
#######################################################
#                                                     #
#                        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   15 (  150),  selected   15 , name T0299TS277_4-D2
# Molecule2: number of CA atoms   89 (  757),  selected   89 , name T0299_D2.pdb
# PARAMETERS: T0299TS277_4-D2.T0299_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      L      79           -
LGA    -       -      E      80           -
LGA    -       -      D      81           -
LGA    -       -      F      82           -
LGA    -       -      E      83           -
LGA    -       -      A      84           -
LGA    -       -      E      85           -
LGA    -       -      L      86           -
LGA    -       -      E      87           -
LGA    -       -      N      88           -
LGA    -       -      L      89           -
LGA    -       -      P      90           -
LGA    -       -      A      91           -
LGA    -       -      W      92           -
LGA    -       -      W      93           -
LGA    -       -      S      94           -
LGA    -       -      R      95           -
LGA    -       -      D      96           -
LGA    -       -      L      97           -
LGA    -       -      A      98           -
LGA    -       -      R      99           -
LGA    -       -      K     100           -
LGA    -       -      D     101           -
LGA    -       -      F     102           -
LGA    -       -      L     103           -
LGA    -       -      F     104           -
LGA    -       -      Y     105           -
LGA    -       -      T     106           -
LGA    -       -      E     107           -
LGA    -       -      G     108           -
LGA    -       -      L     109           -
LGA    -       -      D     110           -
LGA    -       -      V     111           -
LGA    -       -      D     112           -
LGA    -       -      Q     113           -
LGA    -       -      V     114           -
LGA    -       -      I     115           -
LGA    -       -      A     116           -
LGA    -       -      T     117           -
LGA    -       -      V     118           -
LGA    -       -      E     119           -
LGA    -       -      S     120           -
LGA    -       -      L     121           -
LGA    -       -      E     122           -
LGA    -       -      L     123           -
LGA    -       -      K     124           -
LGA    -       -      D     125           -
LGA    -       -      E     126           -
LGA    -       -      V     127           -
LGA    -       -      L     128           -
LGA    -       -      Y     129           -
LGA    -       -      F     130           -
LGA    -       -      G     131           -
LGA    -       -      K     132           -
LGA    -       -      L     133           -
LGA    -       -      G     134           -
LGA    -       -      I     135           -
LGA    -       -      F     136           -
LGA    -       -      W     137           -
LGA    -       -      G     138           -
LGA    -       -      K     139           -
LGA    -       -      F     140           -
LGA    -       -      S     141           -
LGA    -       -      E     142           -
LGA    -       -      E     143           -
LGA    -       -      S     144           -
LGA    -       -      Y     145           -
LGA    -       -      S     146           -
LGA    -       -      K     147           -
LGA    L      79      T     148          4.255
LGA    E      80      A     149          2.778
LGA    D      81      Y     150          2.045
LGA    F      82      H     151          1.550
LGA    E      83      K     152          1.657
LGA    A      84      Y     153          1.453
LGA    E      85      L     154          1.371
LGA    L      86      L     155          2.046
LGA    E      87      K     156          1.458
LGA    N      88      V     157          0.551
LGA    -       -      P     158           -
LGA    L      89      F     159          2.540
LGA    P      90      Y     160          1.316
LGA    -       -      R     161           -
LGA    -       -      H     162           -
LGA    A      91      I     163          4.333
LGA    W      92      T     164          2.732
LGA    W      93      I     165          3.556
LGA    -       -      R     166           -
LGA    -       -      N     167           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   15   89    5.0     15    2.49     6.67     13.481     0.580

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.282412 * X  +   0.404563 * Y  +   0.869812 * Z  + -55.959919
  Y_new =  -0.743912 * X  +   0.664840 * Y  +  -0.067693 * Z  +  29.932858
  Z_new =  -0.605672 * X  +  -0.627946 * Y  +   0.488718 * Z  + -17.092621 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.909441    2.232152  [ DEG:   -52.1071    127.8929 ]
  Theta =   0.650610    2.490983  [ DEG:    37.2772    142.7228 ]
  Phi   =  -1.207973    1.933620  [ DEG:   -69.2117    110.7883 ]
 
# 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: T0299TS277_4-D2                               
REMARK     2: T0299_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299TS277_4-D2.T0299_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   15   89   5.0   15   2.49    6.67  13.481
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS277_4-D2
PFRMAT TS 
TARGET T0299
MODEL 4
PARENT 1DD3_A
ATOM   1439  H   LEU    79      16.211  52.604  -7.980  1.00  0.00                              
ATOM   1441  N   LEU    79      16.580  52.243  -7.189  1.00  0.00                              
ATOM   1443  CA  LEU    79      17.755  52.886  -6.570  1.00  0.00                              
ATOM   1445  CB  LEU    79      18.527  53.666  -7.620  1.00  0.00                              
ATOM   1447  C   LEU    79      17.333  53.813  -5.354  1.00  0.00                              
ATOM   1449  O   LEU    79      16.189  53.751  -4.898  1.00  0.00                              
ATOM   1451  CG  LEU    79      19.054  52.829  -8.797  1.00  0.00                              
ATOM   1453  CD1 LEU    79      19.000  53.630 -10.095  1.00  0.00                              
ATOM   1455  CD2 LEU    79      20.471  52.347  -8.516  1.00  0.00                              
ATOM   1457  H   GLU    80      19.108  54.754  -5.317  1.00  0.00                              
ATOM   1459  N   GLU    80      18.271  54.694  -4.879  1.00  0.00                              
ATOM   1461  CA  GLU    80      18.014  55.571  -3.665  1.00  0.00                              
ATOM   1463  CB  GLU    80      16.820  56.534  -3.881  1.00  0.00                              
ATOM   1465  C   GLU    80      17.804  54.737  -2.375  1.00  0.00                              
ATOM   1467  O   GLU    80      18.384  55.048  -1.331  1.00  0.00                              
ATOM   1469  CG  GLU    80      17.056  57.573  -4.966  1.00  0.00                              
ATOM   1471  CD  GLU    80      15.819  58.399  -5.279  1.00  0.00                              
ATOM   1473  OE1 GLU    80      14.790  58.221  -4.588  1.00  0.00                              
ATOM   1475  OE2 GLU    80      15.870  59.218  -6.223  1.00  0.00                              
ATOM   1477  H   ASP    81      16.464  53.554  -3.240  1.00  0.00                              
ATOM   1479  N   ASP    81      16.941  53.703  -2.441  1.00  0.00                              
ATOM   1481  CA  ASP    81      16.721  52.793  -1.291  1.00  0.00                              
ATOM   1483  CB  ASP    81      15.230  52.415  -1.161  1.00  0.00                              
ATOM   1485  C   ASP    81      17.573  51.533  -1.439  1.00  0.00                              
ATOM   1487  O   ASP    81      17.602  50.690  -0.559  1.00  0.00                              
ATOM   1489  CG  ASP    81      14.341  53.613  -0.905  1.00  0.00                              
ATOM   1491  OD1 ASP    81      14.678  54.431  -0.022  1.00  0.00                              
ATOM   1493  OD2 ASP    81      13.310  53.754  -1.596  1.00  0.00                              
ATOM   1495  H   PHE    82      18.271  52.155  -3.165  1.00  0.00                              
ATOM   1497  N   PHE    82      18.301  51.448  -2.539  1.00  0.00                              
ATOM   1499  CA  PHE    82      19.135  50.279  -2.839  1.00  0.00                              
ATOM   1501  CB  PHE    82      19.822  50.493  -4.213  1.00  0.00                              
ATOM   1503  C   PHE    82      20.183  50.033  -1.738  1.00  0.00                              
ATOM   1505  O   PHE    82      20.507  48.880  -1.427  1.00  0.00                              
ATOM   1507  CG  PHE    82      20.544  49.297  -4.740  1.00  0.00                              
ATOM   1509  CD1 PHE    82      19.850  48.267  -5.344  1.00  0.00                              
ATOM   1511  CE1 PHE    82      20.527  47.114  -5.800  1.00  0.00                              
ATOM   1513  CZ  PHE    82      21.896  47.001  -5.617  1.00  0.00                              
ATOM   1515  CD2 PHE    82      21.936  49.215  -4.664  1.00  0.00                              
ATOM   1517  CE2 PHE    82      22.615  48.075  -5.125  1.00  0.00                              
ATOM   1519  H   GLU    83      20.362  51.971  -1.361  1.00  0.00                              
ATOM   1521  N   GLU    83      20.677  51.114  -1.121  1.00  0.00                              
ATOM   1523  CA  GLU    83      21.713  50.992  -0.097  1.00  0.00                              
ATOM   1525  CB  GLU    83      22.857  51.998  -0.363  1.00  0.00                              
ATOM   1527  C   GLU    83      21.138  51.171   1.331  1.00  0.00                              
ATOM   1529  O   GLU    83      21.894  51.253   2.307  1.00  0.00                              
ATOM   1531  CG  GLU    83      23.745  51.615  -1.563  1.00  0.00                              
ATOM   1533  CD  GLU    83      24.608  52.770  -2.096  1.00  0.00                              
ATOM   1535  OE1 GLU    83      25.247  53.473  -1.278  1.00  0.00                              
ATOM   1537  OE2 GLU    83      24.662  52.954  -3.333  1.00  0.00                              
ATOM   1539  H   ALA    84      19.273  51.179   0.682  1.00  0.00                              
ATOM   1541  N   ALA    84      19.805  51.209   1.450  1.00  0.00                              
ATOM   1543  CA  ALA    84      19.161  51.335   2.767  1.00  0.00                              
ATOM   1545  CB  ALA    84      18.570  52.736   2.934  1.00  0.00                              
ATOM   1547  C   ALA    84      18.065  50.268   2.970  1.00  0.00                              
ATOM   1549  O   ALA    84      17.890  49.757   4.077  1.00  0.00                              
ATOM   1551  H   GLU    85      17.563  50.288   1.051  1.00  0.00                              
ATOM   1553  N   GLU    85      17.344  49.918   1.896  1.00  0.00                              
ATOM   1555  CA  GLU    85      16.233  48.952   1.997  1.00  0.00                              
ATOM   1557  CB  GLU    85      15.532  48.777   0.642  1.00  0.00                              
ATOM   1559  C   GLU    85      16.717  47.598   2.521  1.00  0.00                              
ATOM   1561  O   GLU    85      15.919  46.806   3.040  1.00  0.00                              
ATOM   1563  CG  GLU    85      14.119  48.224   0.742  1.00  0.00                              
ATOM   1565  CD  GLU    85      14.064  46.707   0.776  1.00  0.00                              
ATOM   1567  OE1 GLU    85      14.963  46.061   0.192  1.00  0.00                              
ATOM   1569  OE2 GLU    85      13.110  46.160   1.367  1.00  0.00                              
ATOM   1571  H   LEU    86      18.566  47.969   1.938  1.00  0.00                              
ATOM   1573  N   LEU    86      18.005  47.346   2.401  1.00  0.00                              
ATOM   1575  CA  LEU    86      18.593  46.123   2.916  1.00  0.00                              
ATOM   1577  CB  LEU    86      20.107  46.115   2.652  1.00  0.00                              
ATOM   1579  C   LEU    86      18.340  45.974   4.423  1.00  0.00                              
ATOM   1581  O   LEU    86      18.146  44.853   4.916  1.00  0.00                              
ATOM   1583  CG  LEU    86      20.846  44.838   3.032  1.00  0.00                              
ATOM   1585  CD1 LEU    86      20.249  43.672   2.276  1.00  0.00                              
ATOM   1587  CD2 LEU    86      22.331  44.976   2.727  1.00  0.00                              
ATOM   1589  H   GLU    87      18.503  47.926   4.739  1.00  0.00                              
ATOM   1591  N   GLU    87      18.373  47.090   5.161  1.00  0.00                              
ATOM   1593  CA  GLU    87      18.227  47.036   6.618  1.00  0.00                              
ATOM   1595  CB  GLU    87      19.571  47.376   7.304  1.00  0.00                              
ATOM   1597  C   GLU    87      17.107  47.966   7.147  1.00  0.00                              
ATOM   1599  O   GLU    87      16.571  47.728   8.236  1.00  0.00                              
ATOM   1601  CG  GLU    87      20.695  46.383   6.980  1.00  0.00                              
ATOM   1603  CD  GLU    87      22.038  46.741   7.620  1.00  0.00                              
ATOM   1605  OE1 GLU    87      22.479  47.911   7.493  1.00  0.00                              
ATOM   1607  OE2 GLU    87      22.663  45.849   8.232  1.00  0.00                              
ATOM   1609  H   ASN    88      17.213  49.184   5.555  1.00  0.00                              
ATOM   1611  N   ASN    88      16.780  49.062   6.382  1.00  0.00                              
ATOM   1613  CA  ASN    88      15.755  50.093   6.832  1.00  0.00                              
ATOM   1615  CB  ASN    88      15.881  51.405   5.988  1.00  0.00                              
ATOM   1617  C   ASN    88      14.303  49.554   6.781  1.00  0.00                              
ATOM   1619  O   ASN    88      13.979  48.563   7.434  1.00  0.00                              
ATOM   1621  CG  ASN    88      15.010  52.587   6.520  1.00  0.00                              
ATOM   1623  ND2 ASN    88      14.752  53.567   5.659  1.00  0.00                              
ATOM   1625 HD21 ASN    88      15.104  53.506   4.787  1.00  0.00                              
ATOM   1627 HD22 ASN    88      14.221  54.296   5.931  1.00  0.00                              
ATOM   1629  OD1 ASN    88      14.612  52.621   7.696  1.00  0.00                              
ATOM   1631  H   LEU    89      13.736  50.969   5.507  1.00  0.00                              
ATOM   1633  N   LEU    89      13.430  50.239   6.022  1.00  0.00                              
ATOM   1635  CA  LEU    89      12.004  49.867   5.964  1.00  0.00                              
ATOM   1637  CB  LEU    89      11.132  51.079   6.296  1.00  0.00                              
ATOM   1639  C   LEU    89      11.609  49.308   4.585  1.00  0.00                              
ATOM   1641  O   LEU    89      12.081  49.791   3.545  1.00  0.00                              
ATOM   1643  CG  LEU    89      11.352  51.721   7.667  1.00  0.00                              
ATOM   1645  CD1 LEU    89      10.537  53.002   7.782  1.00  0.00                              
ATOM   1647  CD2 LEU    89      10.972  50.745   8.771  1.00  0.00                              
ATOM   1649  N   PRO    90      10.724  48.313   4.555  1.00  0.00                              
ATOM   1651  CA  PRO    90      10.293  47.725   3.291  1.00  0.00                              
ATOM   1653  CB  PRO    90       9.561  46.459   3.721  1.00  0.00                              
ATOM   1655  C   PRO    90       9.378  48.655   2.497  1.00  0.00                              
ATOM   1657  O   PRO    90       8.275  48.976   2.943  1.00  0.00                              
ATOM   1659  CG  PRO    90       8.998  46.816   5.061  1.00  0.00                              
ATOM   1661  CD  PRO    90      10.082  47.651   5.711  1.00  0.00                              
ATOM   1663  H   ALA    91      10.737  48.938   1.112  1.00  0.00                              
ATOM   1665  N   ALA    91       9.859  49.123   1.341  1.00  0.00                              
ATOM   1667  CA  ALA    91       9.046  49.985   0.438  1.00  0.00                              
ATOM   1669  CB  ALA    91       9.965  50.824  -0.437  1.00  0.00                              
ATOM   1671  C   ALA    91       8.079  49.134  -0.444  1.00  0.00                              
ATOM   1673  O   ALA    91       8.195  47.903  -0.482  1.00  0.00                              
ATOM   1675  H   TRP    92       7.012  50.753  -1.061  1.00  0.00                              
ATOM   1677  N   TRP    92       7.069  49.808  -1.120  1.00  0.00                              
ATOM   1679  CA  TRP    92       6.047  49.065  -1.957  1.00  0.00                              
ATOM   1681  CB  TRP    92       5.374  48.004  -1.093  1.00  0.00                              
ATOM   1683  C   TRP    92       4.927  50.007  -2.511  1.00  0.00                              
ATOM   1685  O   TRP    92       4.931  51.220  -2.257  1.00  0.00                              
ATOM   1687  CG  TRP    92       4.752  48.565   0.133  1.00  0.00                              
ATOM   1689  CD1 TRP    92       4.893  49.838   0.617  1.00  0.00                              
ATOM   1691  NE1 TRP    92       4.130  49.998   1.735  1.00  0.00                              
ATOM   1693  HE1 TRP    92       4.083  50.794   2.256  1.00  0.00                              
ATOM   1695  CD2 TRP    92       3.926  47.874   1.060  1.00  0.00                              
ATOM   1697  CE2 TRP    92       3.494  48.820   2.010  1.00  0.00                              
ATOM   1699  CE3 TRP    92       3.444  46.566   1.142  1.00  0.00                              
ATOM   1701  CZ3 TRP    92       2.527  46.258   2.128  1.00  0.00                              
ATOM   1703  CH2 TRP    92       2.065  47.238   3.013  1.00  0.00                              
ATOM   1705  CZ2 TRP    92       2.514  48.532   2.945  1.00  0.00                              
ATOM   1707  H   TRP    93       4.110  48.502  -3.579  1.00  0.00                              
ATOM   1709  N   TRP    93       3.980  49.407  -3.329  1.00  0.00                              
ATOM   1711  CA  TRP    93       2.778  50.133  -3.847  1.00  0.00                              
ATOM   1713  CB  TRP    93       1.677  50.254  -2.710  1.00  0.00                              
ATOM   1715  C   TRP    93       3.146  51.523  -4.364  1.00  0.00                              
ATOM   1717  O   TRP    93       3.069  51.784  -5.568  1.00  0.00                              
ATOM   1719  CG  TRP    93       1.198  48.915  -2.116  1.00  0.00                              
ATOM   1721  CD1 TRP    93       1.450  47.665  -2.613  1.00  0.00                              
ATOM   1723  NE1 TRP    93       0.820  46.712  -1.836  1.00  0.00                              
ATOM   1725  HE1 TRP    93       0.856  45.771  -1.987  1.00  0.00                              
ATOM   1727  CD2 TRP    93       0.358  48.728  -0.956  1.00  0.00                              
ATOM   1729  CE2 TRP    93       0.171  47.337  -0.799  1.00  0.00                              
ATOM   1731  CE3 TRP    93      -0.268  49.610  -0.047  1.00  0.00                              
ATOM   1733  CZ3 TRP    93      -1.092  49.074   0.942  1.00  0.00                              
ATOM   1735  CH2 TRP    93      -1.270  47.684   1.060  1.00  0.00                              
ATOM   1737  CZ2 TRP    93      -0.613  46.798   0.232  1.00  0.00                              
TER 
END
