
#######################################################
#                                                     #
#                        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  125 (  125),  selected  125 , name T0367TS393_5
# Molecule2: number of CA atoms  125 ( 1016),  selected  125 , name T0367.pdb
# PARAMETERS: T0367TS393_5.T0367.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      M       1           -
LGA    D       2      D       2           -
LGA    E       3      E       3           -
LGA    L       4      L       4           -
LGA    E       5      E       5           -
LGA    L       6      L       6           -
LGA    R       7      R       7           -
LGA    I       8      I       8           -
LGA    R       9      R       9           -
LGA    K      10      K      10           -
LGA    A      11      A      11           -
LGA    E      12      E      12           -
LGA    K      13      K      13           -
LGA    L      14      L      14           -
LGA    V      15      V      15           -
LGA    Q      16      Q      16           -
LGA    D      17      D      17           -
LGA    A      18      A      18           -
LGA    K      19      K      19           -
LGA    -       -      K      20           -
LGA    -       -      E      21           -
LGA    K      20      F      22           #
LGA    E      21      E      23           -
LGA    F      22      M      24           -
LGA    -       -      G      25           -
LGA    -       -      L      26           -
LGA    -       -      Y      27           -
LGA    -       -      E      28           -
LGA    -       -      R      29           -
LGA    -       -      C      30           -
LGA    E      23      C      31           #
LGA    M      24      S      32           -
LGA    G      25      T      33           -
LGA    L      26      -       -           -
LGA    Y      27      A      34           #
LGA    E      28      Y      35           -
LGA    R      29      Y      36           -
LGA    C      30      A      37           #
LGA    C      31      M      38          4.158
LGA    S      32      F      39           -
LGA    T      33      -       -           -
LGA    A      34      H      40          4.003
LGA    Y      35      A      41          2.722
LGA    Y      36      A      42          3.592
LGA    A      37      K      43          2.498
LGA    M      38      A      44          1.265
LGA    F      39      M      45          2.370
LGA    H      40      L      46          1.068
LGA    A      41      L      47          2.694
LGA    A      42      G      48          4.124
LGA    -       -      Y      49           -
LGA    K      43      G      50          1.367
LGA    A      44      R      51          3.829
LGA    M      45      D      52           #
LGA    L      46      -       -           -
LGA    L      47      -       -           -
LGA    G      48      -       -           -
LGA    Y      49      -       -           -
LGA    G      50      -       -           -
LGA    R      51      S      53          5.068
LGA    D      52      K      54          5.280
LGA    S      53      -       -           -
LGA    K      54      -       -           -
LGA    T      55      T      55          3.384
LGA    H      56      -       -           -
LGA    R      57      -       -           -
LGA    G      58      -       -           -
LGA    T      59      H      56           #
LGA    I      60      R      57           #
LGA    Y      61      G      58           #
LGA    L      62      T      59          4.614
LGA    I      63      I      60          4.097
LGA    W      64      Y      61          4.529
LGA    E      65      L      62          3.459
LGA    C      66      I      63          3.012
LGA    R      67      -       -           -
LGA    E      68      W      64          3.216
LGA    E      69      E      65          2.497
LGA    L      70      C      66          1.618
LGA    G      71      R      67          2.383
LGA    -       -      E      68           -
LGA    -       -      E      69           -
LGA    -       -      L      70           -
LGA    -       -      G      71           -
LGA    L      72      L      72          2.674
LGA    S      73      S      73          1.014
LGA    D      74      D      74          2.072
LGA    D      75      D      75          2.221
LGA    D      76      D      76          1.392
LGA    C      77      C      77          1.895
LGA    S      78      S      78          2.319
LGA    K      79      K      79          1.829
LGA    L      80      L      80          2.085
LGA    S      81      S      81          2.162
LGA    R      82      R      82          2.011
LGA    A      83      A      83          1.541
LGA    F      84      F      84          1.826
LGA    D      85      D      85          1.792
LGA    L      86      L      86          1.721
LGA    R      87      R      87          1.733
LGA    E      88      E      88          1.832
LGA    E      89      E      89          1.561
LGA    S      90      S      90          2.722
LGA    D      91      D      91          2.754
LGA    Y      92      Y      92          1.278
LGA    G      93      G      93          4.280
LGA    I      94      I      94          2.031
LGA    Y      95      Y      95          1.846
LGA    K      96      -       -           -
LGA    E      97      K      96          3.860
LGA    V      98      E      97          1.826
LGA    S      99      V      98          4.211
LGA    K     100      S      99          3.623
LGA    D     101      K     100          3.143
LGA    L     102      D     101          2.924
LGA    A     103      L     102          2.922
LGA    I     104      A     103          3.045
LGA    K     105      -       -           -
LGA    I     106      I     104          4.593
LGA    L     107      K     105           -
LGA    K     108      I     106           -
LGA    D     109      L     107          3.625
LGA    -       -      K     108           -
LGA    -       -      D     109           -
LGA    A     110      A     110           #
LGA    E     111      -       -           -
LGA    I     112      -       -           -
LGA    F     113      E     111           #
LGA    V     114      I     112           -
LGA    Q     115      F     113           -
LGA    K     116      V     114           -
LGA    A     117      Q     115           -
LGA    K     118      K     116           -
LGA    N     119      A     117           -
LGA    A     120      K     118           -
LGA    V     121      N     119           -
LGA    N     122      A     120           -
LGA    K     123      V     121           -
LGA    N     124      N     122           -
LGA    R     125      K     123           -
LGA    -       -      N     124           -
LGA    -       -      R     125           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  125  125    5.0     58    2.95    48.28     30.086     1.899

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.720660 * X  +  -0.649616 * Y  +  -0.242173 * Z  +  35.306007
  Y_new =   0.540656 * X  +   0.307940 * Y  +   0.782857 * Z  +  33.014515
  Z_new =  -0.433982 * X  +  -0.695106 * Y  +   0.573138 * Z  +  28.031303 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.881274    2.260319  [ DEG:   -50.4933    129.5067 ]
  Theta =   0.448908    2.692685  [ DEG:    25.7205    154.2795 ]
  Phi   =   0.643643   -2.497949  [ DEG:    36.8781   -143.1219 ]
 
# 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: T0367TS393_5                                  
REMARK     2: T0367.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0367TS393_5.T0367.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  125  125   5.0   58   2.95   48.28  30.086
REMARK  ---------------------------------------------------------- 
MOLECULE T0367TS393_5
PFRMAT TS
TARGET T0367
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1      -4.183  22.796  16.137  1.00 25.00           C
ATOM      2  CA  ASP     2      -1.848  25.819  15.993  1.00 25.00           C
ATOM      3  CA  GLU     3       0.549  25.391  13.036  1.00 25.00           C
ATOM      4  CA  LEU     4       1.712  29.020  13.421  1.00 25.00           C
ATOM      5  CA  GLU     5       2.298  28.462  17.164  1.00 25.00           C
ATOM      6  CA  LEU     6       4.320  25.299  16.400  1.00 25.00           C
ATOM      7  CA  ARG     7       6.418  27.229  13.844  1.00 25.00           C
ATOM      8  CA  ILE     8       7.056  29.993  16.416  1.00 25.00           C
ATOM      9  CA  ARG     9       8.123  27.376  19.000  1.00 25.00           C
ATOM     10  CA  LYS    10      10.503  25.793  16.450  1.00 25.00           C
ATOM     11  CA  ALA    11      11.996  29.232  15.673  1.00 25.00           C
ATOM     12  CA  GLU    12      12.486  29.894  19.413  1.00 25.00           C
ATOM     13  CA  LYS    13      14.210  26.497  19.813  1.00 25.00           C
ATOM     14  CA  LEU    14      16.509  27.289  16.854  1.00 25.00           C
ATOM     15  CA  VAL    15      17.374  30.683  18.403  1.00 25.00           C
ATOM     16  CA  GLN    16      18.162  28.985  21.744  1.00 25.00           C
ATOM     17  CA  ASP    17      20.411  26.453  19.956  1.00 25.00           C
ATOM     18  CA  ALA    18      22.229  29.303  18.156  1.00 25.00           C
ATOM     19  CA  LYS    19      22.736  31.117  21.491  1.00 25.00           C
ATOM     20  CA  LYS    20      24.129  27.911  23.053  1.00 25.00           C
ATOM     21  CA  GLU    21      26.526  27.483  20.096  1.00 25.00           C
ATOM     22  CA  PHE    22      27.688  31.111  20.482  1.00 25.00           C
ATOM     23  CA  GLU    23      28.275  30.551  24.225  1.00 25.00           C
ATOM     24  CA  MET    24      30.296  27.390  23.460  1.00 25.00           C
ATOM     25  CA  GLY    25      32.395  29.320  20.903  1.00 25.00           C
ATOM     26  CA  LEU    26      33.033  32.084  23.477  1.00 25.00           C
ATOM     27  CA  TYR    27      34.100  29.467  26.060  1.00 25.00           C
ATOM     28  CA  GLU    28      36.479  27.883  23.511  1.00 25.00           C
ATOM     29  CA  ARG    29      37.973  31.324  22.733  1.00 25.00           C
ATOM     30  CA  CYS    30      38.462  31.984  26.474  1.00 25.00           C
ATOM     31  CA  CYS    31      40.186  28.588  26.873  1.00 25.00           C
ATOM     32  CA  SER    32      42.486  29.379  23.915  1.00 25.00           C
ATOM     33  CA  THR    33      43.350  32.773  25.463  1.00 25.00           C
ATOM     34  CA  ALA    34      44.138  31.075  28.804  1.00 25.00           C
ATOM     35  CA  TYR    35      46.387  28.544  27.016  1.00 25.00           C
ATOM     36  CA  TYR    36      48.206  31.394  25.217  1.00 25.00           C
ATOM     37  CA  ALA    37      48.713  33.208  28.551  1.00 25.00           C
ATOM     38  CA  MET    38      50.106  30.001  30.113  1.00 25.00           C
ATOM     39  CA  PHE    39      52.503  29.573  27.157  1.00 25.00           C
ATOM     40  CA  HIS    40      53.665  33.202  27.542  1.00 25.00           C
ATOM     41  CA  ALA    41      54.252  32.642  31.285  1.00 25.00           C
ATOM     42  CA  ALA    42      56.273  29.480  30.520  1.00 25.00           C
ATOM     43  CA  LYS    43      58.372  31.411  27.964  1.00 25.00           C
ATOM     44  CA  ALA    44      59.008  34.174  30.537  1.00 25.00           C
ATOM     45  CA  MET    45      60.076  31.557  33.121  1.00 25.00           C
ATOM     46  CA  LEU    46      62.455  29.975  30.571  1.00 25.00           C
ATOM     47  CA  LEU    47      63.950  33.414  29.793  1.00 25.00           C
ATOM     48  CA  GLY    48      64.439  34.075  33.534  1.00 25.00           C
ATOM     49  CA  TYR    49      61.491  36.103  34.948  1.00 25.00           C
ATOM     50  CA  GLY    50      58.256  37.745  35.994  1.00 25.00           C
ATOM     51  CA  ARG    51      55.077  39.731  36.916  1.00 25.00           C
ATOM     52  CA  ASP    52      54.466  42.039  39.918  1.00 25.00           C
ATOM     53  CA  SER    53      51.791  41.414  42.467  1.00 25.00           C
ATOM     54  CA  LYS    54      47.967  41.660  42.123  1.00 25.00           C
ATOM     55  CA  THR    55      47.378  41.798  38.369  1.00 25.00           C
ATOM     56  CA  HIS    56      44.801  39.740  36.472  1.00 25.00           C
ATOM     57  CA  ARG    57      42.187  37.079  36.824  1.00 25.00           C
ATOM     58  CA  GLY    58      44.488  34.755  34.831  1.00 25.00           C
ATOM     59  CA  THR    59      41.803  34.376  32.126  1.00 25.00           C
ATOM     60  CA  ILE    60      41.405  38.181  31.954  1.00 25.00           C
ATOM     61  CA  TYR    61      45.198  38.588  31.615  1.00 25.00           C
ATOM     62  CA  LEU    62      45.249  35.989  28.801  1.00 25.00           C
ATOM     63  CA  ILE    63      42.409  37.835  27.013  1.00 25.00           C
ATOM     64  CA  TRP    64      44.315  41.140  27.343  1.00 25.00           C
ATOM     65  CA  GLU    65      47.463  39.496  25.912  1.00 25.00           C
ATOM     66  CA  CYS    66      45.435  38.110  22.975  1.00 25.00           C
ATOM     67  CA  ARG    67      43.961  41.584  22.322  1.00 25.00           C
ATOM     68  CA  GLU    68      47.472  43.112  22.382  1.00 25.00           C
ATOM     69  CA  GLU    69      48.697  40.456  19.910  1.00 25.00           C
ATOM     70  CA  LEU    70      50.472  37.146  19.435  1.00 25.00           C
ATOM     71  CA  GLY    71      49.129  36.787  15.865  1.00 25.00           C
ATOM     72  CA  LEU    72      46.050  35.345  17.611  1.00 25.00           C
ATOM     73  CA  SER    73      43.820  35.021  14.476  1.00 25.00           C
ATOM     74  CA  ASP    74      41.153  37.709  14.037  1.00 25.00           C
ATOM     75  CA  ASP    75      38.026  35.788  15.134  1.00 25.00           C
ATOM     76  CA  ASP    76      39.988  34.185  18.005  1.00 25.00           C
ATOM     77  CA  CYS    77      41.264  37.629  19.088  1.00 25.00           C
ATOM     78  CA  SER    78      37.690  39.003  19.017  1.00 25.00           C
ATOM     79  CA  LYS    79      36.487  36.048  21.136  1.00 25.00           C
ATOM     80  CA  LEU    80      39.311  36.667  23.648  1.00 25.00           C
ATOM     81  CA  SER    81      38.365  40.375  23.834  1.00 25.00           C
ATOM     82  CA  ARG    82      34.701  39.435  24.435  1.00 25.00           C
ATOM     83  CA  ALA    83      35.750  37.022  27.217  1.00 25.00           C
ATOM     84  CA  PHE    84      37.880  39.766  28.828  1.00 25.00           C
ATOM     85  CA  ASP    85      34.923  42.193  28.664  1.00 25.00           C
ATOM     86  CA  LEU    86      32.651  39.573  30.288  1.00 25.00           C
ATOM     87  CA  ARG    87      35.229  39.023  33.066  1.00 25.00           C
ATOM     88  CA  GLU    88      35.437  42.802  33.654  1.00 25.00           C
ATOM     89  CA  GLU    89      31.617  43.006  33.849  1.00 25.00           C
ATOM     90  CA  SER    90      32.135  41.108  37.106  1.00 25.00           C
ATOM     91  CA  ASP    91      33.811  42.588  40.158  1.00 25.00           C
ATOM     92  CA  TYR    92      31.432  45.521  39.587  1.00 25.00           C
ATOM     93  CA  GLY    93      28.911  45.901  42.390  1.00 25.00           C
ATOM     94  CA  ILE    94      25.184  45.739  41.568  1.00 25.00           C
ATOM     95  CA  TYR    95      22.857  46.940  38.744  1.00 25.00           C
ATOM     96  CA  LYS    96      19.362  47.677  37.334  1.00 25.00           C
ATOM     97  CA  GLU    97      19.626  45.464  34.240  1.00 25.00           C
ATOM     98  CA  VAL    98      21.308  42.123  33.357  1.00 25.00           C
ATOM     99  CA  SER    99      24.069  43.563  31.172  1.00 25.00           C
ATOM    100  CA  LYS   100      23.290  40.556  28.962  1.00 25.00           C
ATOM    101  CA  ASP   101      22.000  36.968  28.595  1.00 25.00           C
ATOM    102  CA  LEU   102      24.936  36.123  26.287  1.00 25.00           C
ATOM    103  CA  ALA   103      27.390  37.605  28.825  1.00 25.00           C
ATOM    104  CA  ILE   104      25.786  35.539  31.621  1.00 25.00           C
ATOM    105  CA  LYS   105      26.073  32.375  29.482  1.00 25.00           C
ATOM    106  CA  ILE   106      29.762  33.142  28.798  1.00 25.00           C
ATOM    107  CA  LEU   107      30.378  33.642  32.545  1.00 25.00           C
ATOM    108  CA  LYS   108      28.659  30.302  33.297  1.00 25.00           C
ATOM    109  CA  ASP   109      30.823  28.565  30.658  1.00 25.00           C
ATOM    110  CA  ALA   110      33.975  30.109  32.192  1.00 25.00           C
ATOM    111  CA  GLU   111      32.900  28.912  35.667  1.00 25.00           C
ATOM    112  CA  ILE   112      32.306  25.385  34.295  1.00 25.00           C
ATOM    113  CA  PHE   113      35.771  25.409  32.666  1.00 25.00           C
ATOM    114  CA  VAL   114      37.346  26.528  35.973  1.00 25.00           C
ATOM    115  CA  GLN   115      35.518  23.718  37.823  1.00 25.00           C
ATOM    116  CA  LYS   116      36.762  21.176  35.244  1.00 25.00           C
ATOM    117  CA  ALA   117      40.343  22.472  35.658  1.00 25.00           C
ATOM    118  CA  LYS   118      40.038  22.165  39.464  1.00 25.00           C
ATOM    119  CA  ASN   119      38.748  18.578  39.097  1.00 25.00           C
ATOM    120  CA  ALA   120      41.685  17.732  36.788  1.00 25.00           C
ATOM    121  CA  VAL   121      44.139  19.215  39.326  1.00 25.00           C
ATOM    122  CA  ASN   122      42.534  17.147  42.123  1.00 25.00           C
ATOM    123  CA  LYS   123      41.913  13.567  43.146  1.00 25.00           C
ATOM    124  CA  ASN   124      40.417  10.391  41.790  1.00 25.00           C
ATOM    125  CA  ARG   125      38.414  10.134  38.541  1.00 25.00           C
TER
END
