
#######################################################
#                                                     #
#                        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   26 (  210),  selected   26 , name T0378TS022_2-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS022_2-D1.T0378_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    -       -      M       1           -
LGA    V      64      L       2          4.356
LGA    E      65      S       3          3.029
LGA    L      66      A       4           -
LGA    P      67      N       5           -
LGA    E      68      Q       6          4.549
LGA    S      69      I       7          2.672
LGA    F      70      K       8          3.361
LGA    D      71      F       9          4.085
LGA    F      72      L      10           #
LGA    K      73      R      11          4.031
LGA    R      74      S      12          2.116
LGA    -       -      L      13           -
LGA    -       -      R      14           -
LGA    -       -      E      15           -
LGA    -       -      R      16           -
LGA    -       -      K      17           -
LGA    I      75      Y      18          1.588
LGA    S      76      R      19          3.955
LGA    -       -      L      20           -
LGA    -       -      R      21           -
LGA    -       -      E      22           -
LGA    -       -      Q      23           -
LGA    T      77      A      24          2.529
LGA    Q      78      F      25          1.967
LGA    T      79      A      26          2.413
LGA    T      80      V      27          3.771
LGA    P      81      E      28           #
LGA    -       -      G      29           -
LGA    -       -      P      30           -
LGA    Q      82      K      31          3.685
LGA    P      83      L      32          3.592
LGA    L      84      V      33          3.848
LGA    M      85      G      34          1.417
LGA    -       -      E      35           -
LGA    A      86      M      36          2.391
LGA    V      87      L      37          1.907
LGA    -       -      P      38           -
LGA    F      88      F      39          2.295
LGA    D      89      Y      40          3.409
LGA    -       -      R      41           -
LGA    -       -      C      42           -
LGA    -       -      R      43           -
LGA    -       -      M      44           -
LGA    -       -      L      45           -
LGA    -       -      V      46           -
LGA    -       -      G      47           -
LGA    -       -      T      48           -
LGA    -       -      A      49           -
LGA    -       -      A      50           -
LGA    -       -      M      51           -
LGA    -       -      L      52           -
LGA    -       -      R      53           -
LGA    -       -      A      54           -
LGA    -       -      V      55           -
LGA    -       -      S      56           -
LGA    -       -      T      57           -
LGA    -       -      P      58           -
LGA    -       -      H      59           -
LGA    -       -      D      60           -
LGA    -       -      A      61           -
LGA    -       -      E      62           -
LGA    -       -      V      63           -
LGA    -       -      V      64           -
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    -       -      P      67           -
LGA    -       -      E      68           -
LGA    -       -      S      69           -
LGA    -       -      F      70           -
LGA    -       -      D      71           -
LGA    -       -      F      72           -
LGA    -       -      K      73           -
LGA    -       -      R      74           -
LGA    -       -      I      75           -
LGA    -       -      S      76           -
LGA    -       -      T      77           -
LGA    -       -      Q      78           -
LGA    -       -      T      79           -
LGA    -       -      T      80           -
LGA    -       -      P      81           -
LGA    -       -      Q      82           -
LGA    -       -      P      83           -
LGA    -       -      L      84           -
LGA    -       -      M      85           -
LGA    -       -      A      86           -
LGA    -       -      V      87           -
LGA    -       -      F      88           -
LGA    -       -      D      89           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   26   89    5.0     22    3.18     4.55     14.458     0.670

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.309242 * X  +   0.404328 * Y  +  -0.860748 * Z  +  25.987356
  Y_new =   0.664751 * X  +  -0.555347 * Y  +  -0.499695 * Z  +  28.360159
  Z_new =  -0.680055 * X  +  -0.726711 * Y  +  -0.097041 * Z  +  75.000732 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.703546    1.438047  [ DEG:   -97.6060     82.3940 ]
  Theta =   0.747838    2.393755  [ DEG:    42.8479    137.1521 ]
  Phi   =   2.006218   -1.135375  [ DEG:   114.9478    -65.0522 ]
 
# 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: T0378TS022_2-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS022_2-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   26   89   5.0   22   3.18    4.55  14.458
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS022_2-D1
PFRMAT TS
TARGET T0378
MODEL  2
PARENT 1v2x_A
ATOM      1  N   VAL    64       2.898  35.482  56.715  1.00  0.00
ATOM      2  CA  VAL    64       3.435  35.601  55.341  1.00  0.00
ATOM      3  C   VAL    64       2.428  35.088  54.372  1.00  0.00
ATOM      4  O   VAL    64       1.549  34.309  54.737  1.00  0.00
ATOM      5  CB  VAL    64       4.734  34.791  55.172  1.00  0.00
ATOM      6  CG1 VAL    64       5.810  35.307  56.115  1.00  0.00
ATOM      7  CG2 VAL    64       4.490  33.323  55.478  1.00  0.00
ATOM      8  N   GLU    65       2.514  35.531  53.103  1.00  0.00
ATOM      9  CA  GLU    65       1.589  35.032  52.137  1.00  0.00
ATOM     10  C   GLU    65       1.953  33.603  51.910  1.00  0.00
ATOM     11  O   GLU    65       3.123  33.234  52.000  1.00  0.00
ATOM     12  CB  GLU    65       1.692  35.829  50.835  1.00  0.00
ATOM     13  CG  GLU    65       1.207  37.264  50.944  1.00  0.00
ATOM     14  CD  GLU    65       1.323  38.021  49.635  1.00  0.00
ATOM     15  OE1 GLU    65       1.820  37.433  48.652  1.00  0.00
ATOM     16  OE2 GLU    65       0.916  39.200  49.593  1.00  0.00
ATOM     17  N   LEU    66       0.949  32.757  51.622  1.00  0.00
ATOM     18  CA  LEU    66       1.207  31.354  51.502  1.00  0.00
ATOM     19  C   LEU    66       2.176  31.135  50.391  1.00  0.00
ATOM     20  O   LEU    66       3.116  30.357  50.542  1.00  0.00
ATOM     21  CB  LEU    66      -0.087  30.596  51.199  1.00  0.00
ATOM     22  CG  LEU    66      -1.114  30.529  52.331  1.00  0.00
ATOM     23  CD1 LEU    66      -2.415  29.910  51.840  1.00  0.00
ATOM     24  CD2 LEU    66      -0.591  29.684  53.482  1.00  0.00
ATOM     25  N   PRO    67       2.008  31.802  49.284  1.00  0.00
ATOM     26  CA  PRO    67       2.935  31.595  48.214  1.00  0.00
ATOM     27  C   PRO    67       4.318  32.018  48.583  1.00  0.00
ATOM     28  O   PRO    67       5.270  31.439  48.064  1.00  0.00
ATOM     29  CB  PRO    67       2.384  32.454  47.075  1.00  0.00
ATOM     30  CG  PRO    67       0.920  32.543  47.349  1.00  0.00
ATOM     31  CD  PRO    67       0.780  32.621  48.844  1.00  0.00
ATOM     32  N   GLU    68       4.477  33.021  49.465  1.00  0.00
ATOM     33  CA  GLU    68       5.823  33.376  49.781  1.00  0.00
ATOM     34  C   GLU    68       6.263  32.512  50.911  1.00  0.00
ATOM     35  O   GLU    68       5.553  32.324  51.898  1.00  0.00
ATOM     36  CB  GLU    68       5.908  34.849  50.187  1.00  0.00
ATOM     37  CG  GLU    68       7.313  35.322  50.519  1.00  0.00
ATOM     38  CD  GLU    68       7.352  36.776  50.947  1.00  0.00
ATOM     39  OE1 GLU    68       6.279  37.412  50.989  1.00  0.00
ATOM     40  OE2 GLU    68       8.457  37.279  51.240  1.00  0.00
ATOM     41  N   SER    69       7.468  31.946  50.767  1.00  0.00
ATOM     42  CA  SER    69       8.029  31.100  51.770  1.00  0.00
ATOM     43  C   SER    69       8.751  31.979  52.730  1.00  0.00
ATOM     44  O   SER    69       8.675  33.204  52.639  1.00  0.00
ATOM     45  CB  SER    69       8.999  30.096  51.143  1.00  0.00
ATOM     46  OG  SER    69       9.449  29.154  52.101  1.00  0.00
ATOM     47  N   PHE    70       9.458  31.372  53.702  1.00  0.00
ATOM     48  CA  PHE    70      10.191  32.183  54.623  1.00  0.00
ATOM     49  C   PHE    70      11.471  32.530  53.942  1.00  0.00
ATOM     50  O   PHE    70      12.013  31.738  53.173  1.00  0.00
ATOM     51  CB  PHE    70      10.461  31.413  55.917  1.00  0.00
ATOM     52  CG  PHE    70       9.244  31.229  56.779  1.00  0.00
ATOM     53  CD1 PHE    70       8.545  30.035  56.767  1.00  0.00
ATOM     54  CD2 PHE    70       8.797  32.251  57.598  1.00  0.00
ATOM     55  CE1 PHE    70       7.425  29.865  57.559  1.00  0.00
ATOM     56  CE2 PHE    70       7.677  32.081  58.390  1.00  0.00
ATOM     57  CZ  PHE    70       6.991  30.894  58.373  1.00  0.00
ATOM     58  N   ASP    71      11.974  33.752  54.208  1.00  0.00
ATOM     59  CA  ASP    71      13.170  34.224  53.574  1.00  0.00
ATOM     60  C   ASP    71      14.237  33.215  53.812  1.00  0.00
ATOM     61  O   ASP    71      14.153  32.397  54.727  1.00  0.00
ATOM     62  CB  ASP    71      13.590  35.573  54.160  1.00  0.00
ATOM     63  CG  ASP    71      12.657  36.698  53.760  1.00  0.00
ATOM     64  OD1 ASP    71      11.816  36.482  52.862  1.00  0.00
ATOM     65  OD2 ASP    71      12.765  37.797  54.345  1.00  0.00
ATOM     66  N   PHE    72      15.269  33.242  52.948  1.00  0.00
ATOM     67  CA  PHE    72      16.345  32.309  53.073  1.00  0.00
ATOM     68  C   PHE    72      15.715  30.960  52.998  1.00  0.00
ATOM     69  O   PHE    72      16.177  29.994  53.605  1.00  0.00
ATOM     70  CB  PHE    72      17.068  32.501  54.408  1.00  0.00
ATOM     71  CG  PHE    72      17.647  33.875  54.592  1.00  0.00
ATOM     72  CD1 PHE    72      16.998  34.816  55.373  1.00  0.00
ATOM     73  CD2 PHE    72      18.839  34.227  53.985  1.00  0.00
ATOM     74  CE1 PHE    72      17.531  36.079  55.543  1.00  0.00
ATOM     75  CE2 PHE    72      19.372  35.491  54.154  1.00  0.00
ATOM     76  CZ  PHE    72      18.722  36.415  54.929  1.00  0.00
ATOM     77  N   LYS    73      14.637  30.875  52.204  1.00  0.00
ATOM     78  CA  LYS    73      13.869  29.682  52.056  1.00  0.00
ATOM     79  C   LYS    73      14.715  28.653  51.401  1.00  0.00
ATOM     80  O   LYS    73      14.405  27.467  51.450  1.00  0.00
ATOM     81  CB  LYS    73      12.630  29.945  51.197  1.00  0.00
ATOM     82  CG  LYS    73      12.938  30.232  49.736  1.00  0.00
ATOM     83  CD  LYS    73      11.669  30.521  48.952  1.00  0.00
ATOM     84  CE  LYS    73      11.972  30.769  47.483  1.00  0.00
ATOM     85  NZ  LYS    73      10.734  31.022  46.695  1.00  0.00
ATOM     86  N   ARG    74      15.807  29.082  50.757  1.00  0.00
ATOM     87  CA  ARG    74      16.656  28.180  50.038  1.00  0.00
ATOM     88  C   ARG    74      17.070  27.106  50.994  1.00  0.00
ATOM     89  O   ARG    74      17.162  25.934  50.630  1.00  0.00
ATOM     90  CB  ARG    74      17.889  28.915  49.506  1.00  0.00
ATOM     91  CG  ARG    74      17.594  29.876  48.366  1.00  0.00
ATOM     92  CD  ARG    74      18.846  30.624  47.937  1.00  0.00
ATOM     93  NE  ARG    74      18.575  31.573  46.860  1.00  0.00
ATOM     94  CZ  ARG    74      19.478  32.404  46.352  1.00  0.00
ATOM     95  NH1 ARG    74      19.140  33.233  45.373  1.00  0.00
ATOM     96  NH2 ARG    74      20.718  32.404  46.821  1.00  0.00
ATOM     97  N   ILE    75      17.330  27.471  52.260  1.00  0.00
ATOM     98  CA  ILE    75      17.611  26.396  53.156  1.00  0.00
ATOM     99  C   ILE    75      16.313  26.064  53.811  1.00  0.00
ATOM    100  O   ILE    75      16.064  26.462  54.947  1.00  0.00
ATOM    101  CB  ILE    75      18.656  26.801  54.212  1.00  0.00
ATOM    102  CG1 ILE    75      19.949  27.258  53.535  1.00  0.00
ATOM    103  CG2 ILE    75      18.979  25.624  55.121  1.00  0.00
ATOM    104  CD1 ILE    75      20.929  27.926  54.475  1.00  0.00
ATOM    105  N   SER    76      15.455  25.304  53.100  1.00  0.00
ATOM    106  CA  SER    76      14.203  24.866  53.637  1.00  0.00
ATOM    107  C   SER    76      13.930  23.515  53.051  1.00  0.00
ATOM    108  O   SER    76      14.779  22.928  52.382  1.00  0.00
ATOM    109  CB  SER    76      13.088  25.843  53.261  1.00  0.00
ATOM    110  OG  SER    76      11.900  25.565  53.983  1.00  0.00
ATOM    111  N   THR    77      12.731  22.961  53.288  1.00  0.00
ATOM    112  CA  THR    77      12.477  21.661  52.744  1.00  0.00
ATOM    113  C   THR    77      12.520  21.771  51.254  1.00  0.00
ATOM    114  O   THR    77      12.000  22.726  50.678  1.00  0.00
ATOM    115  CB  THR    77      11.098  21.128  53.175  1.00  0.00
ATOM    116  OG1 THR    77      11.032  21.067  54.605  1.00  0.00
ATOM    117  CG2 THR    77      10.865  19.735  52.610  1.00  0.00
ATOM    118  N   GLN    78      13.177  20.791  50.596  1.00  0.00
ATOM    119  CA  GLN    78      13.247  20.768  49.163  1.00  0.00
ATOM    120  C   GLN    78      12.018  20.066  48.696  1.00  0.00
ATOM    121  O   GLN    78      11.462  19.236  49.413  1.00  0.00
ATOM    122  CB  GLN    78      14.501  20.022  48.700  1.00  0.00
ATOM    123  CG  GLN    78      15.804  20.644  49.177  1.00  0.00
ATOM    124  CD  GLN    78      16.015  22.043  48.634  1.00  0.00
ATOM    125  OE1 GLN    78      15.951  22.266  47.426  1.00  0.00
ATOM    126  NE2 GLN    78      16.270  22.991  49.529  1.00  0.00
ATOM    127  N   THR    79      11.543  20.399  47.482  1.00  0.00
ATOM    128  CA  THR    79      10.367  19.739  47.004  1.00  0.00
ATOM    129  C   THR    79      10.783  18.397  46.516  1.00  0.00
ATOM    130  O   THR    79      11.887  18.217  46.006  1.00  0.00
ATOM    131  CB  THR    79       9.705  20.525  45.857  1.00  0.00
ATOM    132  OG1 THR    79      10.615  20.621  44.754  1.00  0.00
ATOM    133  CG2 THR    79       9.337  21.928  46.315  1.00  0.00
ATOM    134  N   THR    80       9.902  17.399  46.689  1.00  0.00
ATOM    135  CA  THR    80      10.228  16.092  46.216  1.00  0.00
ATOM    136  C   THR    80       9.633  15.962  44.855  1.00  0.00
ATOM    137  O   THR    80       8.949  16.859  44.361  1.00  0.00
ATOM    138  CB  THR    80       9.657  14.999  47.140  1.00  0.00
ATOM    139  OG1 THR    80       8.226  15.058  47.128  1.00  0.00
ATOM    140  CG2 THR    80      10.147  15.200  48.566  1.00  0.00
ATOM    141  N   PRO    81       9.905  14.855  44.233  1.00  0.00
ATOM    142  CA  PRO    81       9.410  14.647  42.903  1.00  0.00
ATOM    143  C   PRO    81       7.937  14.413  42.875  1.00  0.00
ATOM    144  O   PRO    81       7.370  14.007  43.889  1.00  0.00
ATOM    145  CB  PRO    81      10.168  13.411  42.414  1.00  0.00
ATOM    146  CG  PRO    81      10.477  12.647  43.658  1.00  0.00
ATOM    147  CD  PRO    81      10.750  13.673  44.721  1.00  0.00
ATOM    148  N   GLN    82       7.311  14.685  41.714  1.00  0.00
ATOM    149  CA  GLN    82       5.904  14.517  41.518  1.00  0.00
ATOM    150  C   GLN    82       5.209  15.664  42.172  1.00  0.00
ATOM    151  O   GLN    82       5.126  15.780  43.393  1.00  0.00
ATOM    152  CB  GLN    82       5.430  13.202  42.140  1.00  0.00
ATOM    153  CG  GLN    82       5.973  11.959  41.455  1.00  0.00
ATOM    154  CD  GLN    82       5.527  10.677  42.132  1.00  0.00
ATOM    155  OE1 GLN    82       4.808  10.711  43.131  1.00  0.00
ATOM    156  NE2 GLN    82       5.952   9.543  41.589  1.00  0.00
ATOM    157  N   PRO    83       4.719  16.526  41.338  1.00  0.00
ATOM    158  CA  PRO    83       4.032  17.714  41.754  1.00  0.00
ATOM    159  C   PRO    83       2.815  17.385  42.558  1.00  0.00
ATOM    160  O   PRO    83       2.438  18.191  43.409  1.00  0.00
ATOM    161  CB  PRO    83       3.662  18.407  40.441  1.00  0.00
ATOM    162  CG  PRO    83       4.687  17.931  39.466  1.00  0.00
ATOM    163  CD  PRO    83       4.964  16.496  39.819  1.00  0.00
ATOM    164  N   LEU    84       2.164  16.234  42.309  1.00  0.00
ATOM    165  CA  LEU    84       0.943  16.012  43.022  1.00  0.00
ATOM    166  C   LEU    84       1.111  14.946  44.051  1.00  0.00
ATOM    167  O   LEU    84       1.421  13.798  43.728  1.00  0.00
ATOM    168  CB  LEU    84      -0.166  15.579  42.061  1.00  0.00
ATOM    169  CG  LEU    84      -1.520  15.253  42.694  1.00  0.00
ATOM    170  CD1 LEU    84      -2.129  16.493  43.330  1.00  0.00
ATOM    171  CD2 LEU    84      -2.492  14.730  41.646  1.00  0.00
ATOM    172  N   MET    85       0.865  15.336  45.319  1.00  0.00
ATOM    173  CA  MET    85       0.830  14.484  46.473  1.00  0.00
ATOM    174  C   MET    85       2.114  13.757  46.691  1.00  0.00
ATOM    175  O   MET    85       2.840  13.390  45.770  1.00  0.00
ATOM    176  CB  MET    85      -0.269  13.429  46.326  1.00  0.00
ATOM    177  CG  MET    85      -1.676  14.002  46.274  1.00  0.00
ATOM    178  SD  MET    85      -2.139  14.851  47.796  1.00  0.00
ATOM    179  CE  MET    85      -2.266  13.470  48.929  1.00  0.00
ATOM    180  N   ALA    86       2.441  13.577  47.981  1.00  0.00
ATOM    181  CA  ALA    86       3.573  12.797  48.360  1.00  0.00
ATOM    182  C   ALA    86       3.655  12.877  49.848  1.00  0.00
ATOM    183  O   ALA    86       3.434  13.931  50.442  1.00  0.00
ATOM    184  CB  ALA    86       4.837  13.353  47.723  1.00  0.00
ATOM    185  N   VAL    87       3.960  11.745  50.500  1.00  0.00
ATOM    186  CA  VAL    87       4.118  11.783  51.919  1.00  0.00
ATOM    187  C   VAL    87       5.373  11.034  52.198  1.00  0.00
ATOM    188  O   VAL    87       5.567   9.922  51.711  1.00  0.00
ATOM    189  CB  VAL    87       2.926  11.126  52.639  1.00  0.00
ATOM    190  CG1 VAL    87       3.133  11.150  54.145  1.00  0.00
ATOM    191  CG2 VAL    87       1.636  11.868  52.319  1.00  0.00
ATOM    192  N   PHE    88       6.289  11.635  52.977  1.00  0.00
ATOM    193  CA  PHE    88       7.511  10.930  53.218  1.00  0.00
ATOM    194  C   PHE    88       8.009  11.314  54.565  1.00  0.00
ATOM    195  O   PHE    88       7.595  12.321  55.138  1.00  0.00
ATOM    196  CB  PHE    88       8.556  11.293  52.161  1.00  0.00
ATOM    197  CG  PHE    88       8.964  12.739  52.183  1.00  0.00
ATOM    198  CD1 PHE    88      10.060  13.153  52.919  1.00  0.00
ATOM    199  CD2 PHE    88       8.251  13.685  51.467  1.00  0.00
ATOM    200  CE1 PHE    88      10.434  14.484  52.939  1.00  0.00
ATOM    201  CE2 PHE    88       8.626  15.015  51.487  1.00  0.00
ATOM    202  CZ  PHE    88       9.712  15.416  52.219  1.00  0.00
ATOM    203  N   ASP    89       8.906  10.472  55.106  1.00  0.00
ATOM    204  CA  ASP    89       9.635  10.836  56.277  1.00  0.00
ATOM    205  C   ASP    89      10.758  11.597  55.676  1.00  0.00
ATOM    206  O   ASP    89      10.709  11.911  54.489  1.00  0.00
ATOM    207  CB  ASP    89      10.088   9.587  57.035  1.00  0.00
ATOM    208  CG  ASP    89      11.136   8.794  56.279  1.00  0.00
ATOM    209  OD1 ASP    89      10.891   8.457  55.102  1.00  0.00
ATOM    210  OD2 ASP    89      12.202   8.511  56.864  1.00  0.00
TER
END
