
#######################################################
#                                                     #
#                        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  146 (  146),  selected  146 , name T0312TS393_3
# Molecule2: number of CA atoms  140 ( 1114),  selected  140 , name T0312.pdb
# PARAMETERS: T0312TS393_3.T0312.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    K       2      K       2           -
LGA    V       3      V       3           -
LGA    F       4      F       4           -
LGA    E       5      E       5           -
LGA    F       6      F       6           -
LGA    E       7      E       7           -
LGA    V       8      V       8           -
LGA    G       9      G       9           -
LGA    K      10      K      10           -
LGA    G      11      G      11           -
LGA    F      12      F      12           -
LGA    -       -      L      13           -
LGA    -       -      L      14           -
LGA    -       -      R      15           -
LGA    -       -      L      16           -
LGA    -       -      D      17           -
LGA    -       -      Y      18           -
LGA    -       -      G      19           -
LGA    -       -      K      20           -
LGA    -       -      D      21           -
LGA    -       -      L      22           -
LGA    L      13      V      23          4.077
LGA    L      14      R      24          3.412
LGA    R      15      -       -           -
LGA    L      16      -       -           -
LGA    D      17      -       -           -
LGA    Y      18      -       -           -
LGA    G      19      -       -           -
LGA    K      20      -       -           -
LGA    D      21      -       -           -
LGA    L      22      -       -           -
LGA    V      23      -       -           -
LGA    R      24      -       -           -
LGA    Q      25      -       -           -
LGA    I      26      -       -           -
LGA    E      27      -       -           -
LGA    E      28      -       -           -
LGA    F      29      -       -           -
LGA    L      30      -       -           -
LGA    E      31      -       -           -
LGA    E      32      -       -           -
LGA    K      33      -       -           -
LGA    G      34      -       -           -
LGA    I      35      -       -           -
LGA    H      36      -       -           -
LGA    A      37      -       -           -
LGA    A      38      -       -           -
LGA    H      39      -       -           -
LGA    I      40      Q      25          4.373
LGA    S      41      I      26           #
LGA    -       -      E      27           -
LGA    -       -      E      28           -
LGA    A      42      F      29          2.685
LGA    I      43      L      30          4.033
LGA    G      44      E      31          4.206
LGA    -       -      E      32           -
LGA    -       -      K      33           -
LGA    -       -      G      34           -
LGA    -       -      I      35           -
LGA    A      45      H      36          1.108
LGA    V      46      A      37          3.523
LGA    R      47      A      38          3.234
LGA    S      48      H      39          1.424
LGA    A      49      I      40          0.571
LGA    V      50      S      41          1.923
LGA    I      51      A      42          2.648
LGA    G      52      I      43          4.792
LGA    Y      53      G      44          2.696
LGA    Y      54      A      45          1.585
LGA    -       -      V      46           -
LGA    D      55      R      47           #
LGA    Q      56      S      48           -
LGA    E      57      A      49           -
LGA    K      58      V      50           -
LGA    K      59      I      51           -
LGA    E      60      G      52           -
LGA    -       -      Y      53           -
LGA    -       -      Y      54           -
LGA    -       -      D      55           -
LGA    -       -      Q      56           -
LGA    -       -      E      57           -
LGA    -       -      K      58           -
LGA    -       -      K      59           -
LGA    -       -      E      60           -
LGA    -       -      Y      61           -
LGA    -       -      V      62           -
LGA    -       -      K      63           -
LGA    -       -      K      64           -
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    -       -      M      67           -
LGA    -       -      E      68           -
LGA    -       -      P      69           -
LGA    -       -      L      70           -
LGA    Y      61      E      71          4.896
LGA    -       -      I      72           -
LGA    V      62      L      73          2.330
LGA    K      63      S      74          1.947
LGA    K      64      L      75          3.209
LGA    E      65      S      76          3.838
LGA    L      66      G      77           #
LGA    M      67      -       -           -
LGA    E      68      -       -           -
LGA    P      69      -       -           -
LGA    L      70      N      78           #
LGA    E      71      V      79          3.726
LGA    I      72      S      80          2.948
LGA    -       -      M      81           -
LGA    -       -      K      82           -
LGA    -       -      D      83           -
LGA    -       -      S      84           -
LGA    -       -      K      85           -
LGA    -       -      P      86           -
LGA    L      73      F      87          4.796
LGA    S      74      C      88          3.466
LGA    L      75      H      89          3.853
LGA    S      76      I      90          3.234
LGA    G      77      H      91           #
LGA    N      78      V      92          2.559
LGA    V      79      L      93          4.778
LGA    S      80      L      94          1.244
LGA    M      81      G      95          4.270
LGA    -       -      K      96           -
LGA    -       -      D      97           -
LGA    K      82      G      98          3.808
LGA    D      83      E      99          4.582
LGA    S      84      V     100          3.176
LGA    K      85      Y     101          1.140
LGA    P      86      G     102          4.830
LGA    F      87      G     103          4.598
LGA    C      88      H     104          1.685
LGA    H      89      L     105           #
LGA    I      90      -       -           -
LGA    H      91      -       -           -
LGA    V      92      -       -           -
LGA    L      93      -       -           -
LGA    L      94      -       -           -
LGA    G      95      -       -           -
LGA    K      96      -       -           -
LGA    D      97      -       -           -
LGA    G      98      -       -           -
LGA    E      99      -       -           -
LGA    V     100      -       -           -
LGA    Y     101      -       -           -
LGA    G     102      -       -           -
LGA    G     103      -       -           -
LGA    H     104      -       -           -
LGA    L     105      -       -           -
LGA    F     106      F     106          3.043
LGA    S     107      S     107          3.255
LGA    A     108      -       -           -
LGA    E     109      -       -           -
LGA    V     110      -       -           -
LGA    F     111      A     108          4.590
LGA    A     112      E     109          1.561
LGA    C     113      V     110          3.735
LGA    E     114      F     111           -
LGA    V     115      A     112           #
LGA    F     116      C     113          3.974
LGA    V     117      -       -           -
LGA    L     118      -       -           -
LGA    P     119      -       -           -
LGA    L     120      -       -           -
LGA    S     121      -       -           -
LGA    G     122      -       -           -
LGA    E     123      -       -           -
LGA    A     124      E     114           #
LGA    P     125      V     115          4.526
LGA    E     126      F     116           -
LGA    R     127      V     117           -
LGA    A     128      L     118           -
LGA    F     129      P     119           -
LGA    D     130      L     120           -
LGA    E     131      S     121           -
LGA    Q     132      G     122           -
LGA    T     133      E     123           -
LGA    G     134      A     124           -
LGA    L     135      P     125           -
LGA    F     136      E     126           -
LGA    L     137      R     127           -
LGA    W     138      A     128           -
LGA    L     139      F     129           -
LGA    E     140      D     130           -
LGA    H     141      E     131           -
LGA    H     142      Q     132           -
LGA    H     143      T     133           -
LGA    H     144      G     134           -
LGA    H     145      L     135           -
LGA    H     146      F     136           -
LGA    -       -      L     137           -
LGA    -       -      W     138           -
LGA    -       -      L     139           -
LGA    -       -      E     140           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  146  140    5.0     45    3.45     4.44     17.094     1.267

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.580092 * X  +  -0.719013 * Y  +  -0.382771 * Z  +  56.114819
  Y_new =   0.149460 * X  +   0.367983 * Y  +  -0.917742 * Z  +   8.137922
  Z_new =   0.800722 * X  +  -0.589584 * Y  +  -0.106001 * Z  +  10.481580 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.748685    1.392908  [ DEG:  -100.1923     79.8077 ]
  Theta =  -0.928499   -2.213094  [ DEG:   -53.1991   -126.8009 ]
  Phi   =   2.889429   -0.252164  [ DEG:   165.5521    -14.4479 ]
 
# 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: T0312TS393_3                                  
REMARK     2: T0312.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0312TS393_3.T0312.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  146  140   5.0   45   3.45    4.44  17.094
REMARK  ---------------------------------------------------------- 
MOLECULE T0312TS393_3
PFRMAT TS
TARGET T0312
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      50.636   0.781  -0.448  1.00 25.00           C
ATOM      2  CA  LYS     2      50.647  -0.255   3.212  1.00 25.00           C
ATOM      3  CA  VAL     3      51.453  -2.154   6.439  1.00 25.00           C
ATOM      4  CA  PHE     4      53.844  -2.705   9.329  1.00 25.00           C
ATOM      5  CA  GLU     5      57.187  -1.722  10.831  1.00 25.00           C
ATOM      6  CA  PHE     6      60.272  -0.208  12.379  1.00 25.00           C
ATOM      7  CA  GLU     7      59.983  -3.003  14.926  1.00 25.00           C
ATOM      8  CA  VAL     8      59.927  -4.825  18.324  1.00 25.00           C
ATOM      9  CA  GLY     9      63.736  -5.087  17.981  1.00 25.00           C
ATOM     10  CA  LYS    10      64.484  -1.683  19.413  1.00 25.00           C
ATOM     11  CA  GLY    11      64.954   0.625  16.414  1.00 25.00           C
ATOM     12  CA  PHE    12      63.647   4.047  15.416  1.00 25.00           C
ATOM     13  CA  LEU    13      62.241   4.533  11.890  1.00 25.00           C
ATOM     14  CA  LEU    14      61.938   8.118  12.913  1.00 25.00           C
ATOM     15  CA  ARG    15      61.060   8.938   9.357  1.00 25.00           C
ATOM     16  CA  LEU    16      61.143  10.487   5.903  1.00 25.00           C
ATOM     17  CA  ASP    17      62.721  11.703   2.664  1.00 25.00           C
ATOM     18  CA  TYR    18      64.456  13.705  -0.081  1.00 25.00           C
ATOM     19  CA  GLY    19      63.905  13.552  -3.825  1.00 25.00           C
ATOM     20  CA  LYS    20      67.623  12.759  -3.934  1.00 25.00           C
ATOM     21  CA  ASP    21      71.108  11.624  -2.820  1.00 25.00           C
ATOM     22  CA  LEU    22      69.727  10.687   0.628  1.00 25.00           C
ATOM     23  CA  VAL    23      66.901   8.694  -1.019  1.00 25.00           C
ATOM     24  CA  ARG    24      69.440   6.870  -3.229  1.00 25.00           C
ATOM     25  CA  GLN    25      71.563   6.043  -0.151  1.00 25.00           C
ATOM     26  CA  ILE    26      68.464   4.702   1.656  1.00 25.00           C
ATOM     27  CA  GLU    27      67.596   2.542  -1.386  1.00 25.00           C
ATOM     28  CA  GLU    28      71.175   1.181  -1.470  1.00 25.00           C
ATOM     29  CA  PHE    29      70.979   0.361   2.265  1.00 25.00           C
ATOM     30  CA  LEU    30      67.646  -1.446   1.718  1.00 25.00           C
ATOM     31  CA  GLU    31      69.178  -3.451  -1.163  1.00 25.00           C
ATOM     32  CA  GLU    32      72.157  -4.401   1.050  1.00 25.00           C
ATOM     33  CA  LYS    33      74.880  -3.411   3.460  1.00 25.00           C
ATOM     34  CA  GLY    34      76.303  -0.350   5.176  1.00 25.00           C
ATOM     35  CA  ILE    35      73.628   1.574   7.017  1.00 25.00           C
ATOM     36  CA  HIS    36      72.386   3.967   9.750  1.00 25.00           C
ATOM     37  CA  ALA    37      68.684   4.942   9.263  1.00 25.00           C
ATOM     38  CA  ALA    38      65.874   7.405   8.362  1.00 25.00           C
ATOM     39  CA  HIS    39      66.206  10.437   6.041  1.00 25.00           C
ATOM     40  CA  ILE    40      65.990  12.404   9.265  1.00 25.00           C
ATOM     41  CA  SER    41      66.576  14.721  12.233  1.00 25.00           C
ATOM     42  CA  ALA    42      65.923  11.560  14.292  1.00 25.00           C
ATOM     43  CA  ILE    43      66.357   8.215  16.040  1.00 25.00           C
ATOM     44  CA  GLY    44      69.362   9.184  18.226  1.00 25.00           C
ATOM     45  CA  ALA    45      69.516   9.425  22.033  1.00 25.00           C
ATOM     46  CA  VAL    46      66.214  11.137  22.812  1.00 25.00           C
ATOM     47  CA  ARG    47      63.680  13.507  24.253  1.00 25.00           C
ATOM     48  CA  SER    48      60.909  10.972  24.531  1.00 25.00           C
ATOM     49  CA  ALA    49      57.637  11.223  22.603  1.00 25.00           C
ATOM     50  CA  VAL    50      54.671  10.856  20.248  1.00 25.00           C
ATOM     51  CA  ILE    51      52.951  11.261  16.933  1.00 25.00           C
ATOM     52  CA  GLY    52      51.539  11.902  13.415  1.00 25.00           C
ATOM     53  CA  TYR    53      47.878  12.695  14.214  1.00 25.00           C
ATOM     54  CA  TYR    54      46.165  11.876  10.867  1.00 25.00           C
ATOM     55  CA  ASP    55      43.488  14.432  10.124  1.00 25.00           C
ATOM     56  CA  GLN    56      40.738  15.369   7.582  1.00 25.00           C
ATOM     57  CA  GLU    57      36.947  14.800   7.446  1.00 25.00           C
ATOM     58  CA  LYS    58      36.808  18.298   8.781  1.00 25.00           C
ATOM     59  CA  LYS    59      38.643  17.117  11.950  1.00 25.00           C
ATOM     60  CA  GLU    60      39.107  14.211  14.358  1.00 25.00           C
ATOM     61  CA  TYR    61      41.498  11.873  16.172  1.00 25.00           C
ATOM     62  CA  VAL    62      43.198  10.869  19.357  1.00 25.00           C
ATOM     63  CA  LYS    63      46.312   9.938  21.297  1.00 25.00           C
ATOM     64  CA  LYS    64      50.069   9.776  22.028  1.00 25.00           C
ATOM     65  CA  GLU    65      50.862   7.591  25.061  1.00 25.00           C
ATOM     66  CA  LEU    66      53.784   9.978  25.884  1.00 25.00           C
ATOM     67  CA  MET    67      54.404   8.878  29.481  1.00 25.00           C
ATOM     68  CA  GLU    68      58.039   7.803  29.816  1.00 25.00           C
ATOM     69  CA  PRO    69      60.791   5.519  28.581  1.00 25.00           C
ATOM     70  CA  LEU    70      64.590   5.152  28.480  1.00 25.00           C
ATOM     71  CA  GLU    71      65.373   4.733  24.797  1.00 25.00           C
ATOM     72  CA  ILE    72      65.237   6.092  21.228  1.00 25.00           C
ATOM     73  CA  LEU    73      61.915   4.174  20.880  1.00 25.00           C
ATOM     74  CA  SER    74      60.464   1.402  18.657  1.00 25.00           C
ATOM     75  CA  LEU    75      58.583   3.479  16.070  1.00 25.00           C
ATOM     76  CA  SER    76      55.021   4.919  16.010  1.00 25.00           C
ATOM     77  CA  GLY    77      52.369   6.915  14.151  1.00 25.00           C
ATOM     78  CA  ASN    78      49.288   6.812  16.392  1.00 25.00           C
ATOM     79  CA  VAL    79      46.920   7.364  13.505  1.00 25.00           C
ATOM     80  CA  SER    80      43.593   6.226  14.845  1.00 25.00           C
ATOM     81  CA  MET    81      40.434   6.891  16.831  1.00 25.00           C
ATOM     82  CA  LYS    82      37.482   4.580  16.426  1.00 25.00           C
ATOM     83  CA  ASP    83      36.491   0.871  16.221  1.00 25.00           C
ATOM     84  CA  SER    84      39.901   0.340  14.541  1.00 25.00           C
ATOM     85  CA  LYS    85      43.624   1.085  14.291  1.00 25.00           C
ATOM     86  CA  PRO    86      46.844   2.315  12.619  1.00 25.00           C
ATOM     87  CA  PHE    87      50.169   2.217  14.479  1.00 25.00           C
ATOM     88  CA  CYS    88      52.519   0.687  17.007  1.00 25.00           C
ATOM     89  CA  HIS    89      55.339   1.352  19.549  1.00 25.00           C
ATOM     90  CA  ILE    90      56.668   4.260  21.596  1.00 25.00           C
ATOM     91  CA  HIS    91      57.966   7.138  19.468  1.00 25.00           C
ATOM     92  CA  VAL    92      61.294   8.331  17.931  1.00 25.00           C
ATOM     93  CA  LEU    93      63.216  11.558  18.572  1.00 25.00           C
ATOM     94  CA  LEU    94      64.141  15.142  17.772  1.00 25.00           C
ATOM     95  CA  GLY    95      67.839  14.362  18.059  1.00 25.00           C
ATOM     96  CA  LYS    96      70.204  17.083  16.888  1.00 25.00           C
ATOM     97  CA  ASP    97      68.635  19.201  19.599  1.00 25.00           C
ATOM     98  CA  GLY    98      65.730  20.892  17.797  1.00 25.00           C
ATOM     99  CA  GLU    99      63.472  19.912  14.934  1.00 25.00           C
ATOM    100  CA  VAL   100      62.092  16.724  13.268  1.00 25.00           C
ATOM    101  CA  TYR   101      61.564  13.085  12.350  1.00 25.00           C
ATOM    102  CA  GLY   102      58.448  12.815  14.581  1.00 25.00           C
ATOM    103  CA  GLY   103      57.159   9.195  14.461  1.00 25.00           C
ATOM    104  CA  HIS   104      56.638   7.105  11.366  1.00 25.00           C
ATOM    105  CA  LEU   105      57.105   3.359  10.707  1.00 25.00           C
ATOM    106  CA  PHE   106      53.529   2.162  10.740  1.00 25.00           C
ATOM    107  CA  SER   107      52.820   2.812   7.078  1.00 25.00           C
ATOM    108  CA  ALA   108      55.508   0.752   5.310  1.00 25.00           C
ATOM    109  CA  GLU   109      55.286   1.960   1.676  1.00 25.00           C
ATOM    110  CA  VAL   110      54.620   5.572   2.763  1.00 25.00           C
ATOM    111  CA  PHE   111      51.274   6.755   4.140  1.00 25.00           C
ATOM    112  CA  ALA   112      53.325   8.331   6.952  1.00 25.00           C
ATOM    113  CA  CYS   113      56.274  10.822   7.006  1.00 25.00           C
ATOM    114  CA  GLU   114      55.594  12.300  10.461  1.00 25.00           C
ATOM    115  CA  VAL   115      57.761  15.279   9.444  1.00 25.00           C
ATOM    116  CA  PHE   116      56.155  17.003  12.431  1.00 25.00           C
ATOM    117  CA  VAL   117      57.877  17.875  15.707  1.00 25.00           C
ATOM    118  CA  LEU   118      59.489  16.608  18.876  1.00 25.00           C
ATOM    119  CA  PRO   119      60.814  19.647  20.649  1.00 25.00           C
ATOM    120  CA  LEU   120      60.109  18.091  24.101  1.00 25.00           C
ATOM    121  CA  SER   121      59.667  21.370  25.891  1.00 25.00           C
ATOM    122  CA  GLY   122      55.999  22.243  25.419  1.00 25.00           C
ATOM    123  CA  GLU   123      55.336  21.085  21.842  1.00 25.00           C
ATOM    124  CA  ALA   124      52.956  18.627  20.340  1.00 25.00           C
ATOM    125  CA  PRO   125      53.186  19.573  16.689  1.00 25.00           C
ATOM    126  CA  GLU   126      51.293  19.406  13.420  1.00 25.00           C
ATOM    127  CA  ARG   127      51.804  18.115   9.844  1.00 25.00           C
ATOM    128  CA  ALA   128      50.352  14.690   9.112  1.00 25.00           C
ATOM    129  CA  PHE   129      49.298  13.182   5.783  1.00 25.00           C
ATOM    130  CA  ASP   130      48.237  15.986   3.531  1.00 25.00           C
ATOM    131  CA  GLU   131      48.771  18.756   1.052  1.00 25.00           C
ATOM    132  CA  GLN   132      46.211  18.373  -1.733  1.00 25.00           C
ATOM    133  CA  THR   133      46.201  14.601  -1.267  1.00 25.00           C
ATOM    134  CA  GLY   134      47.930  11.237  -1.767  1.00 25.00           C
ATOM    135  CA  LEU   135      45.551  10.872  -4.640  1.00 25.00           C
ATOM    136  CA  PHE   136      44.835  10.053  -8.275  1.00 25.00           C
ATOM    137  CA  LEU   137      42.901   7.667 -10.580  1.00 25.00           C
ATOM    138  CA  TRP   138      41.785   4.018 -11.077  1.00 25.00           C
ATOM    139  CA  LEU   139      43.175   3.883 -14.615  1.00 25.00           C
ATOM    140  CA  GLU   140      43.236   0.891 -16.956  1.00 25.00           C
ATOM    141  CA  HIS   141      39.925  -0.003 -18.532  1.00 25.00           C
ATOM    142  CA  HIS   142      37.726  -1.637 -15.906  1.00 25.00           C
ATOM    143  CA  HIS   143      36.163   1.640 -14.778  1.00 25.00           C
ATOM    144  CA  HIS   144      33.270  -0.231 -13.196  1.00 25.00           C
ATOM    145  CA  HIS   145      31.757  -3.423 -11.814  1.00 25.00           C
ATOM    146  CA  HIS   146      34.138  -3.884  -8.846  1.00 25.00           C
TER
END
