.841  1.00 99.99
ATOM   1793  O   THR   255      11.707  58.786  94.290  1.00 99.99
ATOM   1794  CB  THR   255      12.265  61.744  94.380  1.00 99.99
ATOM   1795  OG1 THR   255      11.905  61.965  95.743  1.00 99.99
ATOM   1796  CG2 THR   255      11.028  61.442  93.579  1.00 99.99
ATOM   1797  N   GLY   256      13.243  58.820  95.928  1.00 99.99
ATOM   1798  CA  GLY   256      12.769  57.586  96.577  1.00 99.99
ATOM   1799  C   GLY   256      13.102  57.636  98.066  1.00 99.99
ATOM   1800  O   GLY   256      13.581  58.646  98.577  1.00 99.99
ATOM   1801  N   THR   257      12.841  56.522  98.734  1.00 99.99
ATOM   1802  CA  THR   257      13.107  56.401 100.180  1.00 99.99
ATOM   1803  C   THR   257      14.611  56.248 100.437  1.00 99.99
ATOM   1804  O   THR   257      15.099  56.549 101.521  1.00 99.99
ATOM   1805  CB  THR   257      12.335  55.211 100.753  1.00 99.99
ATOM   1806  OG1 THR   257      12.526  55.158 102.166  1.00 99.99
ATOM   1807  CG2 THR   257      12.761  53.905 100.100  1.00 99.99
ATOM   1808  N   TYR   258      15.306  55.709  99.435  1.00 99.99
ATOM   1809  CA  TYR   258      16.758  55.495  99.511  1.00 99.99
ATOM   1810  C   TYR   258      17.420  56.027  98.245  1.00 99.99
ATOM   1811  O   TYR   258      17.406  55.384  97.202  1.00 99.99
ATOM   1812  CB  TYR   258      17.051  54.000  99.659  1.00 99.99
ATOM   1813  CG  TYR   258      16.570  53.199  98.442  1.00 99.99
ATOM   1814  CD1 TYR   258      15.290  52.669  98.416  1.00 99.99
ATOM   1815  CD2 TYR   258      17.437  52.957  97.380  1.00 99.99
ATOM   1816  CE1 TYR   258      14.875  51.898  97.338  1.00 99.99
ATOM   1817  CE2 TYR   258      17.022  52.204  96.296  1.00 99.99
ATOM   1818  CZ  TYR   258      15.742  51.667  96.277  1.00 99.99
ATOM   1819  OH  TYR   258      15.337  50.916  95.219  1.00 99.99
ATOM   1820  N   ARG   259      18.000  57.214  98.335  1.00 99.99
ATOM   1821  CA  ARG   259      18.556  57.873  97.131  1.00 99.99
ATOM   1822  C   ARG   259      17.361  58.004  96.177  1.00 99.99
ATOM   1823  O   ARG   259      17.474  57.812  94.973  1.00 99.99
ATOM   1824  CB  ARG   259      19.594  56.963  96.477  1.00 99.99
ATOM   1825  CG  ARG   259      20.654  56.450  97.450  1.00 99.99
ATOM   1826  CD  ARG   259      21.497  57.576  98.044  1.00 99.99
ATOM   1827  NE  ARG   259      22.600  56.988  98.824  1.00 99.99
ATOM   1828  CZ  ARG   259      22.573  56.825 100.151  1.00 99.99
ATOM   1829  NH1 ARG   259      21.494  57.194 100.849  1.00 99.99
ATOM   1830  NH2 ARG   259      23.629  56.310 100.786  1.00 99.99
ATOM   1831  N   GLY   260      16.269  58.519  96.747  1.00 50.00
ATOM   1832  CA  GLY   260      16.358  59.353  97.967  1.00 50.00
ATOM   1833  C   GLY   260      16.963  60.700  97.586  1.00 50.00
ATOM   1834  O   GLY   260      17.562  61.383  98.412  1.00 50.00
ATOM   1835  N   ALA   261      16.822  61.041  96.307  1.00 50.00
ATOM   1836  CA  ALA   261      17.202  62.367  95.802  1.00 50.00
ATOM   1837  C   ALA   261      16.021  63.317  96.015  1.00 50.00
ATOM   1838  O   ALA   261      14.959  63.140  95.429  1.00 50.00
ATOM   1839  CB  ALA   261      17.531  62.284  94.310  1.00 50.00
ATOM   1840  N   GLY   262      16.243  64.332  96.850  1.00 50.00
ATOM   1841  CA  GLY   262      15.159  65.256  97.232  1.00 50.00
ATOM   1842  C   GLY   262      15.461  66.684  96.771  1.00 50.00
ATOM   1843  O   GLY   262      15.156  66.977  95.598  1.00 50.00
ATOM   1844  OXT GLY   262      15.990  67.445  97.608  1.00 99.99
TER    1845      GLY   262                                        
END
