
#######################################################
#                                                     #
#                        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  122 (  122),  selected  122 , name T0304TS393_5
# Molecule2: number of CA atoms  107 (  848),  selected  107 , name T0304.pdb
# PARAMETERS: T0304TS393_5.T0304.pdb  -4  -ie  -o1  -sia  -d:55A/  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      D      16           -
LGA    S       2      R      17           -
LGA    D       3      P      18           -
LGA    T       4      W      19           -
LGA    L       5      W      20           -
LGA    P       6      G      21           -
LGA    G       7      L      22           -
LGA    T       8      P      23           -
LGA    T       9      C      24           -
LGA    L      10      T      25           -
LGA    P      11      V      26           -
LGA    D      12      T      27           -
LGA    D      13      P      28           -
LGA    N      14      C      29           -
LGA    H      15      F      30           -
LGA    D      16      G      31           -
LGA    R      17      A      32           -
LGA    P      18      R      33           -
LGA    W      19      L      34           -
LGA    W      20      V      35           -
LGA    G      21      -       -           -
LGA    L      22      -       -           -
LGA    P      23      -       -           -
LGA    C      24      -       -           -
LGA    T      25      -       -           -
LGA    V      26      Q      36          4.020
LGA    T      27      -       -           -
LGA    P      28      E      37          5.317
LGA    -       -      G      38           -
LGA    -       -      N      39           -
LGA    -       -      R      40           -
LGA    -       -      L      41           -
LGA    C      29      H      42           #
LGA    F      30      -       -           -
LGA    G      31      -       -           -
LGA    A      32      -       -           -
LGA    R      33      Y      43           #
LGA    L      34      L      44          0.713
LGA    V      35      A      45          1.546
LGA    Q      36      D      46          1.827
LGA    E      37      R      47          3.137
LGA    G      38      A      48          3.944
LGA    N      39      -       -           -
LGA    R      40      G      49          1.042
LGA    L      41      -       -           -
LGA    H      42      -       -           -
LGA    Y      43      I      50          1.685
LGA    L      44      R      51          3.836
LGA    A      45      -       -           -
LGA    D      46      -       -           -
LGA    R      47      G      52          2.046
LGA    A      48      L      53           #
LGA    G      49      F      54          5.092
LGA    I      50      S      55           -
LGA    R      51      D      56           -
LGA    G      52      A      57          2.510
LGA    L      53      D      58           #
LGA    F      54      -       -           -
LGA    S      55      -       -           -
LGA    D      56      -       -           -
LGA    A      57      -       -           -
LGA    D      58      -       -           -
LGA    A      59      A      59          4.062
LGA    Y      60      Y      60          3.825
LGA    H      61      H      61          2.744
LGA    L      62      L      62          2.112
LGA    D      63      D      63          0.778
LGA    Q      64      Q      64          1.190
LGA    A      65      A      65          2.146
LGA    F      66      F      66          2.145
LGA    P      67      P      67          2.120
LGA    L      68      L      68          2.232
LGA    L      69      L      69          1.868
LGA    M      70      M      70          1.542
LGA    K      71      K      71          1.722
LGA    Q      72      Q      72          1.589
LGA    L      73      L      73          0.987
LGA    E      74      E      74          1.068
LGA    L      75      L      75          1.269
LGA    M      76      M      76          1.016
LGA    L      77      L      77          0.853
LGA    T      78      T      78          1.132
LGA    S      79      S      79          0.852
LGA    G      80      G      80           #
LGA    E      81      E      81          4.238
LGA    -       -      L      82           -
LGA    L      82      N      83          3.994
LGA    N      83      P      84           -
LGA    P      84      R      85           #
LGA    R      85      -       -           -
LGA    H      86      H      86           #
LGA    Q      87      Q      87          3.387
LGA    H      88      H      88          5.314
LGA    -       -      T      89           -
LGA    -       -      V      90           -
LGA    -       -      T      91           -
LGA    -       -      L      92           -
LGA    -       -      Y      93           -
LGA    -       -      A      94           -
LGA    -       -      K      95           -
LGA    -       -      G      96           -
LGA    -       -      L      97           -
LGA    -       -      T      98           -
LGA    -       -      C      99           -
LGA    -       -      K     100           -
LGA    -       -      A     101           -
LGA    -       -      D     102           -
LGA    T      89      T     103          1.988
LGA    V      90      L     104           -
LGA    T      91      S     105           -
LGA    L      92      S     106           -
LGA    Y      93      C     107           -
LGA    A      94      D     108           -
LGA    K      95      Y     109           -
LGA    G      96      -       -           -
LGA    L      97      -       -           -
LGA    T      98      -       -           -
LGA    C      99      -       -           -
LGA    K     100      -       -           -
LGA    A     101      V     110           #
LGA    D     102      -       -           -
LGA    T     103      -       -           -
LGA    L     104      -       -           -
LGA    S     105      -       -           -
LGA    S     106      -       -           -
LGA    C     107      Y     111           #
LGA    D     108      L     112           #
LGA    Y     109      A     113          0.963
LGA    V     110      V     114          3.842
LGA    Y     111      Y     115           -
LGA    L     112      P     116           -
LGA    A     113      T     117           -
LGA    V     114      P     118           -
LGA    Y     115      E     119           -
LGA    P     116      M     120           -
LGA    T     117      K     121           -
LGA    P     118      N     122           -
LGA    E     119      -       -           -
LGA    M     120      -       -           -
LGA    K     121      -       -           -
LGA    N     122      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  122  107    5.0     41    2.74    65.85     27.576     1.445

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.517459 * X  +  -0.853447 * Y  +   0.062157 * Z  +  46.857784
  Y_new =   0.168251 * X  +  -0.030255 * Y  +   0.985280 * Z  +  22.059549
  Z_new =  -0.839004 * X  +   0.520300 * Y  +   0.159249 * Z  +  48.699059 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.273779   -1.867814  [ DEG:    72.9822   -107.0178 ]
  Theta =   0.995450    2.146142  [ DEG:    57.0351    122.9649 ]
  Phi   =   2.827227   -0.314365  [ DEG:   161.9882    -18.0118 ]
 
# 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: T0304TS393_5                                  
REMARK     2: T0304.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304TS393_5.T0304.pdb -4 -ie -o1 -sia -d:55A/ 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  122  107   5.0   41   2.74   65.85  27.576
REMARK  ---------------------------------------------------------- 
MOLECULE T0304TS393_5
PFRMAT TS
TARGET T0304
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1      44.527   4.486  66.884  1.00 25.00           C
ATOM      2  CA  SER     2      41.546   3.776  64.680  1.00 25.00           C
ATOM      3  CA  ASP     3      41.014   7.289  63.172  1.00 25.00           C
ATOM      4  CA  THR     4      37.252   7.835  63.726  1.00 25.00           C
ATOM      5  CA  LEU     5      36.628  11.555  63.044  1.00 25.00           C
ATOM      6  CA  PRO     6      32.898  11.328  62.461  1.00 25.00           C
ATOM      7  CA  GLY     7      30.921  14.477  63.293  1.00 25.00           C
ATOM      8  CA  THR     8      32.216  15.920  66.593  1.00 25.00           C
ATOM      9  CA  THR     9      33.293  19.548  66.276  1.00 25.00           C
ATOM     10  CA  LEU    10      35.755  22.326  65.287  1.00 25.00           C
ATOM     11  CA  PRO    11      33.565  25.344  66.106  1.00 25.00           C
ATOM     12  CA  ASP    12      31.403  28.461  66.332  1.00 25.00           C
ATOM     13  CA  ASP    13      33.770  29.798  68.926  1.00 25.00           C
ATOM     14  CA  ASN    14      34.718  28.084  72.143  1.00 25.00           C
ATOM     15  CA  HIS    15      32.952  27.632  75.482  1.00 25.00           C
ATOM     16  CA  ASP    16      35.727  25.469  76.932  1.00 25.00           C
ATOM     17  CA  ARG    17      39.119  27.079  77.031  1.00 25.00           C
ATOM     18  CA  PRO    18      42.557  27.853  75.491  1.00 25.00           C
ATOM     19  CA  TRP    19      43.972  25.074  73.266  1.00 25.00           C
ATOM     20  CA  TRP    20      47.366  24.372  71.594  1.00 25.00           C
ATOM     21  CA  GLY    21      49.494  26.337  69.173  1.00 25.00           C
ATOM     22  CA  LEU    22      50.261  24.999  65.635  1.00 25.00           C
ATOM     23  CA  PRO    23      53.111  25.949  63.249  1.00 25.00           C
ATOM     24  CA  CYS    24      52.573  25.602  59.557  1.00 25.00           C
ATOM     25  CA  THR    25      49.754  28.177  60.027  1.00 25.00           C
ATOM     26  CA  VAL    26      49.262  27.956  56.263  1.00 25.00           C
ATOM     27  CA  THR    27      46.329  25.534  56.355  1.00 25.00           C
ATOM     28  CA  PRO    28      48.888  22.813  56.644  1.00 25.00           C
ATOM     29  CA  CYS    29      46.482  20.923  54.415  1.00 25.00           C
ATOM     30  CA  PHE    30      47.437  17.280  55.121  1.00 25.00           C
ATOM     31  CA  GLY    31      48.168  14.309  52.818  1.00 25.00           C
ATOM     32  CA  ALA    32      44.414  13.710  52.357  1.00 25.00           C
ATOM     33  CA  ARG    33      43.903  17.410  51.510  1.00 25.00           C
ATOM     34  CA  LEU    34      46.752  17.245  48.956  1.00 25.00           C
ATOM     35  CA  VAL    35      45.191  14.123  47.380  1.00 25.00           C
ATOM     36  CA  GLN    36      41.801  15.894  47.172  1.00 25.00           C
ATOM     37  CA  GLU    37      43.456  18.922  45.511  1.00 25.00           C
ATOM     38  CA  GLY    38      45.188  16.621  42.986  1.00 25.00           C
ATOM     39  CA  ASN    39      41.849  14.914  42.214  1.00 25.00           C
ATOM     40  CA  ARG    40      40.193  18.329  41.698  1.00 25.00           C
ATOM     41  CA  LEU    41      43.025  19.372  39.339  1.00 25.00           C
ATOM     42  CA  HIS    42      42.614  16.116  37.365  1.00 25.00           C
ATOM     43  CA  TYR    43      38.842  16.724  37.100  1.00 25.00           C
ATOM     44  CA  LEU    44      39.481  20.290  35.856  1.00 25.00           C
ATOM     45  CA  ALA    45      41.948  18.963  33.245  1.00 25.00           C
ATOM     46  CA  ASP    46      39.369  16.380  32.086  1.00 25.00           C
ATOM     47  CA  ARG    47      36.715  19.124  31.791  1.00 25.00           C
ATOM     48  CA  ALA    48      37.578  22.847  31.865  1.00 25.00           C
ATOM     49  CA  GLY    49      39.304  22.612  28.419  1.00 25.00           C
ATOM     50  CA  ILE    50      42.961  22.280  29.445  1.00 25.00           C
ATOM     51  CA  ARG    51      45.947  20.135  28.459  1.00 25.00           C
ATOM     52  CA  GLY    52      44.854  17.395  26.091  1.00 25.00           C
ATOM     53  CA  LEU    53      41.834  15.077  26.391  1.00 25.00           C
ATOM     54  CA  PHE    54      43.233  12.402  28.681  1.00 25.00           C
ATOM     55  CA  SER    55      44.893   9.169  29.865  1.00 25.00           C
ATOM     56  CA  ASP    56      48.528   8.678  28.691  1.00 25.00           C
ATOM     57  CA  ALA    57      50.896  11.225  27.086  1.00 25.00           C
ATOM     58  CA  ASP    58      48.270  13.979  27.525  1.00 25.00           C
ATOM     59  CA  ALA    59      47.830  13.007  31.203  1.00 25.00           C
ATOM     60  CA  TYR    60      51.624  13.124  31.713  1.00 25.00           C
ATOM     61  CA  HIS    61      51.762  16.587  30.083  1.00 25.00           C
ATOM     62  CA  LEU    62      48.936  17.800  32.365  1.00 25.00           C
ATOM     63  CA  ASP    63      50.795  16.448  35.428  1.00 25.00           C
ATOM     64  CA  GLN    64      53.991  18.236  34.309  1.00 25.00           C
ATOM     65  CA  ALA    65      52.037  21.499  33.861  1.00 25.00           C
ATOM     66  CA  PHE    66      50.534  21.110  37.361  1.00 25.00           C
ATOM     67  CA  PRO    67      54.026  20.514  38.819  1.00 25.00           C
ATOM     68  CA  LEU    68      55.331  23.642  37.037  1.00 25.00           C
ATOM     69  CA  LEU    69      52.402  25.683  38.425  1.00 25.00           C
ATOM     70  CA  MET    70      53.129  24.379  41.950  1.00 25.00           C
ATOM     71  CA  LYS    71      56.821  25.322  41.565  1.00 25.00           C
ATOM     72  CA  GLN    72      55.827  28.832  40.399  1.00 25.00           C
ATOM     73  CA  LEU    73      53.496  29.202  43.415  1.00 25.00           C
ATOM     74  CA  GLU    74      56.315  28.096  45.760  1.00 25.00           C
ATOM     75  CA  LEU    75      58.683  30.643  44.155  1.00 25.00           C
ATOM     76  CA  MET    76      56.057  33.395  44.593  1.00 25.00           C
ATOM     77  CA  LEU    77      55.617  32.425  48.272  1.00 25.00           C
ATOM     78  CA  THR    78      59.411  32.540  48.782  1.00 25.00           C
ATOM     79  CA  SER    79      59.405  36.068  47.266  1.00 25.00           C
ATOM     80  CA  GLY    80      58.575  39.757  46.771  1.00 25.00           C
ATOM     81  CA  GLU    81      56.215  39.318  49.772  1.00 25.00           C
ATOM     82  CA  LEU    82      52.435  39.750  49.741  1.00 25.00           C
ATOM     83  CA  ASN    83      52.854  42.881  51.875  1.00 25.00           C
ATOM     84  CA  PRO    84      49.750  44.335  50.292  1.00 25.00           C
ATOM     85  CA  ARG    85      48.948  43.310  46.761  1.00 25.00           C
ATOM     86  CA  HIS    86      47.910  40.083  45.064  1.00 25.00           C
ATOM     87  CA  GLN    87      47.343  38.085  48.211  1.00 25.00           C
ATOM     88  CA  HIS    88      46.283  34.610  49.464  1.00 25.00           C
ATOM     89  CA  THR    89      47.531  31.061  50.225  1.00 25.00           C
ATOM     90  CA  VAL    90      49.818  28.167  51.155  1.00 25.00           C
ATOM     91  CA  THR    91      52.716  25.660  51.144  1.00 25.00           C
ATOM     92  CA  LEU    92      53.245  23.874  47.819  1.00 25.00           C
ATOM     93  CA  TYR    93      54.256  20.377  46.817  1.00 25.00           C
ATOM     94  CA  ALA    94      53.192  16.721  47.412  1.00 25.00           C
ATOM     95  CA  LYS    95      51.741  13.349  48.383  1.00 25.00           C
ATOM     96  CA  GLY    96      50.659  12.387  44.861  1.00 25.00           C
ATOM     97  CA  LEU    97      50.222  15.922  43.384  1.00 25.00           C
ATOM     98  CA  THR    98      49.727  19.626  44.121  1.00 25.00           C
ATOM     99  CA  CYS    99      46.854  21.744  42.855  1.00 25.00           C
ATOM    100  CA  LYS   100      43.879  23.731  44.108  1.00 25.00           C
ATOM    101  CA  ALA   101      41.914  23.980  47.340  1.00 25.00           C
ATOM    102  CA  ASP   102      38.880  24.569  49.521  1.00 25.00           C
ATOM    103  CA  THR   103      37.612  21.453  47.724  1.00 25.00           C
ATOM    104  CA  LEU   104      34.577  23.440  46.677  1.00 25.00           C
ATOM    105  CA  SER   105      34.611  27.192  45.800  1.00 25.00           C
ATOM    106  CA  SER   106      38.346  27.651  45.337  1.00 25.00           C
ATOM    107  CA  CYS   107      38.752  24.419  43.301  1.00 25.00           C
ATOM    108  CA  ASP   108      39.361  26.643  40.226  1.00 25.00           C
ATOM    109  CA  TYR   109      43.096  27.159  40.177  1.00 25.00           C
ATOM    110  CA  VAL   110      46.617  25.884  39.365  1.00 25.00           C
ATOM    111  CA  TYR   111      48.616  26.600  42.483  1.00 25.00           C
ATOM    112  CA  LEU   112      48.568  25.375  46.065  1.00 25.00           C
ATOM    113  CA  ALA   113      48.211  22.253  48.238  1.00 25.00           C
ATOM    114  CA  VAL   114      50.672  20.700  50.737  1.00 25.00           C
ATOM    115  CA  TYR   115      52.637  17.953  52.543  1.00 25.00           C
ATOM    116  CA  PRO   116      56.153  17.341  53.867  1.00 25.00           C
ATOM    117  CA  THR   117      57.652  15.711  56.981  1.00 25.00           C
ATOM    118  CA  PRO   118      60.969  14.487  58.531  1.00 25.00           C
ATOM    119  CA  GLU   119      64.280  15.513  60.134  1.00 25.00           C
ATOM    120  CA  MET   120      64.746  14.776  63.856  1.00 25.00           C
ATOM    121  CA  LYS   121      63.084  13.984  67.185  1.00 25.00           C
ATOM    122  CA  ASN   122      59.755  14.542  68.976  1.00 25.00           C
TER
END
