
#######################################################
#                                                     #
#                        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   17 (  146),  selected   17 , name T0381TS277_3-D1
# Molecule2: number of CA atoms   61 (  477),  selected   61 , name T0381_D1.pdb
# PARAMETERS: T0381TS277_3-D1.T0381_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    -       -      V      17           -
LGA    -       -      Q      18           -
LGA    -       -      S      19           -
LGA    -       -      L      20           -
LGA    -       -      A      21           -
LGA    -       -      R      22           -
LGA    -       -      G      23           -
LGA    -       -      L      24           -
LGA    -       -      A      25           -
LGA    -       -      V      26           -
LGA    -       -      I      27           -
LGA    -       -      R      28           -
LGA    -       -      C      29           -
LGA    -       -      F      30           -
LGA    -       -      D      31           -
LGA    V      61      H      32          1.829
LGA    E      62      R      33          1.666
LGA    L      63      N      34          1.515
LGA    G      64      Q      35          2.760
LGA    Y      65      R      36          2.653
LGA    -       -      R      37           -
LGA    V      66      T      38          1.429
LGA    -       -      L      39           -
LGA    -       -      S      40           -
LGA    -       -      D      41           -
LGA    A      67      V      42          2.253
LGA    T      68      A      43          1.884
LGA    -       -      R      44           -
LGA    -       -      A      45           -
LGA    -       -      T      46           -
LGA    -       -      D      47           -
LGA    -       -      L      48           -
LGA    -       -      T      49           -
LGA    D      69      R      50          3.246
LGA    G      70      A      51          2.264
LGA    -       -      T      52           -
LGA    -       -      A      53           -
LGA    -       -      R      54           -
LGA    S      71      R      55          2.063
LGA    A      72      F      56          3.361
LGA    F      73      L      57          2.108
LGA    -       -      L      58           -
LGA    -       -      T      59           -
LGA    -       -      L      60           -
LGA    -       -      V      61           -
LGA    -       -      E      62           -
LGA    -       -      L      63           -
LGA    -       -      G      64           -
LGA    -       -      Y      65           -
LGA    -       -      V      66           -
LGA    -       -      A      67           -
LGA    -       -      T      68           -
LGA    -       -      D      69           -
LGA    -       -      G      70           -
LGA    -       -      S      71           -
LGA    W      74      A      72           #
LGA    L      75      F      73          2.735
LGA    T      76      W      74          1.991
LGA    P      77      L      75          4.559
LGA    -       -      T      76           -
LGA    -       -      P      77           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   17   61    5.0     16    2.52     0.00     18.361     0.611

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.382589 * X  +   0.888803 * Y  +  -0.252300 * Z  + -16.778948
  Y_new =  -0.301909 * X  +   0.378352 * Y  +   0.875043 * Z  +  71.575943
  Z_new =   0.873199 * X  +  -0.258610 * Y  +   0.413091 * Z  + -10.877723 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.559345    2.582248  [ DEG:   -32.0481    147.9519 ]
  Theta =  -1.061729   -2.079864  [ DEG:   -60.8326   -119.1674 ]
  Phi   =  -0.668072    2.473521  [ DEG:   -38.2777    141.7223 ]
 
# 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: T0381TS277_3-D1                               
REMARK     2: T0381_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0381TS277_3-D1.T0381_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   17   61   5.0   16   2.52    0.00  18.361
REMARK  ---------------------------------------------------------- 
MOLECULE T0381TS277_3-D1
PFRMAT TS 
TARGET T0381
MODEL 3
PARENT 1TF1_A
ATOM      1  H   VAL    61       6.955  42.909   8.736  1.00  0.00                              
ATOM      3  N   VAL    61       7.691  43.169   8.216  1.00  0.00                              
ATOM      5  CA  VAL    61       8.165  44.547   8.302  1.00  0.00                              
ATOM      7  CB  VAL    61       9.237  44.833   7.228  1.00  0.00                              
ATOM      9  C   VAL    61       6.992  45.501   8.103  1.00  0.00                              
ATOM     11  O   VAL    61       6.278  45.408   7.102  1.00  0.00                              
ATOM     13  CG1 VAL    61      10.254  43.700   7.170  1.00  0.00                              
ATOM     15  CG2 VAL    61       8.579  45.035   5.868  1.00  0.00                              
ATOM     17  H   GLU    62       7.290  46.388   9.846  1.00  0.00                              
ATOM     19  N   GLU    62       6.757  46.390   9.065  1.00  0.00                              
ATOM     21  CA  GLU    62       5.687  47.374   8.927  1.00  0.00                              
ATOM     23  CB  GLU    62       4.381  46.699   8.479  1.00  0.00                              
ATOM     25  C   GLU    62       5.455  48.175  10.205  1.00  0.00                              
ATOM     27  O   GLU    62       4.731  47.723  11.095  1.00  0.00                              
ATOM     29  CG  GLU    62       3.726  45.797   9.522  1.00  0.00                              
ATOM     31  CD  GLU    62       2.406  45.187   9.064  1.00  0.00                              
ATOM     33  OE1 GLU    62       1.746  45.784   8.183  1.00  0.00                              
ATOM     35  OE2 GLU    62       2.002  44.124   9.599  1.00  0.00                              
ATOM     37  H   LEU    63       6.598  49.688   9.619  1.00  0.00                              
ATOM     39  N   LEU    63       6.024  49.374  10.303  1.00  0.00                              
ATOM     41  CA  LEU    63       5.758  50.209  11.467  1.00  0.00                              
ATOM     43  CB  LEU    63       5.673  49.351  12.726  1.00  0.00                              
ATOM     45  C   LEU    63       6.795  51.309  11.676  1.00  0.00                              
ATOM     47  O   LEU    63       7.224  51.542  12.809  1.00  0.00                              
ATOM     49  CG  LEU    63       5.597  50.147  14.024  1.00  0.00                              
ATOM     51  CD1 LEU    63       4.326  50.985  14.043  1.00  0.00                              
ATOM     53  CD2 LEU    63       5.642  49.211  15.225  1.00  0.00                              
ATOM     55  H   GLY    64       6.839  51.812   9.772  1.00  0.00                              
ATOM     57  N   GLY    64       7.177  52.016  10.615  1.00  0.00                              
ATOM     59  CA  GLY    64       8.168  53.070  10.761  1.00  0.00                              
ATOM     61  C   GLY    64       7.889  54.352  10.001  1.00  0.00                              
ATOM     63  O   GLY    64       7.857  54.366   8.769  1.00  0.00                              
ATOM     65  H   TYR    65       7.979  55.429  11.646  1.00  0.00                              
ATOM     67  N   TYR    65       7.770  55.454  10.726  1.00  0.00                              
ATOM     69  CA  TYR    65       7.397  56.722  10.123  1.00  0.00                              
ATOM     71  CB  TYR    65       6.217  56.519   9.161  1.00  0.00                              
ATOM     73  C   TYR    65       7.024  57.712  11.223  1.00  0.00                              
ATOM     75  O   TYR    65       7.025  57.350  12.402  1.00  0.00                              
ATOM     77  CG  TYR    65       4.875  56.263   9.820  1.00  0.00                              
ATOM     79  CD1 TYR    65       4.775  55.777  11.125  1.00  0.00                              
ATOM     81  CE1 TYR    65       3.532  55.548  11.714  1.00  0.00                              
ATOM     83  CZ  TYR    65       2.379  55.812  10.996  1.00  0.00                              
ATOM     85  CD2 TYR    65       3.698  56.544   9.130  1.00  0.00                              
ATOM     87  CE2 TYR    65       2.452  56.318   9.709  1.00  0.00                              
ATOM     89  OH  TYR    65       1.148  55.611  11.582  1.00  0.00                              
ATOM     91  H   VAL    66       6.669  59.174   9.951  1.00  0.00                              
ATOM     93  N   VAL    66       6.716  58.955  10.862  1.00  0.00                              
ATOM     95  CA  VAL    66       6.408  59.980  11.858  1.00  0.00                              
ATOM     97  CB  VAL    66       6.329  61.386  11.225  1.00  0.00                              
ATOM     99  C   VAL    66       5.088  59.667  12.561  1.00  0.00                              
ATOM    101  O   VAL    66       4.084  59.359  11.914  1.00  0.00                              
ATOM    103  CG1 VAL    66       7.693  61.830  10.707  1.00  0.00                              
ATOM    105  CG2 VAL    66       5.305  61.400  10.094  1.00  0.00                              
ATOM    107  H   ALA    67       5.904  59.917  14.327  1.00  0.00                              
ATOM    109  N   ALA    67       5.101  59.726  13.891  1.00  0.00                              
ATOM    111  CA  ALA    67       3.900  59.525  14.689  1.00  0.00                              
ATOM    113  CB  ALA    67       3.942  58.170  15.390  1.00  0.00                              
ATOM    115  C   ALA    67       3.788  60.648  15.716  1.00  0.00                              
ATOM    117  O   ALA    67       4.383  61.712  15.528  1.00  0.00                              
ATOM    119  H   THR    68       2.674  59.544  16.902  1.00  0.00                              
ATOM    121  N   THR    68       3.054  60.395  16.799  1.00  0.00                              
ATOM    123  CA  THR    68       2.796  61.395  17.835  1.00  0.00                              
ATOM    125  CB  THR    68       1.987  60.763  18.994  1.00  0.00                              
ATOM    127  C   THR    68       4.099  61.980  18.377  1.00  0.00                              
ATOM    129  O   THR    68       4.947  61.246  18.888  1.00  0.00                              
ATOM    131  CG2 THR    68       1.596  61.781  20.062  1.00  0.00                              
ATOM    133  OG1 THR    68       0.795  60.172  18.460  1.00  0.00                              
ATOM    135  H   ASP    69       3.557  63.823  17.920  1.00  0.00                              
ATOM    137  N   ASP    69       4.244  63.303  18.303  1.00  0.00                              
ATOM    139  CA  ASP    69       5.442  63.976  18.803  1.00  0.00                              
ATOM    141  CB  ASP    69       6.185  64.678  17.663  1.00  0.00                              
ATOM    143  C   ASP    69       5.104  64.995  19.887  1.00  0.00                              
ATOM    145  O   ASP    69       4.853  66.165  19.591  1.00  0.00                              
ATOM    147  CG  ASP    69       7.444  65.387  18.127  1.00  0.00                              
ATOM    149  OD1 ASP    69       7.714  65.393  19.347  1.00  0.00                              
ATOM    151  OD2 ASP    69       8.180  65.925  17.271  1.00  0.00                              
ATOM    153  H   GLY    70       5.390  63.696  21.335  1.00  0.00                              
ATOM    155  N   GLY    70       5.139  64.573  21.148  1.00  0.00                              
ATOM    157  CA  GLY    70       4.807  65.467  22.245  1.00  0.00                              
ATOM    159  C   GLY    70       6.028  66.100  22.888  1.00  0.00                              
ATOM    161  O   GLY    70       5.900  66.995  23.727  1.00  0.00                              
ATOM    163  H   SER    71       7.259  64.994  21.827  1.00  0.00                              
ATOM    165  N   SER    71       7.214  65.654  22.487  1.00  0.00                              
ATOM    167  CA  SER    71       8.456  66.160  23.062  1.00  0.00                              
ATOM    169  CB  SER    71       8.420  66.045  24.589  1.00  0.00                              
ATOM    171  C   SER    71       9.661  65.400  22.519  1.00  0.00                              
ATOM    173  O   SER    71      10.758  65.486  23.074  1.00  0.00                              
ATOM    175  OG  SER    71       7.922  64.777  24.982  1.00  0.00                              
ATOM    177  H   ALA    72       8.611  64.642  21.043  1.00  0.00                              
ATOM    179  N   ALA    72       9.453  64.643  21.446  1.00  0.00                              
ATOM    181  CA  ALA    72      10.518  63.831  20.867  1.00  0.00                              
ATOM    183  CB  ALA    72      11.883  64.415  21.221  1.00  0.00                              
ATOM    185  C   ALA    72      10.423  62.388  21.353  1.00  0.00                              
ATOM    187  O   ALA    72      10.101  62.139  22.517  1.00  0.00                              
ATOM    189  H   PHE    73      10.928  61.680  19.578  1.00  0.00                              
ATOM    191  N   PHE    73      10.681  61.438  20.459  1.00  0.00                              
ATOM    193  CA  PHE    73      10.587  60.024  20.804  1.00  0.00                              
ATOM    195  CB  PHE    73       9.564  59.822  21.929  1.00  0.00                              
ATOM    197  C   PHE    73      10.192  59.197  19.586  1.00  0.00                              
ATOM    199  O   PHE    73      10.109  57.969  19.663  1.00  0.00                              
ATOM    201  CG  PHE    73       9.322  58.378  22.284  1.00  0.00                              
ATOM    203  CD1 PHE    73      10.285  57.648  22.971  1.00  0.00                              
ATOM    205  CE1 PHE    73      10.061  56.316  23.309  1.00  0.00                              
ATOM    207  CZ  PHE    73       8.874  55.700  22.942  1.00  0.00                              
ATOM    209  CD2 PHE    73       8.120  57.761  21.956  1.00  0.00                              
ATOM    211  CE2 PHE    73       7.894  56.425  22.276  1.00  0.00                              
ATOM    213  H   TRP    74      10.036  60.811  18.455  1.00  0.00                              
ATOM    215  N   TRP    74       9.977  59.864  18.457  1.00  0.00                              
ATOM    217  CA  TRP    74       9.620  59.172  17.223  1.00  0.00                              
ATOM    219  CB  TRP    74       8.569  59.972  16.440  1.00  0.00                              
ATOM    221  C   TRP    74      10.850  58.920  16.360  1.00  0.00                              
ATOM    223  O   TRP    74      11.944  59.396  16.672  1.00  0.00                              
ATOM    225  CG  TRP    74       8.950  61.394  16.174  1.00  0.00                              
ATOM    227  CD1 TRP    74       8.609  62.502  16.897  1.00  0.00                              
ATOM    229  NE1 TRP    74       9.154  63.623  16.320  1.00  0.00                              
ATOM    231  HE1 TRP    74       9.072  64.508  16.659  1.00  0.00                              
ATOM    233  CD2 TRP    74       9.806  61.845  15.122  1.00  0.00                              
ATOM    235  CE2 TRP    74       9.868  63.251  15.212  1.00  0.00                              
ATOM    237  CE3 TRP    74      10.440  61.206  14.050  1.00  0.00                              
ATOM    239  CZ3 TRP    74      11.060  61.983  13.084  1.00  0.00                              
ATOM    241  CH2 TRP    74      11.064  63.382  13.175  1.00  0.00                              
ATOM    243  CZ2 TRP    74      10.476  64.034  14.230  1.00  0.00                              
ATOM    245  H   LEU    75       9.853  57.705  15.166  1.00  0.00                              
ATOM    247  N   LEU    75      10.686  58.129  15.306  1.00  0.00                              
ATOM    249  CA  LEU    75      11.775  57.862  14.374  1.00  0.00                              
ATOM    251  CB  LEU    75      12.972  58.773  14.661  1.00  0.00                              
ATOM    253  C   LEU    75      12.206  56.399  14.441  1.00  0.00                              
ATOM    255  O   LEU    75      12.709  55.942  15.470  1.00  0.00                              
ATOM    257  CG  LEU    75      14.158  58.638  13.704  1.00  0.00                              
ATOM    259  CD1 LEU    75      13.726  58.996  12.289  1.00  0.00                              
ATOM    261  CD2 LEU    75      15.303  59.535  14.156  1.00  0.00                              
ATOM    263  H   THR    76      11.573  56.047  12.613  1.00  0.00                              
ATOM    265  N   THR    76      11.989  55.660  13.358  1.00  0.00                              
ATOM    267  CA  THR    76      12.340  54.243  13.307  1.00  0.00                              
ATOM    269  CB  THR    76      11.399  53.404  14.199  1.00  0.00                              
ATOM    271  C   THR    76      12.265  53.719  11.873  1.00  0.00                              
ATOM    273  O   THR    76      11.173  53.502  11.345  1.00  0.00                              
ATOM    275  CG2 THR    76      12.022  52.054  14.531  1.00  0.00                              
ATOM    277  OG1 THR    76      11.144  54.112  15.419  1.00  0.00                              
ATOM    279  N   PRO    77      13.410  53.556  11.203  1.00  0.00                              
ATOM    281  CA  PRO    77      13.442  53.061   9.825  1.00  0.00                              
ATOM    283  CB  PRO    77      14.574  53.916   9.268  1.00  0.00                              
ATOM    285  C   PRO    77      13.833  51.589   9.729  1.00  0.00                              
ATOM    287  O   PRO    77      14.645  51.223   8.871  1.00  0.00                              
ATOM    289  CG  PRO    77      15.582  53.888  10.381  1.00  0.00                              
ATOM    291  CD  PRO    77      14.771  53.889  11.662  1.00  0.00                              
TER 
END
