
#######################################################
#                                                     #
#                        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   18 (  179),  selected   18 , name T0299TS277_5-D2
# Molecule2: number of CA atoms   89 (  757),  selected   89 , name T0299_D2.pdb
# PARAMETERS: T0299TS277_5-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    L      79      E     119          2.331
LGA    E      80      S     120          1.788
LGA    D      81      L     121          2.318
LGA    F      82      E     122          2.875
LGA    E      83      L     123          1.740
LGA    A      84      K     124          4.154
LGA    E      85      D     125          2.440
LGA    L      86      E     126          5.026
LGA    E      87      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    N      88      F     140          0.971
LGA    L      89      S     141          0.913
LGA    P      90      E     142          1.016
LGA    -       -      E     143           -
LGA    -       -      S     144           -
LGA    A      91      Y     145          1.697
LGA    W      92      S     146          3.761
LGA    W      93      K     147          3.087
LGA    -       -      T     148           -
LGA    S      94      A     149          1.725
LGA    -       -      Y     150           -
LGA    -       -      H     151           -
LGA    -       -      K     152           -
LGA    R      95      Y     153          0.910
LGA    D      96      L     154          1.229
LGA    -       -      L     155           -
LGA    -       -      K     156           -
LGA    -       -      V     157           -
LGA    -       -      P     158           -
LGA    -       -      F     159           -
LGA    -       -      Y     160           -
LGA    -       -      R     161           -
LGA    -       -      H     162           -
LGA    -       -      I     163           -
LGA    -       -      T     164           -
LGA    -       -      I     165           -
LGA    -       -      R     166           -
LGA    -       -      N     167           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   18   89    5.0     17    2.53     0.00     13.454     0.647

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.281905 * X  +  -0.318361 * Y  +   0.905083 * Z  +  -7.072351
  Y_new =   0.258969 * X  +   0.883081 * Y  +   0.391283 * Z  + -15.383150
  Z_new =  -0.923831 * X  +   0.344693 * Y  +  -0.166499 * Z  +  15.896331 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.020781   -1.120811  [ DEG:   115.7822    -64.2178 ]
  Theta =   1.177971    1.963621  [ DEG:    67.4928    112.5072 ]
  Phi   =   2.398574   -0.743019  [ DEG:   137.4282    -42.5718 ]
 
# 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_5-D2                               
REMARK     2: T0299_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299TS277_5-D2.T0299_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   18   89   5.0   17   2.53    0.00  13.454
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS277_5-D2
PFRMAT TS 
TARGET T0299
MODEL 5
PARENT 1G0C_A
ATOM   1439  H   LEU    79      16.345  57.539   4.167  1.00  0.00                              
ATOM   1441  N   LEU    79      15.695  58.005   4.670  1.00  0.00                              
ATOM   1443  CA  LEU    79      15.717  59.453   4.661  1.00  0.00                              
ATOM   1445  CB  LEU    79      15.337  60.010   6.025  1.00  0.00                              
ATOM   1447  C   LEU    79      17.113  59.950   4.283  1.00  0.00                              
ATOM   1449  O   LEU    79      17.410  60.145   3.102  1.00  0.00                              
ATOM   1451  CG  LEU    79      15.772  61.450   6.296  1.00  0.00                              
ATOM   1453  CD1 LEU    79      15.390  62.344   5.113  1.00  0.00                              
ATOM   1455  CD2 LEU    79      15.128  61.962   7.586  1.00  0.00                              
ATOM   1457  H   GLU    80      17.702  59.956   6.173  1.00  0.00                              
ATOM   1459  N   GLU    80      17.984  60.115   5.283  1.00  0.00                              
ATOM   1461  CA  GLU    80      19.358  60.545   5.035  1.00  0.00                              
ATOM   1463  CB  GLU    80      20.066  60.885   6.354  1.00  0.00                              
ATOM   1465  C   GLU    80      20.148  59.469   4.281  1.00  0.00                              
ATOM   1467  O   GLU    80      20.115  58.266   4.657  1.00  0.00                              
ATOM   1469  CG  GLU    80      19.291  61.840   7.250  1.00  0.00                              
ATOM   1471  CD  GLU    80      18.510  61.130   8.344  1.00  0.00                              
ATOM   1473  OE1 GLU    80      17.997  60.017   8.088  1.00  0.00                              
ATOM   1475  OE2 GLU    80      18.425  61.674   9.470  1.00  0.00                              
ATOM   1477  H   ASP    81      20.909  60.798   3.015  1.00  0.00                              
ATOM   1479  N   ASP    81      20.886  59.881   3.231  1.00  0.00                              
ATOM   1481  CA  ASP    81      21.638  58.941   2.414  1.00  0.00                              
ATOM   1483  CB  ASP    81      20.962  57.577   2.432  1.00  0.00                              
ATOM   1485  C   ASP    81      21.782  59.449   0.961  1.00  0.00                              
ATOM   1487  O   ASP    81      21.732  60.654   0.707  1.00  0.00                              
ATOM   1489  CG  ASP    81      21.856  56.456   1.943  1.00  0.00                              
ATOM   1491  OD1 ASP    81      22.892  56.185   2.591  1.00  0.00                              
ATOM   1493  OD2 ASP    81      21.506  55.817   0.919  1.00  0.00                              
ATOM   1495  H   PHE    82      21.854  57.612   0.248  1.00  0.00                              
ATOM   1497  N   PHE    82      21.909  58.530   0.017  1.00  0.00                              
ATOM   1499  CA  PHE    82      22.138  58.901  -1.383  1.00  0.00                              
ATOM   1501  CB  PHE    82      23.131  57.918  -2.034  1.00  0.00                              
ATOM   1503  C   PHE    82      20.821  59.016  -2.188  1.00  0.00                              
ATOM   1505  O   PHE    82      20.463  58.118  -2.958  1.00  0.00                              
ATOM   1507  CG  PHE    82      24.393  57.823  -1.242  1.00  0.00                              
ATOM   1509  CD1 PHE    82      24.498  56.922  -0.174  1.00  0.00                              
ATOM   1511  CE1 PHE    82      25.650  56.881   0.617  1.00  0.00                              
ATOM   1513  CZ  PHE    82      26.678  57.776   0.382  1.00  0.00                              
ATOM   1515  CD2 PHE    82      25.482  58.648  -1.536  1.00  0.00                              
ATOM   1517  CE2 PHE    82      26.631  58.613  -0.749  1.00  0.00                              
ATOM   1519  H   GLU    83      20.390  60.768  -1.362  1.00  0.00                              
ATOM   1521  N   GLU    83      20.101  60.131  -1.998  1.00  0.00                              
ATOM   1523  CA  GLU    83      18.853  60.377  -2.754  1.00  0.00                              
ATOM   1525  CB  GLU    83      17.993  61.440  -2.057  1.00  0.00                              
ATOM   1527  C   GLU    83      19.138  60.809  -4.206  1.00  0.00                              
ATOM   1529  O   GLU    83      19.304  59.964  -5.091  1.00  0.00                              
ATOM   1531  CG  GLU    83      17.393  60.969  -0.739  1.00  0.00                              
ATOM   1533  CD  GLU    83      16.595  62.048  -0.017  1.00  0.00                              
ATOM   1535  OE1 GLU    83      16.812  63.246  -0.305  1.00  0.00                              
ATOM   1537  OE2 GLU    83      15.740  61.697   0.826  1.00  0.00                              
ATOM   1539  H   ALA    84      19.080  62.727  -3.737  1.00  0.00                              
ATOM   1541  N   ALA    84      19.181  62.129  -4.447  1.00  0.00                              
ATOM   1543  CA  ALA    84      19.377  62.660  -5.805  1.00  0.00                              
ATOM   1545  CB  ALA    84      19.066  64.154  -5.837  1.00  0.00                              
ATOM   1547  C   ALA    84      20.814  62.408  -6.320  1.00  0.00                              
ATOM   1549  O   ALA    84      21.612  63.350  -6.442  1.00  0.00                              
ATOM   1551  H   GLU    85      20.482  60.460  -6.577  1.00  0.00                              
ATOM   1553  N   GLU    85      21.134  61.142  -6.660  1.00  0.00                              
ATOM   1555  CA  GLU    85      22.476  60.801  -7.169  1.00  0.00                              
ATOM   1557  CB  GLU    85      23.280  59.998  -6.102  1.00  0.00                              
ATOM   1559  C   GLU    85      22.412  60.021  -8.525  1.00  0.00                              
ATOM   1561  O   GLU    85      22.807  60.555  -9.562  1.00  0.00                              
ATOM   1563  CG  GLU    85      24.706  59.663  -6.508  1.00  0.00                              
ATOM   1565  CD  GLU    85      25.450  59.096  -5.407  1.00  0.00                              
ATOM   1567  OE1 GLU    85      24.850  58.343  -4.661  1.00  0.00                              
ATOM   1569  OE2 GLU    85      26.666  59.435  -5.237  1.00  0.00                              
ATOM   1571  H   LEU    86      21.525  58.429  -7.694  1.00  0.00                              
ATOM   1573  N   LEU    86      21.870  58.772  -8.507  1.00  0.00                              
ATOM   1575  CA  LEU    86      21.817  57.917  -9.738  1.00  0.00                              
ATOM   1577  CB  LEU    86      22.770  56.696  -9.596  1.00  0.00                              
ATOM   1579  C   LEU    86      20.407  57.358  -9.987  1.00  0.00                              
ATOM   1581  O   LEU    86      20.167  56.728 -11.018  1.00  0.00                              
ATOM   1583  CG  LEU    86      24.236  56.969  -9.375  1.00  0.00                              
ATOM   1585  CD1 LEU    86      25.033  55.658  -9.372  1.00  0.00                              
ATOM   1587  CD2 LEU    86      24.762  57.919 -10.441  1.00  0.00                              
ATOM   1589  H   GLU    87      19.701  58.105  -8.317  1.00  0.00                              
ATOM   1591  N   GLU    87      19.497  57.563  -9.065  1.00  0.00                              
ATOM   1593  CA  GLU    87      18.163  56.961  -9.180  1.00  0.00                              
ATOM   1595  CB  GLU    87      17.246  57.451  -8.071  1.00  0.00                              
ATOM   1597  C   GLU    87      17.529  57.208 -10.553  1.00  0.00                              
ATOM   1599  O   GLU    87      16.719  56.403 -11.020  1.00  0.00                              
ATOM   1601  CG  GLU    87      17.730  57.123  -6.670  1.00  0.00                              
ATOM   1603  CD  GLU    87      16.946  57.848  -5.585  1.00  0.00                              
ATOM   1605  OE1 GLU    87      16.289  58.868  -5.901  1.00  0.00                              
ATOM   1607  OE2 GLU    87      16.993  57.409  -4.413  1.00  0.00                              
ATOM   1609  H   ASN    88      18.493  58.906 -10.783  1.00  0.00                              
ATOM   1611  N   ASN    88      17.875  58.322 -11.185  1.00  0.00                              
ATOM   1613  CA  ASN    88      17.305  58.672 -12.490  1.00  0.00                              
ATOM   1615  CB  ASN    88      17.312  60.197 -12.691  1.00  0.00                              
ATOM   1617  C   ASN    88      18.049  57.982 -13.654  1.00  0.00                              
ATOM   1619  O   ASN    88      17.705  58.193 -14.819  1.00  0.00                              
ATOM   1621  CG  ASN    88      16.264  60.908 -11.844  1.00  0.00                              
ATOM   1623  ND2 ASN    88      16.216  62.239 -11.946  1.00  0.00                              
ATOM   1625 HD21 ASN    88      16.824  62.671 -12.522  1.00  0.00                              
ATOM   1627 HD22 ASN    88      15.584  62.721 -11.437  1.00  0.00                              
ATOM   1629  OD1 ASN    88      15.488  60.268 -11.131  1.00  0.00                              
ATOM   1631  H   LEU    89      19.231  56.956 -12.429  1.00  0.00                              
ATOM   1633  N   LEU    89      19.050  57.146 -13.338  1.00  0.00                              
ATOM   1635  CA  LEU    89      19.869  56.502 -14.387  1.00  0.00                              
ATOM   1637  CB  LEU    89      21.350  56.920 -14.251  1.00  0.00                              
ATOM   1639  C   LEU    89      19.740  54.933 -14.374  1.00  0.00                              
ATOM   1641  O   LEU    89      18.630  54.388 -14.250  1.00  0.00                              
ATOM   1643  CG  LEU    89      21.660  58.416 -14.376  1.00  0.00                              
ATOM   1645  CD1 LEU    89      23.131  58.668 -14.075  1.00  0.00                              
ATOM   1647  CD2 LEU    89      21.307  58.922 -15.774  1.00  0.00                              
ATOM   1649  N   PRO    90      20.885  54.206 -14.540  1.00  0.00                              
ATOM   1651  CA  PRO    90      20.880  52.707 -14.548  1.00  0.00                              
ATOM   1653  CB  PRO    90      22.244  52.368 -15.129  1.00  0.00                              
ATOM   1655  C   PRO    90      20.682  52.048 -13.139  1.00  0.00                              
ATOM   1657  O   PRO    90      19.566  51.636 -12.801  1.00  0.00                              
ATOM   1659  CG  PRO    90      23.120  53.495 -14.650  1.00  0.00                              
ATOM   1661  CD  PRO    90      22.247  54.735 -14.768  1.00  0.00                              
ATOM   1663  H   ALA    91      22.630  52.221 -12.647  1.00  0.00                              
ATOM   1665  N   ALA    91      21.808  51.903 -12.339  1.00  0.00                              
ATOM   1667  CA  ALA    91      21.747  51.251 -10.989  1.00  0.00                              
ATOM   1669  CB  ALA    91      22.708  50.066 -10.931  1.00  0.00                              
ATOM   1671  C   ALA    91      22.071  52.245  -9.870  1.00  0.00                              
ATOM   1673  O   ALA    91      23.216  52.719  -9.748  1.00  0.00                              
ATOM   1675  H   TRP    92      20.271  52.013  -9.114  1.00  0.00                              
ATOM   1677  N   TRP    92      21.084  52.496  -9.033  1.00  0.00                              
ATOM   1679  CA  TRP    92      21.192  53.488  -7.976  1.00  0.00                              
ATOM   1681  CB  TRP    92      19.810  53.837  -7.470  1.00  0.00                              
ATOM   1683  C   TRP    92      22.013  53.025  -6.807  1.00  0.00                              
ATOM   1685  O   TRP    92      22.832  52.100  -6.916  1.00  0.00                              
ATOM   1687  CG  TRP    92      19.195  52.776  -6.670  1.00  0.00                              
ATOM   1689  CD1 TRP    92      19.693  51.524  -6.412  1.00  0.00                              
ATOM   1691  NE1 TRP    92      18.811  50.820  -5.679  1.00  0.00                              
ATOM   1693  HE1 TRP    92      18.933  49.922  -5.391  1.00  0.00                              
ATOM   1695  CD2 TRP    92      17.930  52.831  -6.074  1.00  0.00                              
ATOM   1697  CE2 TRP    92      17.695  51.575  -5.485  1.00  0.00                              
ATOM   1699  CE3 TRP    92      16.909  53.780  -6.067  1.00  0.00                              
ATOM   1701  CZ3 TRP    92      15.698  53.437  -5.530  1.00  0.00                              
ATOM   1703  CH2 TRP    92      15.474  52.160  -5.021  1.00  0.00                              
ATOM   1705  CZ2 TRP    92      16.456  51.212  -5.008  1.00  0.00                              
ATOM   1707  H   TRP    93      21.091  54.328  -5.641  1.00  0.00                              
ATOM   1709  N   TRP    93      21.767  53.663  -5.655  1.00  0.00                              
ATOM   1711  CA  TRP    93      22.483  53.385  -4.462  1.00  0.00                              
ATOM   1713  CB  TRP    93      23.791  54.126  -4.515  1.00  0.00                              
ATOM   1715  C   TRP    93      21.679  53.858  -3.256  1.00  0.00                              
ATOM   1717  O   TRP    93      21.739  55.039  -2.882  1.00  0.00                              
ATOM   1719  CG  TRP    93      24.689  53.849  -3.377  1.00  0.00                              
ATOM   1721  CD1 TRP    93      24.547  52.868  -2.443  1.00  0.00                              
ATOM   1723  NE1 TRP    93      25.615  52.883  -1.582  1.00  0.00                              
ATOM   1725  HE1 TRP    93      25.725  52.299  -0.839  1.00  0.00                              
ATOM   1727  CD2 TRP    93      25.854  54.585  -3.016  1.00  0.00                              
ATOM   1729  CE2 TRP    93      26.454  53.897  -1.933  1.00  0.00                              
ATOM   1731  CE3 TRP    93      26.539  55.682  -3.593  1.00  0.00                              
ATOM   1733  CZ3 TRP    93      27.804  56.001  -3.114  1.00  0.00                              
ATOM   1735  CH2 TRP    93      28.415  55.230  -2.087  1.00  0.00                              
ATOM   1737  CZ2 TRP    93      27.764  54.178  -1.498  1.00  0.00                              
ATOM   1739  H   SER    94      21.035  52.050  -2.858  1.00  0.00                              
ATOM   1741  N   SER    94      20.968  52.949  -2.616  1.00  0.00                              
ATOM   1743  CA  SER    94      20.105  53.325  -1.538  1.00  0.00                              
ATOM   1745  CB  SER    94      18.701  53.632  -2.064  1.00  0.00                              
ATOM   1747  C   SER    94      20.017  52.254  -0.470  1.00  0.00                              
ATOM   1749  O   SER    94      20.504  51.137  -0.652  1.00  0.00                              
ATOM   1751  OG  SER    94      18.000  52.429  -2.347  1.00  0.00                              
ATOM   1753  H   ARG    95      19.138  53.517   0.776  1.00  0.00                              
ATOM   1755  N   ARG    95      19.423  52.615   0.669  1.00  0.00                              
ATOM   1757  CA  ARG    95      19.190  51.653   1.775  1.00  0.00                              
ATOM   1759  CB  ARG    95      18.859  52.404   3.081  1.00  0.00                              
ATOM   1761  C   ARG    95      18.034  50.628   1.423  1.00  0.00                              
ATOM   1763  O   ARG    95      18.000  50.082   0.318  1.00  0.00                              
ATOM   1765  CG  ARG    95      19.972  53.347   3.556  1.00  0.00                              
ATOM   1767  CD  ARG    95      19.555  54.125   4.808  1.00  0.00                              
ATOM   1769  NE  ARG    95      20.554  55.137   5.189  1.00  0.00                              
ATOM   1771  HE  ARG    95      20.649  55.896   4.627  1.00  0.00                              
ATOM   1773  CZ  ARG    95      21.334  55.064   6.276  1.00  0.00                              
ATOM   1775  NH1 ARG    95      21.206  54.051   7.127  1.00  0.00                              
ATOM   1777  NH2 ARG    95      22.264  55.984   6.487  1.00  0.00                              
ATOM   1779  H   ASP    96      17.094  50.926   3.169  1.00  0.00                              
ATOM   1781  N   ASP    96      17.074  50.413   2.378  1.00  0.00                              
ATOM   1783  CA  ASP    96      15.971  49.390   2.195  1.00  0.00                              
ATOM   1785  CB  ASP    96      15.449  48.912   3.558  1.00  0.00                              
ATOM   1787  C   ASP    96      14.788  49.935   1.355  1.00  0.00                              
ATOM   1789  O   ASP    96      14.885  50.038   0.124  1.00  0.00                              
ATOM   1791  CG  ASP    96      16.517  48.268   4.416  1.00  0.00                              
ATOM   1793  OD1 ASP    96      17.514  47.766   3.856  1.00  0.00                              
ATOM   1795  OD2 ASP    96      16.382  48.285   5.658  1.00  0.00                              
TER 
END
