
#######################################################
#                                                     #
#                        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  101 (  101),  selected  101 , name T0304TS393_1-D1
# Molecule2: number of CA atoms  101 (  799),  selected  101 , name T0304_D1.pdb
# PARAMETERS: T0304TS393_1-D1.T0304_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    R      17      R      17           -
LGA    P      18      P      18           -
LGA    W      19      W      19           -
LGA    W      20      W      20           -
LGA    G      21      G      21           -
LGA    L      22      L      22           -
LGA    P      23      P      23           -
LGA    C      24      C      24           -
LGA    T      25      T      25           -
LGA    -       -      V      26           -
LGA    -       -      T      27           -
LGA    -       -      P      28           -
LGA    -       -      C      29           -
LGA    -       -      F      30           -
LGA    -       -      G      31           -
LGA    -       -      A      32           -
LGA    -       -      R      33           -
LGA    -       -      L      34           -
LGA    -       -      V      35           -
LGA    V      26      Q      36           #
LGA    T      27      E      37          3.237
LGA    P      28      G      38          4.484
LGA    C      29      N      39           #
LGA    F      30      R      40           #
LGA    G      31      -       -           -
LGA    A      32      -       -           -
LGA    R      33      L      41           #
LGA    L      34      H      42          2.972
LGA    V      35      Y      43          3.905
LGA    Q      36      L      44          1.073
LGA    E      37      -       -           -
LGA    G      38      A      45          5.107
LGA    N      39      D      46          5.503
LGA    R      40      R      47          3.828
LGA    L      41      A      48          3.941
LGA    H      42      -       -           -
LGA    Y      43      -       -           -
LGA    L      44      G      49          2.069
LGA    A      45      I      50          2.315
LGA    D      46      -       -           -
LGA    R      47      -       -           -
LGA    A      48      R      51          1.238
LGA    G      49      G      52          4.643
LGA    I      50      L      53           #
LGA    R      51      F      54          4.039
LGA    G      52      S      55          3.653
LGA    L      53      D      56          4.448
LGA    F      54      -       -           -
LGA    S      55      -       -           -
LGA    D      56      -       -           -
LGA    A      57      A      57           #
LGA    D      58      D      58          4.467
LGA    A      59      A      59          2.748
LGA    Y      60      Y      60          3.411
LGA    H      61      H      61          2.306
LGA    L      62      L      62          1.227
LGA    D      63      D      63          1.560
LGA    Q      64      Q      64          2.046
LGA    A      65      A      65          2.202
LGA    F      66      F      66          2.504
LGA    P      67      P      67          2.342
LGA    L      68      L      68          1.821
LGA    L      69      L      69          1.531
LGA    M      70      M      70          1.385
LGA    K      71      K      71          1.123
LGA    Q      72      Q      72          0.603
LGA    L      73      L      73          0.602
LGA    E      74      E      74          0.650
LGA    L      75      L      75          0.856
LGA    M      76      M      76          0.810
LGA    L      77      L      77          0.787
LGA    T      78      T      78          1.323
LGA    S      79      -       -           -
LGA    G      80      -       -           -
LGA    E      81      S      79          3.476
LGA    L      82      G      80          3.539
LGA    N      83      -       -           -
LGA    P      84      -       -           -
LGA    R      85      -       -           -
LGA    H      86      -       -           -
LGA    Q      87      E      81          2.853
LGA    H      88      L      82          1.844
LGA    T      89      N      83          2.980
LGA    -       -      P      84           -
LGA    V      90      R      85           #
LGA    T      91      H      86           -
LGA    L      92      Q      87           -
LGA    Y      93      H      88           -
LGA    A      94      T      89           -
LGA    K      95      V      90           -
LGA    G      96      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    L      97      K     100           #
LGA    T      98      -       -           -
LGA    C      99      -       -           -
LGA    K     100      -       -           -
LGA    A     101      -       -           -
LGA    D     102      -       -           -
LGA    T     103      -       -           -
LGA    L     104      -       -           -
LGA    S     105      -       -           -
LGA    S     106      -       -           -
LGA    C     107      -       -           -
LGA    D     108      -       -           -
LGA    Y     109      -       -           -
LGA    V     110      -       -           -
LGA    Y     111      -       -           -
LGA    L     112      -       -           -
LGA    A     113      -       -           -
LGA    V     114      A     101          0.474
LGA    Y     115      -       -           -
LGA    P     116      D     102          4.475
LGA    -       -      T     103           -
LGA    T     117      L     104           #
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    -       -      C     107           -
LGA    -       -      D     108           -
LGA    -       -      Y     109           -
LGA    -       -      V     110           -
LGA    -       -      Y     111           -
LGA    -       -      L     112           -
LGA    -       -      A     113           -
LGA    -       -      V     114           -
LGA    -       -      Y     115           -
LGA    -       -      P     116           -
LGA    -       -      T     117           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  101  101    5.0     44    2.91    52.27     29.261     1.461

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.302350 * X  +  -0.713577 * Y  +   0.631975 * Z  +  45.397976
  Y_new =  -0.611652 * X  +   0.363263 * Y  +   0.702796 * Z  +  25.012951
  Z_new =  -0.731072 * X  +  -0.599039 * Y  +  -0.326628 * Z  +  48.683701 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.069987    1.071605  [ DEG:  -118.6015     61.3985 ]
  Theta =   0.819892    2.321701  [ DEG:    46.9764    133.0237 ]
  Phi   =  -1.111705    2.029888  [ DEG:   -63.6960    116.3040 ]
 
# 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_1-D1                               
REMARK     2: T0304_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304TS393_1-D1.T0304_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  101  101   5.0   44   2.91   52.27  29.261
REMARK  ---------------------------------------------------------- 
MOLECULE T0304TS393_1-D1
PFRMAT TS
TARGET T0304
MODEL 1
PARENT N/A
ATOM     17  CA  ARG    17      30.587  34.106  67.110  1.00 25.00           C
ATOM     18  CA  PRO    18      32.561  36.189  64.646  1.00 25.00           C
ATOM     19  CA  TRP    19      36.263  35.426  64.161  1.00 25.00           C
ATOM     20  CA  TRP    20      38.868  37.031  61.862  1.00 25.00           C
ATOM     21  CA  GLY    21      41.606  39.522  62.715  1.00 25.00           C
ATOM     22  CA  LEU    22      44.023  38.149  60.065  1.00 25.00           C
ATOM     23  CA  PRO    23      46.424  35.510  61.425  1.00 25.00           C
ATOM     24  CA  CYS    24      47.311  33.165  58.568  1.00 25.00           C
ATOM     25  CA  THR    25      48.749  30.321  60.557  1.00 25.00           C
ATOM     26  CA  VAL    26      48.274  27.937  57.680  1.00 25.00           C
ATOM     27  CA  THR    27      51.956  27.147  58.225  1.00 25.00           C
ATOM     28  CA  PRO    28      54.031  24.380  56.638  1.00 25.00           C
ATOM     29  CA  CYS    29      54.235  22.974  53.162  1.00 25.00           C
ATOM     30  CA  PHE    30      55.879  19.526  52.712  1.00 25.00           C
ATOM     31  CA  GLY    31      56.125  16.580  50.276  1.00 25.00           C
ATOM     32  CA  ALA    32      52.874  15.119  51.675  1.00 25.00           C
ATOM     33  CA  ARG    33      51.144  18.511  51.266  1.00 25.00           C
ATOM     34  CA  LEU    34      52.383  18.733  47.649  1.00 25.00           C
ATOM     35  CA  VAL    35      51.070  15.204  46.956  1.00 25.00           C
ATOM     36  CA  GLN    36      47.674  16.145  48.454  1.00 25.00           C
ATOM     37  CA  GLU    37      47.553  19.287  46.268  1.00 25.00           C
ATOM     38  CA  GLY    38      48.378  17.194  43.170  1.00 25.00           C
ATOM     39  CA  ASN    39      45.600  14.718  44.073  1.00 25.00           C
ATOM     40  CA  ARG    40      43.127  17.610  44.498  1.00 25.00           C
ATOM     41  CA  LEU    41      44.151  19.021  41.088  1.00 25.00           C
ATOM     42  CA  HIS    42      43.656  15.577  39.488  1.00 25.00           C
ATOM     43  CA  TYR    43      40.190  15.302  41.095  1.00 25.00           C
ATOM     44  CA  LEU    44      39.277  18.780  39.777  1.00 25.00           C
ATOM     45  CA  ALA    45      40.446  17.786  36.269  1.00 25.00           C
ATOM     46  CA  ASP    46      38.341  14.593  36.445  1.00 25.00           C
ATOM     47  CA  ARG    47      35.289  16.634  37.534  1.00 25.00           C
ATOM     48  CA  ALA    48      34.885  20.417  37.082  1.00 25.00           C
ATOM     49  CA  GLY    49      36.897  22.554  34.595  1.00 25.00           C
ATOM     50  CA  ILE    50      40.199  21.687  32.981  1.00 25.00           C
ATOM     51  CA  ARG    51      43.234  20.827  30.758  1.00 25.00           C
ATOM     52  CA  GLY    52      41.034  17.977  29.437  1.00 25.00           C
ATOM     53  CA  LEU    53      41.414  14.254  29.227  1.00 25.00           C
ATOM     54  CA  PHE    54      41.884  12.032  32.332  1.00 25.00           C
ATOM     55  CA  SER    55      44.492   9.273  32.121  1.00 25.00           C
ATOM     56  CA  ASP    56      46.811   9.756  29.144  1.00 25.00           C
ATOM     57  CA  ALA    57      49.610  11.930  27.690  1.00 25.00           C
ATOM     58  CA  ASP    58      47.414  15.045  28.057  1.00 25.00           C
ATOM     59  CA  ALA    59      46.661  14.116  31.694  1.00 25.00           C
ATOM     60  CA  TYR    60      50.399  13.649  32.376  1.00 25.00           C
ATOM     61  CA  HIS    61      51.137  17.066  30.812  1.00 25.00           C
ATOM     62  CA  LEU    62      48.423  18.673  32.985  1.00 25.00           C
ATOM     63  CA  ASP    63      49.911  17.024  36.106  1.00 25.00           C
ATOM     64  CA  GLN    64      53.389  18.316  35.160  1.00 25.00           C
ATOM     65  CA  ALA    65      51.975  21.843  34.680  1.00 25.00           C
ATOM     66  CA  PHE    66      50.270  21.652  38.103  1.00 25.00           C
ATOM     67  CA  PRO    67      53.559  20.518  39.706  1.00 25.00           C
ATOM     68  CA  LEU    68      55.404  23.429  38.038  1.00 25.00           C
ATOM     69  CA  LEU    69      52.757  25.879  39.326  1.00 25.00           C
ATOM     70  CA  MET    70      53.113  24.443  42.858  1.00 25.00           C
ATOM     71  CA  LYS    71      56.918  24.818  42.654  1.00 25.00           C
ATOM     72  CA  GLN    72      56.523  28.450  41.504  1.00 25.00           C
ATOM     73  CA  LEU    73      54.136  29.140  44.418  1.00 25.00           C
ATOM     74  CA  GLU    74      56.642  27.595  46.868  1.00 25.00           C
ATOM     75  CA  LEU    75      59.441  29.768  45.413  1.00 25.00           C
ATOM     76  CA  MET    76      57.245  32.884  45.780  1.00 25.00           C
ATOM     77  CA  LEU    77      56.491  31.955  49.418  1.00 25.00           C
ATOM     78  CA  THR    78      60.230  31.488  50.099  1.00 25.00           C
ATOM     79  CA  SER    79      63.108  32.205  47.811  1.00 25.00           C
ATOM     80  CA  GLY    80      63.037  34.502  44.802  1.00 25.00           C
ATOM     81  CA  GLU    81      62.549  37.834  46.627  1.00 25.00           C
ATOM     82  CA  LEU    82      59.563  39.196  48.586  1.00 25.00           C
ATOM     83  CA  ASN    83      59.976  42.906  49.574  1.00 25.00           C
ATOM     84  CA  PRO    84      59.422  44.552  46.180  1.00 25.00           C
ATOM     85  CA  ARG    85      56.081  43.845  44.502  1.00 25.00           C
ATOM     86  CA  HIS    86      55.749  40.076  44.515  1.00 25.00           C
ATOM     87  CA  GLN    87      53.894  39.815  47.842  1.00 25.00           C
ATOM     88  CA  HIS    88      51.517  36.869  47.673  1.00 25.00           C
ATOM     89  CA  THR    89      49.847  34.009  49.578  1.00 25.00           C
ATOM     90  CA  VAL    90      47.300  31.664  51.265  1.00 25.00           C
ATOM     91  CA  THR    91      48.747  28.371  52.605  1.00 25.00           C
ATOM     92  CA  LEU    92      45.924  26.877  50.522  1.00 25.00           C
ATOM     93  CA  TYR    93      43.134  25.107  52.484  1.00 25.00           C
ATOM     94  CA  ALA    94      41.219  25.163  49.197  1.00 25.00           C
ATOM     95  CA  LYS    95      37.456  25.736  49.010  1.00 25.00           C
ATOM     96  CA  GLY    96      37.881  26.523  45.342  1.00 25.00           C
ATOM     97  CA  LEU    97      40.757  25.675  43.068  1.00 25.00           C
ATOM     98  CA  THR    98      44.534  25.430  43.264  1.00 25.00           C
ATOM     99  CA  CYS    99      44.267  23.085  46.205  1.00 25.00           C
ATOM    100  CA  LYS   100      44.646  21.037  49.435  1.00 25.00           C
ATOM    101  CA  ALA   101      40.951  20.094  49.001  1.00 25.00           C
ATOM    102  CA  ASP   102      38.725  20.993  51.953  1.00 25.00           C
ATOM    103  CA  THR   103      36.887  17.637  51.753  1.00 25.00           C
ATOM    104  CA  LEU   104      39.396  15.240  50.179  1.00 25.00           C
ATOM    105  CA  SER   105      40.550  13.161  53.112  1.00 25.00           C
ATOM    106  CA  SER   106      44.097  13.083  51.608  1.00 25.00           C
ATOM    107  CA  CYS   107      43.981  16.797  52.394  1.00 25.00           C
ATOM    108  CA  ASP   108      46.240  19.314  54.143  1.00 25.00           C
ATOM    109  CA  TYR   109      49.562  20.676  55.549  1.00 25.00           C
ATOM    110  CA  VAL   110      49.247  22.967  52.520  1.00 25.00           C
ATOM    111  CA  TYR   111      50.443  23.229  48.936  1.00 25.00           C
ATOM    112  CA  LEU   112      48.690  25.088  46.137  1.00 25.00           C
ATOM    113  CA  ALA   113      48.926  28.308  44.148  1.00 25.00           C
ATOM    114  CA  VAL   114      46.301  30.573  42.640  1.00 25.00           C
ATOM    115  CA  TYR   115      45.229  34.044  41.479  1.00 25.00           C
ATOM    116  CA  PRO   116      42.043  33.869  43.501  1.00 25.00           C
ATOM    117  CA  THR   117      39.010  35.885  44.758  1.00 25.00           C
TER
END
