
#######################################################
#                                                     #
#                        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  130 (  130),  selected  130 , name T0354TS393_5
# Molecule2: number of CA atoms  122 (  928),  selected  122 , name T0354.pdb
# PARAMETERS: T0354TS393_5.T0354.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    E       2      -       -           -
LGA    I       3      -       -           -
LGA    Q       4      -       -           -
LGA    E       5      M       1           #
LGA    I       6      E       2           #
LGA    S       7      I       3          3.540
LGA    K       8      Q       4          1.166
LGA    L       9      E       5          1.649
LGA    A      10      I       6          2.515
LGA    I      11      S       7          2.577
LGA    E      12      K       8          2.427
LGA    A      13      L       9          2.062
LGA    L      14      A      10          5.091
LGA    E      15      I      11           #
LGA    D      16      -       -           -
LGA    I      17      E      12          4.689
LGA    K      18      A      13          3.500
LGA    G      19      L      14          2.715
LGA    -       -      E      15           -
LGA    K      20      D      16          1.953
LGA    D      21      I      17          3.102
LGA    I      22      K      18          2.768
LGA    I      23      G      19          2.462
LGA    -       -      K      20           -
LGA    -       -      D      21           -
LGA    E      24      I      22           #
LGA    L      25      -       -           -
LGA    D      26      -       -           -
LGA    T      27      -       -           -
LGA    S      28      -       -           -
LGA    K      29      -       -           -
LGA    L      30      -       -           -
LGA    T      31      -       -           -
LGA    S      32      -       -           -
LGA    L      33      -       -           -
LGA    F      34      I      23          2.763
LGA    Q      35      E      24          4.229
LGA    R      36      L      25          4.876
LGA    -       -      D      26           -
LGA    -       -      T      27           -
LGA    -       -      S      28           -
LGA    -       -      K      29           -
LGA    -       -      L      30           -
LGA    -       -      T      31           -
LGA    -       -      S      32           -
LGA    -       -      L      33           -
LGA    -       -      F      34           -
LGA    -       -      Q      35           -
LGA    -       -      R      36           -
LGA    -       -      M      37           -
LGA    M      37      I      38          2.924
LGA    I      38      V      39          1.718
LGA    V      39      A      40           #
LGA    A      40      T      41          4.249
LGA    T      41      G      42           #
LGA    G      42      -       -           -
LGA    D      43      D      43          3.329
LGA    S      44      S      44          2.865
LGA    N      45      N      45          2.598
LGA    R      46      R      46          1.629
LGA    Q      47      Q      47          1.423
LGA    V      48      V      48          1.310
LGA    K      49      K      49          1.394
LGA    A      50      A      50          0.902
LGA    L      51      L      51          0.337
LGA    A      52      A      52          0.778
LGA    N      53      N      53          0.990
LGA    S      54      S      54          0.552
LGA    V      55      V      55          1.089
LGA    Q      56      Q      56          1.732
LGA    V      57      V      57          1.025
LGA    K      58      K      58          2.000
LGA    L      59      L      59          3.050
LGA    K      60      K      60          2.592
LGA    E      61      E      61          2.374
LGA    -       -      A      62           -
LGA    A      62      G      63          1.703
LGA    G      63      V      64          2.679
LGA    V      64      D      65          2.143
LGA    D      65      I      66          1.792
LGA    -       -      V      67           -
LGA    -       -      G      68           -
LGA    -       -      S      69           -
LGA    -       -      E      70           -
LGA    -       -      G      71           -
LGA    -       -      H      72           -
LGA    -       -      E      73           -
LGA    -       -      S      74           -
LGA    -       -      G      75           -
LGA    -       -      E      76           -
LGA    -       -      W      77           -
LGA    -       -      V      78           -
LGA    -       -      L      79           -
LGA    I      66      V      80          2.938
LGA    V      67      D      81          3.250
LGA    -       -      A      82           -
LGA    -       -      G      83           -
LGA    -       -      D      84           -
LGA    -       -      V      85           -
LGA    -       -      V      86           -
LGA    -       -      V      87           -
LGA    G      68      H      88           #
LGA    S      69      V      89           #
LGA    E      70      M      90           -
LGA    -       -      L      91           -
LGA    -       -      P      92           -
LGA    -       -      A      93           -
LGA    G      71      V      94          5.225
LGA    H      72      R      95          4.670
LGA    -       -      D      96           -
LGA    -       -      Y      97           -
LGA    E      73      Y      98          2.692
LGA    S      74      D      99          2.819
LGA    G      75      I     100           #
LGA    -       -      E     101           -
LGA    -       -      A     102           -
LGA    -       -      L     103           -
LGA    -       -      W     104           -
LGA    -       -      G     105           -
LGA    -       -      G     106           -
LGA    E      76      Q     107          5.220
LGA    W      77      K     108          1.461
LGA    V      78      P     109          1.702
LGA    L      79      S     110           #
LGA    V      80      -       -           -
LGA    D      81      -       -           -
LGA    A      82      -       -           -
LGA    G      83      -       -           -
LGA    D      84      -       -           -
LGA    V      85      -       -           -
LGA    V      86      -       -           -
LGA    V      87      -       -           -
LGA    H      88      -       -           -
LGA    V      89      F     111          4.901
LGA    M      90      A     112           -
LGA    -       -      V     113           -
LGA    -       -      G     114           -
LGA    L      91      A     115          5.217
LGA    -       -      A     116           -
LGA    -       -      K     117           -
LGA    P      92      P     118          5.417
LGA    A      93      W     119          5.432
LGA    V      94      S     120          6.185
LGA    R      95      A     121           #
LGA    D      96      V     122           -
LGA    Y      97      -       -           -
LGA    Y      98      -       -           -
LGA    D      99      -       -           -
LGA    I     100      -       -           -
LGA    E     101      -       -           -
LGA    A     102      -       -           -
LGA    L     103      -       -           -
LGA    W     104      -       -           -
LGA    G     105      -       -           -
LGA    G     106      -       -           -
LGA    Q     107      -       -           -
LGA    K     108      -       -           -
LGA    P     109      -       -           -
LGA    S     110      -       -           -
LGA    F     111      -       -           -
LGA    A     112      -       -           -
LGA    V     113      -       -           -
LGA    G     114      -       -           -
LGA    A     115      -       -           -
LGA    A     116      -       -           -
LGA    K     117      -       -           -
LGA    P     118      -       -           -
LGA    W     119      -       -           -
LGA    S     120      -       -           -
LGA    A     121      -       -           -
LGA    V     122      -       -           -
LGA    L     123      -       -           -
LGA    E     124      -       -           -
LGA    H     125      -       -           -
LGA    H     126      -       -           -
LGA    H     127      -       -           -
LGA    H     128      -       -           -
LGA    H     129      -       -           -
LGA    H     130      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  130  122    5.0     58    3.12    34.48     30.948     1.803

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.306758 * X  +  -0.923244 * Y  +  -0.231346 * Z  +  38.659454
  Y_new =  -0.926763 * X  +  -0.345105 * Y  +   0.148369 * Z  +  27.247257
  Z_new =  -0.216819 * X  +   0.168890 * Y  +  -0.961491 * Z  +  23.029699 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.967712   -0.173880  [ DEG:   170.0374     -9.9626 ]
  Theta =   0.218555    2.923038  [ DEG:    12.5223    167.4777 ]
  Phi   =  -1.251148    1.890445  [ DEG:   -71.6855    108.3145 ]
 
# 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: T0354TS393_5                                  
REMARK     2: T0354.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0354TS393_5.T0354.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  130  122   5.0   58   3.12   34.48  30.948
REMARK  ---------------------------------------------------------- 
MOLECULE T0354TS393_5
PFRMAT TS
TARGET T0354
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1      53.152  21.644   8.536  1.00 25.00           C
ATOM      2  CA  GLU     2      50.296  23.930   9.489  1.00 25.00           C
ATOM      3  CA  ILE     3      49.394  24.938  13.022  1.00 25.00           C
ATOM      4  CA  GLN     4      49.557  21.228  13.959  1.00 25.00           C
ATOM      5  CA  GLU     5      52.833  21.825  15.852  1.00 25.00           C
ATOM      6  CA  ILE     6      51.245  24.766  17.722  1.00 25.00           C
ATOM      7  CA  SER     7      48.234  22.586  18.643  1.00 25.00           C
ATOM      8  CA  LYS     8      50.582  19.842  19.918  1.00 25.00           C
ATOM      9  CA  LEU     9      52.490  22.414  22.017  1.00 25.00           C
ATOM     10  CA  ALA    10      49.193  23.704  23.477  1.00 25.00           C
ATOM     11  CA  ILE    11      48.143  20.122  24.335  1.00 25.00           C
ATOM     12  CA  GLU    12      51.518  19.514  26.041  1.00 25.00           C
ATOM     13  CA  ALA    13      51.109  22.746  28.055  1.00 25.00           C
ATOM     14  CA  LEU    14      47.589  21.671  29.114  1.00 25.00           C
ATOM     15  CA  GLU    15      48.933  18.251  30.196  1.00 25.00           C
ATOM     16  CA  ASP    16      51.699  19.954  32.225  1.00 25.00           C
ATOM     17  CA  ILE    17      53.191  23.375  32.990  1.00 25.00           C
ATOM     18  CA  LYS    18      49.567  24.579  32.724  1.00 25.00           C
ATOM     19  CA  GLY    19      47.249  27.384  31.634  1.00 25.00           C
ATOM     20  CA  LYS    20      48.032  28.873  35.087  1.00 25.00           C
ATOM     21  CA  ASP    21      45.525  26.420  36.593  1.00 25.00           C
ATOM     22  CA  ILE    22      42.033  27.834  36.079  1.00 25.00           C
ATOM     23  CA  ILE    23      42.059  25.613  33.049  1.00 25.00           C
ATOM     24  CA  GLU    24      42.694  26.547  29.455  1.00 25.00           C
ATOM     25  CA  LEU    25      40.532  29.180  27.758  1.00 25.00           C
ATOM     26  CA  ASP    26      38.979  28.497  24.352  1.00 25.00           C
ATOM     27  CA  THR    27      37.123  28.529  21.087  1.00 25.00           C
ATOM     28  CA  SER    28      36.542  29.498  17.411  1.00 25.00           C
ATOM     29  CA  LYS    29      33.352  27.434  16.933  1.00 25.00           C
ATOM     30  CA  LEU    30      32.075  24.218  18.615  1.00 25.00           C
ATOM     31  CA  THR    31      33.155  23.568  22.174  1.00 25.00           C
ATOM     32  CA  SER    32      36.073  21.224  21.230  1.00 25.00           C
ATOM     33  CA  LEU    33      35.273  19.063  24.297  1.00 25.00           C
ATOM     34  CA  PHE    34      37.141  17.510  27.150  1.00 25.00           C
ATOM     35  CA  GLN    35      40.800  17.972  28.247  1.00 25.00           C
ATOM     36  CA  ARG    36      41.056  19.797  24.922  1.00 25.00           C
ATOM     37  CA  MET    37      38.726  22.523  26.194  1.00 25.00           C
ATOM     38  CA  ILE    38      35.882  24.928  26.591  1.00 25.00           C
ATOM     39  CA  VAL    39      33.905  28.043  25.742  1.00 25.00           C
ATOM     40  CA  ALA    40      33.123  28.500  29.464  1.00 25.00           C
ATOM     41  CA  THR    41      31.680  30.675  32.257  1.00 25.00           C
ATOM     42  CA  GLY    42      29.484  32.103  35.092  1.00 25.00           C
ATOM     43  CA  ASP    43      30.662  29.003  36.973  1.00 25.00           C
ATOM     44  CA  SER    44      33.747  31.158  37.538  1.00 25.00           C
ATOM     45  CA  ASN    45      33.734  34.750  36.351  1.00 25.00           C
ATOM     46  CA  ARG    46      36.947  36.140  37.905  1.00 25.00           C
ATOM     47  CA  GLN    47      38.616  32.708  37.585  1.00 25.00           C
ATOM     48  CA  VAL    48      37.548  32.505  33.912  1.00 25.00           C
ATOM     49  CA  LYS    49      38.974  36.002  33.278  1.00 25.00           C
ATOM     50  CA  ALA    50      42.272  34.985  34.941  1.00 25.00           C
ATOM     51  CA  LEU    51      42.425  31.835  32.766  1.00 25.00           C
ATOM     52  CA  ALA    52      41.799  33.941  29.630  1.00 25.00           C
ATOM     53  CA  ASN    53      44.588  36.353  30.662  1.00 25.00           C
ATOM     54  CA  SER    54      46.969  33.404  31.211  1.00 25.00           C
ATOM     55  CA  VAL    55      46.079  32.010  27.757  1.00 25.00           C
ATOM     56  CA  GLN    56      46.731  35.438  26.178  1.00 25.00           C
ATOM     57  CA  VAL    57      50.120  35.636  27.951  1.00 25.00           C
ATOM     58  CA  LYS    58      51.016  32.134  26.684  1.00 25.00           C
ATOM     59  CA  LEU    59      50.039  33.146  23.121  1.00 25.00           C
ATOM     60  CA  LYS    60      52.208  36.292  23.394  1.00 25.00           C
ATOM     61  CA  GLU    61      55.155  34.181  24.632  1.00 25.00           C
ATOM     62  CA  ALA    62      56.043  33.401  21.001  1.00 25.00           C
ATOM     63  CA  GLY    63      53.855  33.597  17.914  1.00 25.00           C
ATOM     64  CA  VAL    64      50.044  33.860  18.033  1.00 25.00           C
ATOM     65  CA  ASP    65      47.326  35.997  19.729  1.00 25.00           C
ATOM     66  CA  ILE    66      44.064  34.414  20.994  1.00 25.00           C
ATOM     67  CA  VAL    67      40.649  32.723  21.131  1.00 25.00           C
ATOM     68  CA  GLY    68      36.941  33.708  21.353  1.00 25.00           C
ATOM     69  CA  SER    69      34.079  32.735  23.663  1.00 25.00           C
ATOM     70  CA  GLU    70      30.856  32.210  21.698  1.00 25.00           C
ATOM     71  CA  GLY    71      29.091  29.866  24.074  1.00 25.00           C
ATOM     72  CA  HIS    72      27.864  26.330  23.692  1.00 25.00           C
ATOM     73  CA  GLU    73      24.224  25.289  23.513  1.00 25.00           C
ATOM     74  CA  SER    74      25.506  21.749  23.285  1.00 25.00           C
ATOM     75  CA  GLY    75      26.862  22.302  26.839  1.00 25.00           C
ATOM     76  CA  GLU    76      27.029  18.647  27.998  1.00 25.00           C
ATOM     77  CA  TRP    77      30.472  17.761  26.646  1.00 25.00           C
ATOM     78  CA  VAL    78      31.573  18.749  30.181  1.00 25.00           C
ATOM     79  CA  LEU    79      33.240  18.040  33.534  1.00 25.00           C
ATOM     80  CA  VAL    80      35.518  17.617  36.515  1.00 25.00           C
ATOM     81  CA  ASP    81      32.647  19.094  38.618  1.00 25.00           C
ATOM     82  CA  ALA    82      33.363  22.683  39.633  1.00 25.00           C
ATOM     83  CA  GLY    83      35.615  25.023  41.621  1.00 25.00           C
ATOM     84  CA  ASP    84      38.560  25.688  39.223  1.00 25.00           C
ATOM     85  CA  VAL    85      39.289  23.023  36.598  1.00 25.00           C
ATOM     86  CA  VAL    86      35.908  23.804  35.081  1.00 25.00           C
ATOM     87  CA  VAL    87      33.630  23.062  32.145  1.00 25.00           C
ATOM     88  CA  HIS    88      30.792  23.854  29.760  1.00 25.00           C
ATOM     89  CA  VAL    89      29.071  25.431  32.734  1.00 25.00           C
ATOM     90  CA  MET    90      27.080  28.512  31.694  1.00 25.00           C
ATOM     91  CA  LEU    91      24.954  31.590  31.174  1.00 25.00           C
ATOM     92  CA  PRO    92      26.663  35.016  31.598  1.00 25.00           C
ATOM     93  CA  ALA    93      27.385  34.675  27.852  1.00 25.00           C
ATOM     94  CA  VAL    94      27.807  38.470  27.562  1.00 25.00           C
ATOM     95  CA  ARG    95      30.212  38.456  30.542  1.00 25.00           C
ATOM     96  CA  ASP    96      32.230  35.627  28.932  1.00 25.00           C
ATOM     97  CA  TYR    97      32.399  37.586  25.645  1.00 25.00           C
ATOM     98  CA  TYR    98      33.597  40.696  27.531  1.00 25.00           C
ATOM     99  CA  ASP    99      36.286  38.619  29.297  1.00 25.00           C
ATOM    100  CA  ILE   100      37.428  37.192  25.931  1.00 25.00           C
ATOM    101  CA  GLU   101      37.617  40.727  24.468  1.00 25.00           C
ATOM    102  CA  ALA   102      39.684  41.888  27.476  1.00 25.00           C
ATOM    103  CA  LEU   103      42.052  38.911  27.028  1.00 25.00           C
ATOM    104  CA  TRP   104      42.437  39.745  23.310  1.00 25.00           C
ATOM    105  CA  GLY   105      41.835  43.340  22.267  1.00 25.00           C
ATOM    106  CA  GLY   106      41.582  42.052  18.657  1.00 25.00           C
ATOM    107  CA  GLN   107      40.402  42.790  15.073  1.00 25.00           C
ATOM    108  CA  LYS   108      40.059  40.727  11.934  1.00 25.00           C
ATOM    109  CA  PRO   109      38.274  38.377   9.491  1.00 25.00           C
ATOM    110  CA  SER   110      37.659  34.658   9.582  1.00 25.00           C
ATOM    111  CA  PHE   111      34.618  32.402   9.622  1.00 25.00           C
ATOM    112  CA  ALA   112      32.138  29.535   9.150  1.00 25.00           C
ATOM    113  CA  VAL   113      29.928  29.789   6.026  1.00 25.00           C
ATOM    114  CA  GLY   114      27.664  29.872   2.938  1.00 25.00           C
ATOM    115  CA  ALA   115      25.729  27.875   0.337  1.00 25.00           C
ATOM    116  CA  ALA   116      24.498  24.516   1.678  1.00 25.00           C
ATOM    117  CA  LYS   117      25.003  20.689   1.572  1.00 25.00           C
ATOM    118  CA  PRO   118      24.527  17.238   3.138  1.00 25.00           C
ATOM    119  CA  TRP   119      27.793  16.493   1.296  1.00 25.00           C
ATOM    120  CA  SER   120      26.661  13.850  -1.194  1.00 25.00           C
ATOM    121  CA  ALA   121      29.492  11.828  -2.731  1.00 25.00           C
ATOM    122  CA  VAL   122      32.791  12.590  -4.399  1.00 25.00           C
ATOM    123  CA  LEU   123      33.761   9.070  -3.500  1.00 25.00           C
ATOM    124  CA  GLU   124      33.748   9.550   0.301  1.00 25.00           C
ATOM    125  CA  HIS   125      37.212  11.174   0.132  1.00 25.00           C
ATOM    126  CA  HIS   126      37.319  12.817   3.614  1.00 25.00           C
ATOM    127  CA  HIS   127      39.340   9.922   4.914  1.00 25.00           C
ATOM    128  CA  HIS   128      38.440   6.470   6.221  1.00 25.00           C
ATOM    129  CA  HIS   129      40.566   7.238   9.300  1.00 25.00           C
ATOM    130  CA  HIS   130      39.104   9.238  12.105  1.00 25.00           C
TER
END
