
#######################################################
#                                                     #
#                        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_3-D2
# Molecule2: number of CA atoms   89 (  757),  selected   89 , name T0299_D2.pdb
# PARAMETERS: T0299TS277_3-D2.T0299_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      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    L      79      A      98          3.964
LGA    E      80      R      99          3.564
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    D      81      F     140          2.097
LGA    F      82      S     141          2.168
LGA    -       -      E     142           -
LGA    E      83      E     143          1.144
LGA    A      84      S     144          1.057
LGA    E      85      Y     145          1.053
LGA    L      86      S     146          1.079
LGA    E      87      K     147          1.057
LGA    N      88      T     148          1.847
LGA    L      89      A     149          1.364
LGA    -       -      Y     150           -
LGA    -       -      H     151           -
LGA    -       -      K     152           -
LGA    P      90      Y     153          1.975
LGA    A      91      L     154          1.569
LGA    W      92      L     155          1.972
LGA    -       -      K     156           -
LGA    W      93      V     157          4.220
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)   15   89    5.0     15    2.26     6.67     14.647     0.635

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.005599 * X  +  -0.980145 * Y  +  -0.198203 * Z  +  12.625134
  Y_new =  -0.956704 * X  +   0.052430 * Y  +  -0.286302 * Z  +  57.941219
  Z_new =   0.291010 * X  +   0.191225 * Y  +  -0.937415 * Z  + -18.511698 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.940361   -0.201231  [ DEG:   168.4703    -11.5297 ]
  Theta =  -0.295282   -2.846311  [ DEG:   -16.9184   -163.0816 ]
  Phi   =  -1.564944    1.576649  [ DEG:   -89.6647     90.3353 ]
 
# 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_3-D2                               
REMARK     2: T0299_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299TS277_3-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   2.26    6.67  14.647
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS277_3-D2
PFRMAT TS 
TARGET T0299
MODEL 3
PARENT 1CTF
ATOM   1439  H   LEU    79      13.043  52.972 -10.848  1.00  0.00                              
ATOM   1441  N   LEU    79      12.961  52.540 -11.687  1.00  0.00                              
ATOM   1443  CA  LEU    79      12.716  53.282 -12.883  1.00  0.00                              
ATOM   1445  CB  LEU    79      11.347  52.958 -13.394  1.00  0.00                              
ATOM   1447  C   LEU    79      12.887  54.755 -12.756  1.00  0.00                              
ATOM   1449  O   LEU    79      12.252  55.409 -11.922  1.00  0.00                              
ATOM   1451  CG  LEU    79      10.993  53.536 -14.702  1.00  0.00                              
ATOM   1453  CD1 LEU    79      10.564  54.955 -14.535  1.00  0.00                              
ATOM   1455  CD2 LEU    79      12.158  53.404 -15.666  1.00  0.00                              
ATOM   1457  H   GLU    80      14.214  54.777 -14.190  1.00  0.00                              
ATOM   1459  N   GLU    80      13.703  55.309 -13.597  1.00  0.00                              
ATOM   1461  CA  GLU    80      13.841  56.714 -13.612  1.00  0.00                              
ATOM   1463  CB  GLU    80      13.226  57.296 -12.356  1.00  0.00                              
ATOM   1465  C   GLU    80      15.249  57.124 -13.721  1.00  0.00                              
ATOM   1467  O   GLU    80      15.689  58.032 -13.013  1.00  0.00                              
ATOM   1469  CG  GLU    80      13.105  58.797 -12.375  1.00  0.00                              
ATOM   1471  CD  GLU    80      12.258  59.339 -11.232  1.00  0.00                              
ATOM   1473  OE1 GLU    80      12.035  58.599 -10.250  1.00  0.00                              
ATOM   1475  OE2 GLU    80      11.797  60.503 -11.324  1.00  0.00                              
ATOM   1477  H   ASP    81      15.618  55.797 -15.113  1.00  0.00                              
ATOM   1479  N   ASP    81      15.991  56.499 -14.603  1.00  0.00                              
ATOM   1481  CA  ASP    81      17.366  56.868 -14.806  1.00  0.00                              
ATOM   1483  CB  ASP    81      17.995  57.276 -13.473  1.00  0.00                              
ATOM   1485  C   ASP    81      18.166  55.706 -15.463  1.00  0.00                              
ATOM   1487  O   ASP    81      18.059  55.481 -16.683  1.00  0.00                              
ATOM   1489  CG  ASP    81      19.356  57.912 -13.639  1.00  0.00                              
ATOM   1491  OD1 ASP    81      19.742  58.210 -14.797  1.00  0.00                              
ATOM   1493  OD2 ASP    81      20.041  58.144 -12.619  1.00  0.00                              
ATOM   1495  H   PHE    82      19.129  55.265 -13.776  1.00  0.00                              
ATOM   1497  N   PHE    82      19.001  55.003 -14.673  1.00  0.00                              
ATOM   1499  CA  PHE    82      19.724  53.828 -15.190  1.00  0.00                              
ATOM   1501  CB  PHE    82      19.784  53.828 -16.708  1.00  0.00                              
ATOM   1503  C   PHE    82      21.151  53.681 -14.626  1.00  0.00                              
ATOM   1505  O   PHE    82      21.371  52.971 -13.634  1.00  0.00                              
ATOM   1507  CG  PHE    82      20.566  52.674 -17.225  1.00  0.00                              
ATOM   1509  CD1 PHE    82      20.232  51.376 -16.860  1.00  0.00                              
ATOM   1511  CE1 PHE    82      20.971  50.300 -17.313  1.00  0.00                              
ATOM   1513  CZ  PHE    82      22.067  50.512 -18.145  1.00  0.00                              
ATOM   1515  CD2 PHE    82      21.675  52.878 -18.048  1.00  0.00                              
ATOM   1517  CE2 PHE    82      22.426  51.808 -18.500  1.00  0.00                              
ATOM   1519  H   GLU    83      21.890  54.870 -16.017  1.00  0.00                              
ATOM   1521  N   GLU    83      22.118  54.311 -15.289  1.00  0.00                              
ATOM   1523  CA  GLU    83      23.503  54.172 -14.917  1.00  0.00                              
ATOM   1525  CB  GLU    83      24.329  55.300 -15.539  1.00  0.00                              
ATOM   1527  C   GLU    83      23.674  54.173 -13.405  1.00  0.00                              
ATOM   1529  O   GLU    83      24.258  53.246 -12.846  1.00  0.00                              
ATOM   1531  CG  GLU    83      25.806  54.980 -15.686  1.00  0.00                              
ATOM   1533  CD  GLU    83      26.637  56.185 -16.109  1.00  0.00                              
ATOM   1535  OE1 GLU    83      26.049  57.269 -16.326  1.00  0.00                              
ATOM   1537  OE2 GLU    83      27.880  56.053 -16.210  1.00  0.00                              
ATOM   1539  H   ALA    84      22.665  55.861 -13.188  1.00  0.00                              
ATOM   1541  N   ALA    84      23.136  55.198 -12.726  1.00  0.00                              
ATOM   1543  CA  ALA    84      23.247  55.285 -11.257  1.00  0.00                              
ATOM   1545  CB  ALA    84      22.912  56.694 -10.781  1.00  0.00                              
ATOM   1547  C   ALA    84      22.328  54.256 -10.562  1.00  0.00                              
ATOM   1549  O   ALA    84      21.493  54.635  -9.714  1.00  0.00                              
ATOM   1551  H   GLU    85      23.013  52.756 -11.685  1.00  0.00                              
ATOM   1553  N   GLU    85      22.444  52.953 -10.971  1.00  0.00                              
ATOM   1555  CA  GLU    85      21.641  51.850 -10.366  1.00  0.00                              
ATOM   1557  CB  GLU    85      21.590  50.626 -11.333  1.00  0.00                              
ATOM   1559  C   GLU    85      22.176  51.409  -8.978  1.00  0.00                              
ATOM   1561  O   GLU    85      21.430  51.379  -8.010  1.00  0.00                              
ATOM   1563  CG  GLU    85      20.779  49.428 -10.808  1.00  0.00                              
ATOM   1565  CD  GLU    85      20.491  48.368 -11.876  1.00  0.00                              
ATOM   1567  OE1 GLU    85      20.581  48.689 -13.088  1.00  0.00                              
ATOM   1569  OE2 GLU    85      20.146  47.228 -11.504  1.00  0.00                              
ATOM   1571  H   LEU    86      24.018  51.097  -9.645  1.00  0.00                              
ATOM   1573  N   LEU    86      23.453  51.049  -8.886  1.00  0.00                              
ATOM   1575  CA  LEU    86      23.996  50.561  -7.602  1.00  0.00                              
ATOM   1577  CB  LEU    86      24.486  49.119  -7.713  1.00  0.00                              
ATOM   1579  C   LEU    86      25.100  51.473  -7.081  1.00  0.00                              
ATOM   1581  O   LEU    86      26.179  51.010  -6.703  1.00  0.00                              
ATOM   1583  CG  LEU    86      23.933  48.293  -8.876  1.00  0.00                              
ATOM   1585  CD1 LEU    86      25.047  47.453  -9.488  1.00  0.00                              
ATOM   1587  CD2 LEU    86      22.793  47.397  -8.388  1.00  0.00                              
ATOM   1589  H   GLU    87      23.984  53.068  -7.365  1.00  0.00                              
ATOM   1591  N   GLU    87      24.819  52.767  -7.040  1.00  0.00                              
ATOM   1593  CA  GLU    87      25.767  53.738  -6.523  1.00  0.00                              
ATOM   1595  CB  GLU    87      26.492  54.422  -7.678  1.00  0.00                              
ATOM   1597  C   GLU    87      25.050  54.783  -5.669  1.00  0.00                              
ATOM   1599  O   GLU    87      25.693  55.595  -4.997  1.00  0.00                              
ATOM   1601  CG  GLU    87      27.222  53.461  -8.589  1.00  0.00                              
ATOM   1603  CD  GLU    87      28.525  52.941  -7.981  1.00  0.00                              
ATOM   1605  OE1 GLU    87      28.914  53.428  -6.895  1.00  0.00                              
ATOM   1607  OE2 GLU    87      29.170  52.060  -8.599  1.00  0.00                              
ATOM   1609  H   ASN    88      23.274  54.072  -6.174  1.00  0.00                              
ATOM   1611  N   ASN    88      23.709  54.756  -5.696  1.00  0.00                              
ATOM   1613  CA  ASN    88      22.899  55.737  -4.968  1.00  0.00                              
ATOM   1615  CB  ASN    88      22.730  57.011  -5.808  1.00  0.00                              
ATOM   1617  C   ASN    88      21.517  55.158  -4.605  1.00  0.00                              
ATOM   1619  O   ASN    88      20.581  55.241  -5.401  1.00  0.00                              
ATOM   1621  CG  ASN    88      21.959  58.096  -5.082  1.00  0.00                              
ATOM   1623  ND2 ASN    88      21.917  59.287  -5.665  1.00  0.00                              
ATOM   1625 HD21 ASN    88      22.366  59.404  -6.485  1.00  0.00                              
ATOM   1627 HD22 ASN    88      21.439  59.989  -5.254  1.00  0.00                              
ATOM   1629  OD1 ASN    88      21.399  57.864  -4.010  1.00  0.00                              
ATOM   1631  H   LEU    89      22.157  54.487  -2.846  1.00  0.00                              
ATOM   1633  N   LEU    89      21.401  54.552  -3.410  1.00  0.00                              
ATOM   1635  CA  LEU    89      20.108  53.989  -2.958  1.00  0.00                              
ATOM   1637  CB  LEU    89      19.485  53.141  -4.107  1.00  0.00                              
ATOM   1639  C   LEU    89      20.278  53.114  -1.669  1.00  0.00                              
ATOM   1641  O   LEU    89      20.855  52.021  -1.731  1.00  0.00                              
ATOM   1643  CG  LEU    89      18.087  52.542  -3.867  1.00  0.00                              
ATOM   1645  CD1 LEU    89      17.102  53.645  -3.469  1.00  0.00                              
ATOM   1647  CD2 LEU    89      17.607  51.761  -5.137  1.00  0.00                              
ATOM   1649  N   PRO    90      19.742  53.575  -0.493  1.00  0.00                              
ATOM   1651  CA  PRO    90      19.861  52.801   0.760  1.00  0.00                              
ATOM   1653  CB  PRO    90      19.755  53.880   1.812  1.00  0.00                              
ATOM   1655  C   PRO    90      18.714  51.804   0.912  1.00  0.00                              
ATOM   1657  O   PRO    90      18.817  50.828   1.654  1.00  0.00                              
ATOM   1659  CG  PRO    90      18.707  54.800   1.246  1.00  0.00                              
ATOM   1661  CD  PRO    90      19.022  54.852  -0.262  1.00  0.00                              
ATOM   1663  H   ALA    91      17.562  52.899  -0.266  1.00  0.00                              
ATOM   1665  N   ALA    91      17.593  52.102   0.221  1.00  0.00                              
ATOM   1667  CA  ALA    91      16.398  51.225   0.209  1.00  0.00                              
ATOM   1669  CB  ALA    91      15.960  51.007  -1.227  1.00  0.00                              
ATOM   1671  C   ALA    91      16.655  49.869   0.862  1.00  0.00                              
ATOM   1673  O   ALA    91      17.264  48.982   0.236  1.00  0.00                              
ATOM   1675  H   TRP    92      15.685  50.352   2.552  1.00  0.00                              
ATOM   1677  N   TRP    92      16.145  49.659   2.098  1.00  0.00                              
ATOM   1679  CA  TRP    92      16.321  48.365   2.753  1.00  0.00                              
ATOM   1681  CB  TRP    92      17.758  48.200   3.258  1.00  0.00                              
ATOM   1683  C   TRP    92      15.318  48.086   3.883  1.00  0.00                              
ATOM   1685  O   TRP    92      14.749  48.999   4.467  1.00  0.00                              
ATOM   1687  CG  TRP    92      18.116  48.983   4.472  1.00  0.00                              
ATOM   1689  CD1 TRP    92      17.407  49.992   5.089  1.00  0.00                              
ATOM   1691  NE1 TRP    92      18.117  50.479   6.131  1.00  0.00                              
ATOM   1693  HE1 TRP    92      17.844  51.199   6.693  1.00  0.00                              
ATOM   1695  CD2 TRP    92      19.291  48.840   5.180  1.00  0.00                              
ATOM   1697  CE2 TRP    92      19.289  49.827   6.202  1.00  0.00                              
ATOM   1699  CE3 TRP    92      20.398  48.022   5.041  1.00  0.00                              
ATOM   1701  CZ3 TRP    92      21.472  48.223   5.871  1.00  0.00                              
ATOM   1703  CH2 TRP    92      21.466  49.247   6.823  1.00  0.00                              
ATOM   1705  CZ2 TRP    92      20.382  50.065   6.988  1.00  0.00                              
ATOM   1707  H   TRP    93      15.522  46.132   3.631  1.00  0.00                              
ATOM   1709  N   TRP    93      15.114  46.793   4.174  1.00  0.00                              
ATOM   1711  CA  TRP    93      14.263  46.385   5.281  1.00  0.00                              
ATOM   1713  CB  TRP    93      13.355  45.220   4.896  1.00  0.00                              
ATOM   1715  C   TRP    93      15.116  45.994   6.488  1.00  0.00                              
ATOM   1717  O   TRP    93      15.377  44.807   6.713  1.00  0.00                              
ATOM   1719  CG  TRP    93      12.072  45.200   5.626  1.00  0.00                              
ATOM   1721  CD1 TRP    93      10.990  45.976   5.420  1.00  0.00                              
ATOM   1723  NE1 TRP    93      10.046  45.708   6.355  1.00  0.00                              
ATOM   1725  HE1 TRP    93       9.193  46.120   6.404  1.00  0.00                              
ATOM   1727  CD2 TRP    93      11.738  44.318   6.660  1.00  0.00                              
ATOM   1729  CE2 TRP    93      10.498  44.731   7.162  1.00  0.00                              
ATOM   1731  CE3 TRP    93      12.452  43.345   7.358  1.00  0.00                              
ATOM   1733  CZ3 TRP    93      11.952  42.885   8.529  1.00  0.00                              
ATOM   1735  CH2 TRP    93      10.738  43.358   9.028  1.00  0.00                              
ATOM   1737  CZ2 TRP    93       9.995  44.263   8.348  1.00  0.00                              
TER 
END
