
#######################################################
#                                                     #
#                        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 T0354TS599_5
# Molecule2: number of CA atoms  122 (  928),  selected  122 , name T0354.pdb
# PARAMETERS: T0354TS599_5.T0354.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           #
LGA    E       2      E       2          4.312
LGA    I       3      I       3          3.316
LGA    Q       4      Q       4          1.426
LGA    E       5      E       5          1.429
LGA    I       6      I       6          1.628
LGA    S       7      S       7          1.505
LGA    K       8      K       8          0.842
LGA    L       9      L       9          1.721
LGA    A      10      A      10          2.137
LGA    I      11      I      11          1.777
LGA    E      12      E      12          1.819
LGA    A      13      A      13          2.615
LGA    L      14      L      14          2.585
LGA    E      15      E      15          2.612
LGA    D      16      D      16          3.667
LGA    I      17      I      17          2.827
LGA    K      18      K      18          1.836
LGA    G      19      G      19          1.577
LGA    K      20      K      20          1.408
LGA    D      21      D      21          1.892
LGA    I      22      I      22          2.036
LGA    I      23      I      23          3.121
LGA    E      24      E      24          3.399
LGA    L      25      L      25          4.522
LGA    D      26      D      26          4.058
LGA    T      27      T      27          3.969
LGA    S      28      S      28          2.850
LGA    -       -      K      29           -
LGA    -       -      L      30           -
LGA    K      29      T      31          5.300
LGA    L      30      S      32           #
LGA    T      31      -       -           -
LGA    S      32      L      33          4.296
LGA    L      33      F      34          1.527
LGA    F      34      Q      35           #
LGA    Q      35      -       -           -
LGA    R      36      -       -           -
LGA    M      37      R      36           #
LGA    I      38      M      37          4.206
LGA    V      39      I      38          3.704
LGA    A      40      V      39          2.569
LGA    T      41      A      40          2.735
LGA    G      42      T      41          1.972
LGA    D      43      G      42          2.801
LGA    S      44      D      43          1.682
LGA    N      45      S      44          3.605
LGA    R      46      N      45          3.399
LGA    -       -      R      46           -
LGA    Q      47      Q      47          2.139
LGA    V      48      V      48          2.682
LGA    K      49      K      49          1.764
LGA    A      50      A      50          1.090
LGA    L      51      L      51          1.868
LGA    A      52      A      52          1.482
LGA    N      53      N      53          0.987
LGA    S      54      S      54          1.545
LGA    V      55      V      55          1.370
LGA    Q      56      Q      56          1.201
LGA    V      57      V      57          2.117
LGA    K      58      K      58          2.596
LGA    L      59      L      59          2.200
LGA    K      60      K      60          2.842
LGA    E      61      E      61          3.634
LGA    -       -      A      62           -
LGA    A      62      G      63          1.364
LGA    G      63      V      64          3.016
LGA    V      64      D      65          3.433
LGA    D      65      I      66          2.857
LGA    I      66      V      67          3.052
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    -       -      V      80           -
LGA    -       -      D      81           -
LGA    V      67      A      82          3.340
LGA    G      68      G      83           -
LGA    S      69      D      84           -
LGA    -       -      V      85           -
LGA    -       -      V      86           -
LGA    -       -      V      87           -
LGA    E      70      H      88          4.116
LGA    -       -      V      89           -
LGA    G      71      M      90          3.232
LGA    H      72      L      91           -
LGA    -       -      P      92           -
LGA    -       -      A      93           -
LGA    -       -      V      94           -
LGA    E      73      R      95          1.434
LGA    S      74      D      96          3.686
LGA    -       -      Y      97           -
LGA    G      75      Y      98           #
LGA    E      76      D      99          3.956
LGA    W      77      I     100          5.064
LGA    V      78      E     101          3.338
LGA    L      79      A     102           #
LGA    V      80      L     103           -
LGA    D      81      -       -           -
LGA    A      82      -       -           -
LGA    G      83      -       -           -
LGA    D      84      -       -           -
LGA    V      85      -       -           -
LGA    V      86      W     104           #
LGA    V      87      G     105          4.053
LGA    H      88      G     106          3.471
LGA    V      89      Q     107          1.050
LGA    M      90      K     108          2.479
LGA    L      91      P     109           #
LGA    P      92      S     110          2.513
LGA    A      93      F     111          5.200
LGA    V      94      A     112           #
LGA    R      95      -       -           -
LGA    D      96      -       -           -
LGA    Y      97      V     113           #
LGA    Y      98      G     114           -
LGA    D      99      A     115           -
LGA    I     100      A     116           -
LGA    E     101      K     117           -
LGA    A     102      P     118           -
LGA    L     103      W     119           -
LGA    W     104      S     120           -
LGA    G     105      A     121           -
LGA    G     106      V     122           -
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     73    2.89    57.53     37.243     2.445

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.123412 * X  +  -0.842809 * Y  +  -0.523873 * Z  +  39.887417
  Y_new =  -0.058904 * X  +   0.533200 * Y  +  -0.843936 * Z  +  22.590126
  Z_new =   0.990606 * X  +  -0.073294 * Y  +  -0.115448 * Z  +  23.759987 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.575931    0.565662  [ DEG:  -147.5900     32.4100 ]
  Theta =  -1.433618   -1.707974  [ DEG:   -82.1403    -97.8597 ]
  Phi   =  -2.696275    0.445318  [ DEG:  -154.4852     25.5148 ]
 
# 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: T0354TS599_5                                  
REMARK     2: T0354.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0354TS599_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   73   2.89   57.53  37.243
REMARK  ---------------------------------------------------------- 
MOLECULE T0354TS599_5
PFRMAT TS                                                                       
TARGET T0354                                                                    
MODEL  5                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      54.357  18.249  18.245  1.00  0.00              
ATOM      2  CA  GLU     2      50.795  20.285  18.291  1.00  0.00              
ATOM      3  CA  ILE     3      49.914  23.760  18.426  1.00  0.00              
ATOM      4  CA  GLN     4      50.326  20.196  20.603  1.00  0.00              
ATOM      5  CA  GLU     5      52.938  21.985  22.798  1.00  0.00              
ATOM      6  CA  ILE     6      50.667  24.935  23.324  1.00  0.00              
ATOM      7  CA  SER     7      47.755  22.804  24.315  1.00  0.00              
ATOM      8  CA  LYS     8      49.830  20.895  26.891  1.00  0.00              
ATOM      9  CA  LEU     9      51.115  24.141  28.377  1.00  0.00              
ATOM     10  CA  ALA    10      47.546  25.560  28.642  1.00  0.00              
ATOM     11  CA  ILE    11      46.238  22.434  30.239  1.00  0.00              
ATOM     12  CA  GLU    12      49.021  22.486  32.771  1.00  0.00              
ATOM     13  CA  ALA    13      48.413  26.161  33.584  1.00  0.00              
ATOM     14  CA  LEU    14      44.709  25.537  34.139  1.00  0.00              
ATOM     15  CA  GLU    15      45.389  22.549  36.355  1.00  0.00              
ATOM     16  CA  ASP    16      47.876  24.448  38.531  1.00  0.00              
ATOM     17  CA  ILE    17      45.504  27.351  38.995  1.00  0.00              
ATOM     18  CA  LYS    18      42.502  25.182  39.742  1.00  0.00              
ATOM     19  CA  GLY    19      40.425  25.930  36.648  1.00  0.00              
ATOM     20  CA  LYS    20      38.275  22.846  36.476  1.00  0.00              
ATOM     21  CA  ASP    21      37.256  22.437  32.945  1.00  0.00              
ATOM     22  CA  ILE    22      39.165  23.336  29.813  1.00  0.00              
ATOM     23  CA  ILE    23      37.921  22.125  26.463  1.00  0.00              
ATOM     24  CA  GLU    24      40.109  22.165  23.436  1.00  0.00              
ATOM     25  CA  LEU    25      38.639  22.557  19.972  1.00  0.00              
ATOM     26  CA  ASP    26      40.412  21.042  16.920  1.00  0.00              
ATOM     27  CA  THR    27      40.057  22.660  13.722  1.00  0.00              
ATOM     28  CA  SER    28      39.586  19.852  11.275  1.00  0.00              
ATOM     29  CA  LYS    29      42.436  20.272   8.854  1.00  0.00              
ATOM     30  CA  LEU    30      45.159  20.568  11.443  1.00  0.00              
ATOM     31  CA  THR    31      47.394  23.311   9.925  1.00  0.00              
ATOM     32  CA  SER    32      44.416  25.730   9.682  1.00  0.00              
ATOM     33  CA  LEU    33      43.623  24.855  13.259  1.00  0.00              
ATOM     34  CA  PHE    34      47.185  25.527  14.533  1.00  0.00              
ATOM     35  CA  GLN    35      47.139  29.129  13.303  1.00  0.00              
ATOM     36  CA  ARG    36      43.879  29.427  15.294  1.00  0.00              
ATOM     37  CA  MET    37      43.547  27.747  18.701  1.00  0.00              
ATOM     38  CA  ILE    38      40.061  27.342  20.155  1.00  0.00              
ATOM     39  CA  VAL    39      39.666  27.122  23.789  1.00  0.00              
ATOM     40  CA  ALA    40      36.415  26.508  25.373  1.00  0.00              
ATOM     41  CA  THR    41      36.246  27.216  29.005  1.00  0.00              
ATOM     42  CA  GLY    42      34.022  25.689  31.491  1.00  0.00              
ATOM     43  CA  ASP    43      35.085  26.951  34.860  1.00  0.00              
ATOM     44  CA  SER    44      34.138  30.277  36.164  1.00  0.00              
ATOM     45  CA  ASN    45      34.518  33.269  33.905  1.00  0.00              
ATOM     46  CA  ARG    46      37.260  34.984  35.886  1.00  0.00              
ATOM     47  CA  GLN    47      39.412  31.806  36.086  1.00  0.00              
ATOM     48  CA  VAL    48      39.054  31.300  32.375  1.00  0.00              
ATOM     49  CA  LYS    49      39.993  34.918  31.630  1.00  0.00              
ATOM     50  CA  ALA    50      43.184  34.613  33.627  1.00  0.00              
ATOM     51  CA  LEU    51      44.057  31.435  31.843  1.00  0.00              
ATOM     52  CA  ALA    52      43.404  33.048  28.405  1.00  0.00              
ATOM     53  CA  ASN    53      45.736  35.872  29.226  1.00  0.00              
ATOM     54  CA  SER    54      48.422  33.382  30.189  1.00  0.00              
ATOM     55  CA  VAL    55      47.935  31.469  27.041  1.00  0.00              
ATOM     56  CA  GLN    56      47.980  34.324  24.753  1.00  0.00              
ATOM     57  CA  VAL    57      51.188  35.633  26.204  1.00  0.00              
ATOM     58  CA  LYS    58      52.915  32.207  25.983  1.00  0.00              
ATOM     59  CA  LEU    59      51.828  31.767  22.400  1.00  0.00              
ATOM     60  CA  LYS    60      52.974  35.193  21.380  1.00  0.00              
ATOM     61  CA  GLU    61      56.354  34.417  22.835  1.00  0.00              
ATOM     62  CA  ALA    62      56.460  31.197  20.739  1.00  0.00              
ATOM     63  CA  GLY    63      55.345  33.028  17.573  1.00  0.00              
ATOM     64  CA  VAL    64      51.918  31.360  17.412  1.00  0.00              
ATOM     65  CA  ASP    65      49.024  33.437  16.386  1.00  0.00              
ATOM     66  CA  ILE    66      45.589  33.048  17.517  1.00  0.00              
ATOM     67  CA  VAL    67      43.917  31.973  20.547  1.00  0.00              
ATOM     68  CA  GLY    68      40.231  32.159  20.427  1.00  0.00              
ATOM     69  CA  SER    69      38.231  31.931  23.591  1.00  0.00              
ATOM     70  CA  GLU    70      34.516  31.202  23.414  1.00  0.00              
ATOM     71  CA  GLY    71      32.308  30.729  26.415  1.00  0.00              
ATOM     72  CA  HIS    72      29.841  28.249  24.836  1.00  0.00              
ATOM     73  CA  GLU    73      27.853  27.017  27.745  1.00  0.00              
ATOM     74  CA  SER    74      24.745  26.183  25.658  1.00  0.00              
ATOM     75  CA  GLY    75      24.294  22.620  26.682  1.00  0.00              
ATOM     76  CA  GLU    76      27.891  21.638  27.089  1.00  0.00              
ATOM     77  CA  TRP    77      30.017  20.343  24.166  1.00  0.00              
ATOM     78  CA  VAL    78      33.799  20.128  24.493  1.00  0.00              
ATOM     79  CA  LEU    79      35.971  19.170  21.440  1.00  0.00              
ATOM     80  CA  VAL    80      39.258  17.628  22.153  1.00  0.00              
ATOM     81  CA  ASP    81      41.608  16.928  19.339  1.00  0.00              
ATOM     82  CA  ALA    82      43.899  14.102  19.816  1.00  0.00              
ATOM     83  CA  GLY    83      44.457  12.520  16.450  1.00  0.00              
ATOM     84  CA  ASP    84      41.054  11.040  15.813  1.00  0.00              
ATOM     85  CA  VAL    85      38.804  13.677  17.412  1.00  0.00              
ATOM     86  CA  VAL    86      37.406  13.192  20.868  1.00  0.00              
ATOM     87  CA  VAL    87      34.133  14.653  21.672  1.00  0.00              
ATOM     88  CA  HIS    88      33.181  15.297  25.235  1.00  0.00              
ATOM     89  CA  VAL    89      29.593  15.845  26.015  1.00  0.00              
ATOM     90  CA  MET    90      28.628  17.595  29.194  1.00  0.00              
ATOM     91  CA  LEU    91      24.994  17.462  30.442  1.00  0.00              
ATOM     92  CA  PRO    92      24.890  17.982  34.230  1.00  0.00              
ATOM     93  CA  ALA    93      21.461  19.574  34.323  1.00  0.00              
ATOM     94  CA  VAL    94      19.906  17.121  31.940  1.00  0.00              
ATOM     95  CA  ARG    95      21.342  14.058  33.596  1.00  0.00              
ATOM     96  CA  ASP    96      20.140  15.356  37.012  1.00  0.00              
ATOM     97  CA  TYR    97      16.672  16.109  35.681  1.00  0.00              
ATOM     98  CA  TYR    98      16.033  12.962  33.604  1.00  0.00              
ATOM     99  CA  ASP    99      17.834  10.140  35.324  1.00  0.00              
ATOM    100  CA  ILE   100      21.600   9.858  34.607  1.00  0.00              
ATOM    101  CA  GLU   101      21.489   6.697  32.589  1.00  0.00              
ATOM    102  CA  ALA   102      18.789   8.164  30.382  1.00  0.00              
ATOM    103  CA  LEU   103      20.732  11.333  29.843  1.00  0.00              
ATOM    104  CA  TRP   104      24.012   9.637  28.894  1.00  0.00              
ATOM    105  CA  GLY   105      22.165   7.524  26.370  1.00  0.00              
ATOM    106  CA  GLY   106      20.343  10.534  24.809  1.00  0.00              
ATOM    107  CA  GLN   107      23.357  12.728  24.369  1.00  0.00              
ATOM    108  CA  LYS   108      25.872  10.175  23.167  1.00  0.00              
ATOM    109  CA  PRO   109      28.877  10.710  25.418  1.00  0.00              
ATOM    110  CA  SER   110      32.072  10.798  23.465  1.00  0.00              
ATOM    111  CA  PHE   111      35.113   9.640  25.305  1.00  0.00              
ATOM    112  CA  ALA   112      38.050  11.995  25.414  1.00  0.00              
ATOM    113  CA  VAL   113      41.136  10.208  24.275  1.00  0.00              
ATOM    114  CA  GLY   114      44.618  11.604  24.397  1.00  0.00              
ATOM    115  CA  ALA   115      45.839  10.536  20.953  1.00  0.00              
ATOM    116  CA  ALA   116      49.491  10.680  21.063  1.00  0.00              
ATOM    117  CA  LYS   117      51.939  13.415  20.592  1.00  0.00              
ATOM    118  CA  PRO   118      51.578  15.144  17.382  1.00  0.00              
ATOM    119  CA  TRP   119      54.232  14.774  14.757  1.00  0.00              
ATOM    120  CA  SER   120      51.963  14.351  11.702  1.00  0.00              
ATOM    121  CA  ALA   121      53.055  16.948   9.232  1.00  0.00              
ATOM    122  CA  VAL   122      50.293  19.503   8.478  1.00  0.00              
ATOM    123  CA  LEU   123      51.696  23.039   8.001  1.00  0.00              
ATOM    124  CA  GLU   124      51.013  23.589   4.359  1.00  0.00              
ATOM    125  CA  HIS   125      48.841  26.682   4.455  1.00  0.00              
ATOM    126  CA  HIS   126      45.750  25.840   2.434  1.00  0.00              
ATOM    127  CA  HIS   127      45.247  29.575   1.951  1.00  0.00              
ATOM    128  CA  HIS   128      47.021  32.133   4.790  1.00  0.00              
ATOM    129  CA  HIS   129      45.241  33.858   7.403  1.00  0.00              
ATOM    130  CA  HIS   130      43.336  35.171  10.161  1.00  0.00              
TER                                                                             
END
