
#######################################################
#                                                     #
#                        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   13 (   94),  selected   13 , name T0382TS009_3_3-D1
# Molecule2: number of CA atoms  119 (  920),  selected  119 , name T0382_D1.pdb
# PARAMETERS: T0382TS009_3_3-D1.T0382_D1.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       4           -
LGA    -       -      D       5           -
LGA    -       -      L       6           -
LGA    -       -      H       7           -
LGA    -       -      Q       8           -
LGA    -       -      M       9           -
LGA    -       -      T      10           -
LGA    -       -      T      11           -
LGA    -       -      Q      12           -
LGA    -       -      D      13           -
LGA    -       -      L      14           -
LGA    -       -      V      15           -
LGA    -       -      A      16           -
LGA    -       -      L      17           -
LGA    -       -      F      18           -
LGA    -       -      A      19           -
LGA    -       -      K      20           -
LGA    -       -      V      21           -
LGA    -       -      T      22           -
LGA    -       -      V      23           -
LGA    -       -      E      24           -
LGA    -       -      Q      25           -
LGA    -       -      D      26           -
LGA    -       -      D      27           -
LGA    -       -      A      28           -
LGA    -       -      L      29           -
LGA    -       -      L      30           -
LGA    -       -      G      31           -
LGA    -       -      N      32           -
LGA    -       -      Q      33           -
LGA    -       -      I      34           -
LGA    -       -      S      35           -
LGA    -       -      R      36           -
LGA    -       -      F      37           -
LGA    -       -      N      38           -
LGA    -       -      R      39           -
LGA    -       -      L      40           -
LGA    -       -      F      41           -
LGA    -       -      G      42           -
LGA    -       -      V      43           -
LGA    -       -      M      44           -
LGA    -       -      A      45           -
LGA    -       -      E      46           -
LGA    -       -      I      47           -
LGA    -       -      A      48           -
LGA    -       -      D      49           -
LGA    -       -      E      50           -
LGA    -       -      L      51           -
LGA    -       -      K      52           -
LGA    -       -      A      53           -
LGA    -       -      R      54           -
LGA    -       -      D      55           -
LGA    -       -      G      56           -
LGA    -       -      D      57           -
LGA    -       -      Q      58           -
LGA    -       -      R      59           -
LGA    -       -      T      60           -
LGA    -       -      A      61           -
LGA    -       -      L      62           -
LGA    -       -      L      63           -
LGA    -       -      S      64           -
LGA    V      73      L      65          2.269
LGA    -       -      F      66           -
LGA    R      74      E      67           #
LGA    L      75      Y      68          3.750
LGA    Q      76      P      69          0.879
LGA    A      77      N      70          1.587
LGA    -       -      M      71           -
LGA    -       -      Q      72           -
LGA    A      78      V      73          3.930
LGA    K      79      R      74          2.141
LGA    L      80      L      75          2.071
LGA    T      81      Q      76          2.225
LGA    L      82      A      77          1.898
LGA    A      83      A      78          1.727
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      T      81           -
LGA    -       -      L      82           -
LGA    -       -      A      83           -
LGA    -       -      V      84           -
LGA    -       -      A      85           -
LGA    -       -      P      86           -
LGA    -       -      V      87           -
LGA    -       -      K      88           -
LGA    -       -      A      89           -
LGA    -       -      R      90           -
LGA    -       -      E      91           -
LGA    V      84      Q      92          3.199
LGA    A      85      L      93          2.760
LGA    -       -      E      94           -
LGA    -       -      A      95           -
LGA    -       -      I      96           -
LGA    -       -      V      97           -
LGA    -       -      S      98           -
LGA    -       -      S      99           -
LGA    -       -      K     100           -
LGA    -       -      W     101           -
LGA    -       -      F     102           -
LGA    -       -      P     103           -
LGA    -       -      Q     104           -
LGA    -       -      A     105           -
LGA    -       -      G     106           -
LGA    -       -      D     107           -
LGA    -       -      A     108           -
LGA    -       -      G     109           -
LGA    -       -      M     110           -
LGA    -       -      C     111           -
LGA    -       -      L     112           -
LGA    -       -      D     113           -
LGA    -       -      L     114           -
LGA    -       -      L     115           -
LGA    -       -      D     116           -
LGA    -       -      D     117           -
LGA    -       -      G     118           -
LGA    -       -      T     119           -
LGA    -       -      F     120           -
LGA    -       -      K     121           -
LGA    -       -      P     122           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   13  119    5.0     12    2.52    16.67      7.546     0.458

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.512366 * X  +  -0.680914 * Y  +  -0.523295 * Z  +   4.266509
  Y_new =  -0.512656 * X  +  -0.246345 * Y  +   0.822495 * Z  +  50.857643
  Z_new =  -0.688959 * X  +   0.689688 * Y  +  -0.222856 * Z  +  11.021848 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.883332   -1.258261  [ DEG:   107.9070    -72.0930 ]
  Theta =   0.760052    2.381540  [ DEG:    43.5478    136.4522 ]
  Phi   =  -2.355911    0.785681  [ DEG:  -134.9838     45.0162 ]
 
# 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: T0382TS009_3_3-D1                             
REMARK     2: T0382_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0382TS009_3_3-D1.T0382_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   13  119   5.0   12   2.52   16.67   7.546
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS009_3_3-D1
REMARK PARENT number 3
PFRMAT TS                                                                       
TARGET T0382                                                                    
PARENT N/A  
ATOM    572  N   VAL    73     -21.578  43.017   0.684  1.00  0.00             
ATOM    573  CA  VAL    73     -20.378  42.187   0.993  1.00  0.00             
ATOM    574  C   VAL    73     -20.635  40.713   0.694  1.00  0.00             
ATOM    575  O   VAL    73     -21.105  40.362  -0.388  1.00  0.00             
ATOM    576  CB  VAL    73     -19.146  42.655   0.194  1.00  0.00             
ATOM    577  CG1 VAL    73     -18.074  43.188   1.133  1.00  0.00             
ATOM    578  CG2 VAL    73     -19.544  43.709  -0.828  1.00  0.00             
ATOM    579  N   ARG    74     -20.325  39.856   1.661  1.00  0.00             
ATOM    580  CA  ARG    74     -20.522  38.420   1.505  1.00  0.00             
ATOM    581  C   ARG    74     -21.878  37.987   2.050  1.00  0.00             
ATOM    582  O   ARG    74     -22.911  38.207   1.418  1.00  0.00             
ATOM    583  CB  ARG    74     -20.394  38.019   0.033  1.00  0.00             
ATOM    584  CG  ARG    74     -19.466  36.842  -0.211  1.00  0.00             
ATOM    585  CD  ARG    74     -19.121  36.705  -1.685  1.00  0.00             
ATOM    586  NE  ARG    74     -18.501  35.418  -1.986  1.00  0.00             
ATOM    587  CZ  ARG    74     -19.172  34.279  -2.120  1.00  0.00             
ATOM    588  NH1 ARG    74     -20.490  34.265  -1.978  1.00  0.00             
ATOM    589  NH2 ARG    74     -18.523  33.155  -2.393  1.00  0.00             
ATOM    590  N   LEU    75     -21.868  37.370   3.227  1.00  0.00             
ATOM    591  CA  LEU    75     -23.096  36.904   3.860  1.00  0.00             
ATOM    592  C   LEU    75     -23.736  38.007   4.697  1.00  0.00             
ATOM    593  O   LEU    75     -24.447  38.865   4.173  1.00  0.00             
ATOM    594  CB  LEU    75     -24.084  36.402   2.806  1.00  0.00             
ATOM    595  CG  LEU    75     -24.619  34.982   3.001  1.00  0.00             
ATOM    596  CD1 LEU    75     -26.124  34.939   2.784  1.00  0.00             
ATOM    597  CD2 LEU    75     -24.255  34.454   4.380  1.00  0.00             
ATOM    598  N   GLN    76     -23.480  37.978   6.001  1.00  0.00             
ATOM    599  CA  GLN    76     -24.032  38.973   6.912  1.00  0.00             
ATOM    600  C   GLN    76     -23.025  40.086   7.188  1.00  0.00             
ATOM    601  O   GLN    76     -23.173  41.205   6.697  1.00  0.00             
ATOM    602  CB  GLN    76     -25.324  39.562   6.344  1.00  0.00             
ATOM    603  CG  GLN    76     -26.590  39.006   6.975  1.00  0.00             
ATOM    604  CD  GLN    76     -27.848  39.497   6.286  1.00  0.00             
ATOM    605  OE1 GLN    76     -28.956  39.303   6.786  1.00  0.00             
ATOM    606  NE2 GLN    76     -27.681  40.135   5.134  1.00  0.00             
ATOM    607  N   ALA    77     -22.002  39.769   7.976  1.00  0.00             
ATOM    608  CA  ALA    77     -20.971  40.741   8.318  1.00  0.00             
ATOM    609  C   ALA    77     -20.973  41.914   7.346  1.00  0.00             
ATOM    610  O   ALA    77     -20.497  43.002   7.669  1.00  0.00             
ATOM    611  CB  ALA    77     -21.164  41.239   9.743  1.00  0.00             
ATOM    612  N   ALA    78     -21.512  41.686   6.152  1.00  0.00             
ATOM    613  CA  ALA    78     -21.578  42.724   5.130  1.00  0.00             
ATOM    614  C   ALA    78     -20.975  44.031   5.632  1.00  0.00             
ATOM    615  O   ALA    78     -19.868  44.406   5.242  1.00  0.00             
ATOM    616  CB  ALA    78     -20.864  42.268   3.865  1.00  0.00             
ATOM    617  N   LYS    79     -21.708  44.722   6.498  1.00  0.00             
ATOM    618  CA  LYS    79     -21.248  45.988   7.055  1.00  0.00             
ATOM    619  C   LYS    79     -19.725  46.057   7.082  1.00  0.00             
ATOM    620  O   LYS    79     -19.141  47.140   7.035  1.00  0.00             
ATOM    621  CB  LYS    79     -21.814  47.163   6.254  1.00  0.00             
ATOM    622  CG  LYS    79     -22.668  48.117   7.072  1.00  0.00             
ATOM    623  CD  LYS    79     -22.718  49.496   6.436  1.00  0.00             
ATOM    624  CE  LYS    79     -23.319  50.521   7.384  1.00  0.00             
ATOM    625  NZ  LYS    79     -23.300  51.892   6.806  1.00  0.00             
ATOM    626  N   LEU    80     -19.086  44.894   7.157  1.00  0.00             
ATOM    627  CA  LEU    80     -17.630  44.820   7.191  1.00  0.00             
ATOM    628  C   LEU    80     -17.001  46.145   6.777  1.00  0.00             
ATOM    629  O   LEU    80     -16.812  47.039   7.603  1.00  0.00             
ATOM    630  CB  LEU    80     -17.146  44.420   8.586  1.00  0.00             
ATOM    631  CG  LEU    80     -15.928  43.496   8.643  1.00  0.00             
ATOM    632  CD1 LEU    80     -15.494  43.265  10.083  1.00  0.00             
ATOM    633  CD2 LEU    80     -14.784  44.063   7.817  1.00  0.00             
ATOM    634  N   THR    81     -16.678  46.266   5.494  1.00  0.00             
ATOM    635  CA  THR    81     -16.056  47.510   4.956  1.00  0.00             
ATOM    636  C   THR    81     -16.966  48.185   3.935  1.00  0.00             
ATOM    637  O   THR    81     -17.278  49.369   4.053  1.00  0.00             
ATOM    638  CB  THR    81     -15.733  48.511   6.081  1.00  0.00             
ATOM    639  OG1 THR    81     -16.879  48.673   6.925  1.00  0.00             
ATOM    640  CG2 THR    81     -14.561  48.017   6.914  1.00  0.00             
ATOM    641  N   LEU    82     -17.388  47.422   2.931  1.00  0.00             
ATOM    642  CA  LEU    82     -18.261  47.944   1.887  1.00  0.00             
ATOM    643  C   LEU    82     -18.508  49.438   2.070  1.00  0.00             
ATOM    644  O   LEU    82     -19.610  49.929   1.831  1.00  0.00             
ATOM    645  CB  LEU    82     -17.665  47.674   0.505  1.00  0.00             
ATOM    646  CG  LEU    82     -18.323  46.561  -0.313  1.00  0.00             
ATOM    647  CD1 LEU    82     -18.717  47.068  -1.692  1.00  0.00             
ATOM    648  CD2 LEU    82     -19.530  45.997   0.421  1.00  0.00             
ATOM    649  N   ALA    83     -17.472  50.156   2.495  1.00  0.00             
ATOM    650  CA  ALA    83     -17.575  51.594   2.710  1.00  0.00             
ATOM    651  C   ALA    83     -18.812  51.942   3.529  1.00  0.00             
ATOM    652  O   ALA    83     -19.929  51.956   3.011  1.00  0.00             
ATOM    653  CB  ALA    83     -16.325  52.116   3.400  1.00  0.00             
ATOM    654  N   VAL    84     -18.607  52.223   4.812  1.00  0.00             
ATOM    655  CA  VAL    84     -19.730  52.580   5.726  1.00  0.00             
ATOM    656  C   VAL    84     -19.852  51.576   6.868  1.00  0.00             
ATOM    657  O   VAL    84     -20.939  51.072   7.149  1.00  0.00             
ATOM    658  CB  VAL    84     -19.552  53.992   6.313  1.00  0.00             
ATOM    659  CG1 VAL    84     -20.045  55.043   5.332  1.00  0.00             
ATOM    660  CG2 VAL    84     -18.097  54.237   6.682  1.00  0.00             
ATOM    661  N   ALA    85     -18.730  51.291   7.522  1.00  0.00             
ATOM    662  CA  ALA    85     -18.710  50.348   8.633  1.00  0.00             
ATOM    663  C   ALA    85     -19.463  49.068   8.284  1.00  0.00             
ATOM    664  O   ALA    85     -20.295  49.047   7.378  1.00  0.00             
ATOM    665  CB  ALA    85     -17.277  50.023   9.026  1.00  0.00             
TER
END
