
#######################################################
#                                                     #
#                        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   22 (  179),  selected   22 , name T0378TS022_1-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS022_1-D1.T0378_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    E      68      M       1           -
LGA    -       -      L       2           -
LGA    -       -      S       3           -
LGA    -       -      A       4           -
LGA    -       -      N       5           -
LGA    -       -      Q       6           -
LGA    -       -      I       7           -
LGA    -       -      K       8           -
LGA    -       -      F       9           -
LGA    -       -      L      10           -
LGA    -       -      R      11           -
LGA    -       -      S      12           -
LGA    -       -      L      13           -
LGA    -       -      R      14           -
LGA    -       -      E      15           -
LGA    -       -      R      16           -
LGA    -       -      K      17           -
LGA    -       -      Y      18           -
LGA    -       -      R      19           -
LGA    -       -      L      20           -
LGA    -       -      R      21           -
LGA    -       -      E      22           -
LGA    -       -      Q      23           -
LGA    -       -      A      24           -
LGA    -       -      F      25           -
LGA    -       -      A      26           -
LGA    -       -      V      27           -
LGA    -       -      E      28           -
LGA    -       -      G      29           -
LGA    -       -      P      30           -
LGA    -       -      K      31           -
LGA    -       -      L      32           -
LGA    -       -      V      33           -
LGA    -       -      G      34           -
LGA    -       -      E      35           -
LGA    -       -      M      36           -
LGA    -       -      L      37           -
LGA    -       -      P      38           -
LGA    S      69      F      39           #
LGA    F      70      Y      40          4.039
LGA    D      71      -       -           -
LGA    F      72      -       -           -
LGA    K      73      R      41          2.949
LGA    R      74      C      42          3.627
LGA    I      75      R      43          4.241
LGA    S      76      M      44          3.491
LGA    T      77      L      45          1.136
LGA    Q      78      V      46          0.883
LGA    T      79      G      47          2.357
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    T      80      L      66          2.216
LGA    P      81      P      67          2.379
LGA    Q      82      E      68          4.615
LGA    P      83      S      69          1.609
LGA    L      84      F      70          5.012
LGA    M      85      D      71          3.040
LGA    A      86      F      72          1.922
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    V      87      P      83          4.019
LGA    -       -      L      84           -
LGA    F      88      M      85          4.163
LGA    D      89      A      86          3.677
LGA    -       -      V      87           -
LGA    -       -      F      88           -
LGA    -       -      D      89           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   22   89    5.0     18    3.30     5.56     13.355     0.530

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.978597 * X  +  -0.180378 * Y  +   0.099049 * Z  +   6.363265
  Y_new =  -0.199371 * X  +  -0.950277 * Y  +   0.239216 * Z  +   4.921569
  Z_new =   0.050975 * X  +  -0.253843 * Y  +  -0.965901 * Z  +  81.124741 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.884599    0.256993  [ DEG:  -165.2754     14.7246 ]
  Theta =  -0.050997   -3.090596  [ DEG:    -2.9219   -177.0781 ]
  Phi   =  -0.200981    2.940612  [ DEG:   -11.5153    168.4847 ]
 
# 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_1-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS022_1-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   22   89   5.0   18   3.30    5.56  13.355
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS022_1-D1
PFRMAT TS
TARGET T0378
MODEL  1
PARENT 1ipa_A
ATOM      1  N   GLU    68      11.771   5.877  57.594  1.00  0.00
ATOM      2  CA  GLU    68      12.664   5.236  56.605  1.00  0.00
ATOM      3  C   GLU    68      12.843   6.132  55.431  1.00  0.00
ATOM      4  O   GLU    68      13.489   7.173  55.529  1.00  0.00
ATOM      5  CB  GLU    68      12.068   3.910  56.125  1.00  0.00
ATOM      6  CG  GLU    68      12.015   2.832  57.195  1.00  0.00
ATOM      7  CD  GLU    68      11.370   1.552  56.700  1.00  0.00
ATOM      8  OE1 GLU    68      10.926   1.524  55.532  1.00  0.00
ATOM      9  OE2 GLU    68      11.308   0.578  57.478  1.00  0.00
ATOM     10  N   SER    69      12.271   5.749  54.277  1.00  0.00
ATOM     11  CA  SER    69      12.415   6.594  53.135  1.00  0.00
ATOM     12  C   SER    69      11.785   7.895  53.491  1.00  0.00
ATOM     13  O   SER    69      12.361   8.960  53.275  1.00  0.00
ATOM     14  CB  SER    69      11.719   5.976  51.921  1.00  0.00
ATOM     15  OG  SER    69      12.367   4.783  51.514  1.00  0.00
ATOM     16  N   PHE    70      10.574   7.836  54.075  1.00  0.00
ATOM     17  CA  PHE    70       9.913   9.053  54.421  1.00  0.00
ATOM     18  C   PHE    70      10.523   9.522  55.695  1.00  0.00
ATOM     19  O   PHE    70      10.759   8.736  56.611  1.00  0.00
ATOM     20  CB  PHE    70       8.413   8.814  54.605  1.00  0.00
ATOM     21  CG  PHE    70       7.676   8.571  53.319  1.00  0.00
ATOM     22  CD1 PHE    70       7.363   7.283  52.916  1.00  0.00
ATOM     23  CD2 PHE    70       7.296   9.628  52.510  1.00  0.00
ATOM     24  CE1 PHE    70       6.686   7.058  51.733  1.00  0.00
ATOM     25  CE2 PHE    70       6.619   9.403  51.327  1.00  0.00
ATOM     26  CZ  PHE    70       6.314   8.126  50.937  1.00  0.00
ATOM     27  N   ASP    71      10.811  10.832  55.775  1.00  0.00
ATOM     28  CA  ASP    71      11.394  11.357  56.969  1.00  0.00
ATOM     29  C   ASP    71      10.284  11.526  57.948  1.00  0.00
ATOM     30  O   ASP    71       9.114  11.567  57.572  1.00  0.00
ATOM     31  CB  ASP    71      12.068  12.702  56.690  1.00  0.00
ATOM     32  CG  ASP    71      13.346  12.558  55.885  1.00  0.00
ATOM     33  OD1 ASP    71      13.841  11.419  55.758  1.00  0.00
ATOM     34  OD2 ASP    71      13.851  13.584  55.385  1.00  0.00
ATOM     35  N   PHE    72      10.622  11.614  59.245  1.00  0.00
ATOM     36  CA  PHE    72       9.584  11.819  60.203  1.00  0.00
ATOM     37  C   PHE    72       9.258  13.266  60.032  1.00  0.00
ATOM     38  O   PHE    72      10.139  14.111  60.163  1.00  0.00
ATOM     39  CB  PHE    72      10.085  11.500  61.614  1.00  0.00
ATOM     40  CG  PHE    72      10.315  10.036  61.858  1.00  0.00
ATOM     41  CD1 PHE    72      11.575   9.484  61.711  1.00  0.00
ATOM     42  CD2 PHE    72       9.269   9.210  62.234  1.00  0.00
ATOM     43  CE1 PHE    72      11.786   8.137  61.937  1.00  0.00
ATOM     44  CE2 PHE    72       9.480   7.863  62.460  1.00  0.00
ATOM     45  CZ  PHE    72      10.732   7.326  62.312  1.00  0.00
ATOM     46  N   LYS    73       8.000  13.597  59.676  1.00  0.00
ATOM     47  CA  LYS    73       7.697  14.982  59.456  1.00  0.00
ATOM     48  C   LYS    73       6.236  15.129  59.182  1.00  0.00
ATOM     49  O   LYS    73       5.490  14.153  59.143  1.00  0.00
ATOM     50  CB  LYS    73       8.486  15.520  58.262  1.00  0.00
ATOM     51  CG  LYS    73       8.125  14.872  56.936  1.00  0.00
ATOM     52  CD  LYS    73       8.926  15.472  55.791  1.00  0.00
ATOM     53  CE  LYS    73       8.609  14.782  54.474  1.00  0.00
ATOM     54  NZ  LYS    73       9.401  15.347  53.347  1.00  0.00
ATOM     55  N   ARG    74       5.801  16.392  59.009  1.00  0.00
ATOM     56  CA  ARG    74       4.436  16.705  58.703  1.00  0.00
ATOM     57  C   ARG    74       4.463  17.325  57.343  1.00  0.00
ATOM     58  O   ARG    74       5.456  17.942  56.962  1.00  0.00
ATOM     59  CB  ARG    74       3.864  17.677  59.736  1.00  0.00
ATOM     60  CG  ARG    74       3.765  17.103  61.141  1.00  0.00
ATOM     61  CD  ARG    74       3.200  18.123  62.115  1.00  0.00
ATOM     62  NE  ARG    74       4.108  19.249  62.317  1.00  0.00
ATOM     63  CZ  ARG    74       3.813  20.327  63.037  1.00  0.00
ATOM     64  NH1 ARG    74       4.703  21.301  63.165  1.00  0.00
ATOM     65  NH2 ARG    74       2.630  20.428  63.626  1.00  0.00
ATOM     66  N   ILE    75       3.380  17.157  56.556  1.00  0.00
ATOM     67  CA  ILE    75       3.382  17.714  55.234  1.00  0.00
ATOM     68  C   ILE    75       2.217  18.640  55.095  1.00  0.00
ATOM     69  O   ILE    75       1.128  18.370  55.599  1.00  0.00
ATOM     70  CB  ILE    75       3.270  16.616  54.158  1.00  0.00
ATOM     71  CG1 ILE    75       4.466  15.665  54.242  1.00  0.00
ATOM     72  CG2 ILE    75       3.242  17.234  52.769  1.00  0.00
ATOM     73  CD1 ILE    75       4.315  14.420  53.397  1.00  0.00
ATOM     74  N   SER    76       2.438  19.786  54.419  1.00  0.00
ATOM     75  CA  SER    76       1.373  20.714  54.174  1.00  0.00
ATOM     76  C   SER    76       1.599  21.281  52.810  1.00  0.00
ATOM     77  O   SER    76       2.720  21.270  52.303  1.00  0.00
ATOM     78  CB  SER    76       1.383  21.830  55.221  1.00  0.00
ATOM     79  OG  SER    76       2.560  22.612  55.121  1.00  0.00
ATOM     80  N   THR    77       0.527  21.787  52.170  1.00  0.00
ATOM     81  CA  THR    77       0.660  22.328  50.848  1.00  0.00
ATOM     82  C   THR    77       0.187  23.744  50.904  1.00  0.00
ATOM     83  O   THR    77      -0.562  24.122  51.804  1.00  0.00
ATOM     84  CB  THR    77      -0.182  21.540  49.828  1.00  0.00
ATOM     85  OG1 THR    77      -1.570  21.639  50.172  1.00  0.00
ATOM     86  CG2 THR    77       0.221  20.073  49.825  1.00  0.00
ATOM     87  N   GLN    78       0.642  24.573  49.945  1.00  0.00
ATOM     88  CA  GLN    78       0.243  25.948  49.919  1.00  0.00
ATOM     89  C   GLN    78      -0.499  26.177  48.640  1.00  0.00
ATOM     90  O   GLN    78      -0.268  25.500  47.640  1.00  0.00
ATOM     91  CB  GLN    78       1.467  26.864  49.984  1.00  0.00
ATOM     92  CG  GLN    78       2.340  26.648  51.211  1.00  0.00
ATOM     93  CD  GLN    78       1.643  27.048  52.497  1.00  0.00
ATOM     94  OE1 GLN    78       0.979  28.083  52.559  1.00  0.00
ATOM     95  NE2 GLN    78       1.795  26.227  53.530  1.00  0.00
ATOM     96  N   THR    79      -1.436  27.144  48.654  1.00  0.00
ATOM     97  CA  THR    79      -2.178  27.462  47.471  1.00  0.00
ATOM     98  C   THR    79      -1.897  28.896  47.177  1.00  0.00
ATOM     99  O   THR    79      -1.376  29.619  48.024  1.00  0.00
ATOM    100  CB  THR    79      -3.690  27.249  47.679  1.00  0.00
ATOM    101  OG1 THR    79      -4.162  28.130  48.705  1.00  0.00
ATOM    102  CG2 THR    79      -3.973  25.813  48.092  1.00  0.00
ATOM    103  N   THR    80      -2.209  29.348  45.948  1.00  0.00
ATOM    104  CA  THR    80      -1.907  30.710  45.631  1.00  0.00
ATOM    105  C   THR    80      -3.179  31.446  45.374  1.00  0.00
ATOM    106  O   THR    80      -4.077  30.983  44.673  1.00  0.00
ATOM    107  CB  THR    80      -1.016  30.815  44.379  1.00  0.00
ATOM    108  OG1 THR    80       0.218  30.125  44.609  1.00  0.00
ATOM    109  CG2 THR    80      -0.716  32.270  44.059  1.00  0.00
ATOM    110  N   PRO    81      -3.263  32.590  45.989  1.00  0.00
ATOM    111  CA  PRO    81      -4.397  33.442  45.768  1.00  0.00
ATOM    112  C   PRO    81      -4.175  34.145  44.471  1.00  0.00
ATOM    113  O   PRO    81      -3.055  34.085  43.966  1.00  0.00
ATOM    114  CB  PRO    81      -4.389  34.387  46.971  1.00  0.00
ATOM    115  CG  PRO    81      -2.947  34.529  47.327  1.00  0.00
ATOM    116  CD  PRO    81      -2.326  33.180  47.092  1.00  0.00
ATOM    117  N   GLN    82      -5.227  34.780  43.910  1.00  0.00
ATOM    118  CA  GLN    82      -5.119  35.528  42.688  1.00  0.00
ATOM    119  C   GLN    82      -5.311  34.579  41.558  1.00  0.00
ATOM    120  O   GLN    82      -5.649  33.413  41.755  1.00  0.00
ATOM    121  CB  GLN    82      -3.744  36.190  42.584  1.00  0.00
ATOM    122  CG  GLN    82      -3.495  37.273  43.620  1.00  0.00
ATOM    123  CD  GLN    82      -2.103  37.866  43.522  1.00  0.00
ATOM    124  OE1 GLN    82      -1.307  37.468  42.671  1.00  0.00
ATOM    125  NE2 GLN    82      -1.806  38.821  44.395  1.00  0.00
ATOM    126  N   PRO    83      -5.133  35.069  40.364  1.00  0.00
ATOM    127  CA  PRO    83      -5.228  34.193  39.236  1.00  0.00
ATOM    128  C   PRO    83      -4.039  33.298  39.304  1.00  0.00
ATOM    129  O   PRO    83      -3.043  33.686  39.913  1.00  0.00
ATOM    130  CB  PRO    83      -5.212  35.137  38.032  1.00  0.00
ATOM    131  CG  PRO    83      -4.446  36.328  38.501  1.00  0.00
ATOM    132  CD  PRO    83      -4.800  36.508  39.950  1.00  0.00
ATOM    133  N   LEU    84      -4.117  32.097  38.705  1.00  0.00
ATOM    134  CA  LEU    84      -3.034  31.173  38.845  1.00  0.00
ATOM    135  C   LEU    84      -1.814  31.744  38.211  1.00  0.00
ATOM    136  O   LEU    84      -1.791  32.042  37.018  1.00  0.00
ATOM    137  CB  LEU    84      -3.373  29.844  38.169  1.00  0.00
ATOM    138  CG  LEU    84      -2.344  28.721  38.325  1.00  0.00
ATOM    139  CD1 LEU    84      -2.220  28.307  39.783  1.00  0.00
ATOM    140  CD2 LEU    84      -2.755  27.499  37.517  1.00  0.00
ATOM    141  N   MET    85      -0.757  31.922  39.023  1.00  0.00
ATOM    142  CA  MET    85       0.490  32.359  38.484  1.00  0.00
ATOM    143  C   MET    85       1.559  31.829  39.383  1.00  0.00
ATOM    144  O   MET    85       1.792  32.354  40.471  1.00  0.00
ATOM    145  CB  MET    85       0.547  33.887  38.435  1.00  0.00
ATOM    146  CG  MET    85       1.818  34.443  37.816  1.00  0.00
ATOM    147  SD  MET    85       1.849  36.245  37.785  1.00  0.00
ATOM    148  CE  MET    85       2.133  36.608  39.516  1.00  0.00
ATOM    149  N   ALA    86       2.243  30.761  38.933  1.00  0.00
ATOM    150  CA  ALA    86       3.300  30.169  39.698  1.00  0.00
ATOM    151  C   ALA    86       2.748  29.618  40.974  1.00  0.00
ATOM    152  O   ALA    86       1.677  30.009  41.436  1.00  0.00
ATOM    153  CB  ALA    86       4.361  31.208  40.028  1.00  0.00
ATOM    154  N   VAL    87       3.476  28.643  41.553  1.00  0.00
ATOM    155  CA  VAL    87       3.123  28.058  42.813  1.00  0.00
ATOM    156  C   VAL    87       4.418  27.765  43.493  1.00  0.00
ATOM    157  O   VAL    87       5.461  27.700  42.842  1.00  0.00
ATOM    158  CB  VAL    87       2.308  26.765  42.627  1.00  0.00
ATOM    159  CG1 VAL    87       0.994  27.061  41.920  1.00  0.00
ATOM    160  CG2 VAL    87       3.087  25.759  41.791  1.00  0.00
ATOM    161  N   PHE    88       4.407  27.601  44.830  1.00  0.00
ATOM    162  CA  PHE    88       5.664  27.325  45.455  1.00  0.00
ATOM    163  C   PHE    88       5.385  26.213  46.414  1.00  0.00
ATOM    164  O   PHE    88       4.244  26.035  46.839  1.00  0.00
ATOM    165  CB  PHE    88       6.184  28.566  46.185  1.00  0.00
ATOM    166  CG  PHE    88       5.320  29.000  47.334  1.00  0.00
ATOM    167  CD1 PHE    88       5.558  28.528  48.613  1.00  0.00
ATOM    168  CD2 PHE    88       4.270  29.880  47.136  1.00  0.00
ATOM    169  CE1 PHE    88       4.762  28.927  49.671  1.00  0.00
ATOM    170  CE2 PHE    88       3.476  30.279  48.194  1.00  0.00
ATOM    171  CZ  PHE    88       3.718  29.807  49.457  1.00  0.00
ATOM    172  N   ASP    89       6.410  25.413  46.767  1.00  0.00
ATOM    173  CA  ASP    89       6.164  24.315  47.656  1.00  0.00
ATOM    174  C   ASP    89       7.086  24.420  48.829  1.00  0.00
ATOM    175  O   ASP    89       8.289  24.621  48.666  1.00  0.00
ATOM    176  CB  ASP    89       6.409  22.983  46.943  1.00  0.00
ATOM    177  CG  ASP    89       5.455  22.757  45.787  1.00  0.00
ATOM    178  OD1 ASP    89       4.227  22.798  46.013  1.00  0.00
ATOM    179  OD2 ASP    89       5.934  22.539  44.655  1.00  0.00
TER
END
