
#######################################################
#                                                     #
#                        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_5
# Molecule2: number of CA atoms  140 ( 1114),  selected  140 , name T0312.pdb
# PARAMETERS: T0312TS393_5.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           -
LGA    -       -      F       4           -
LGA    -       -      E       5           -
LGA    -       -      F       6           -
LGA    -       -      E       7           -
LGA    -       -      V       8           -
LGA    -       -      G       9           -
LGA    -       -      K      10           -
LGA    -       -      G      11           -
LGA    V       3      F      12          5.603
LGA    F       4      L      13          3.278
LGA    E       5      L      14          3.712
LGA    F       6      R      15          2.068
LGA    -       -      L      16           -
LGA    E       7      D      17          4.132
LGA    V       8      -       -           -
LGA    G       9      -       -           -
LGA    K      10      -       -           -
LGA    G      11      -       -           -
LGA    F      12      -       -           -
LGA    L      13      -       -           -
LGA    L      14      Y      18           #
LGA    -       -      G      19           -
LGA    R      15      K      20           #
LGA    L      16      D      21          3.772
LGA    D      17      L      22           -
LGA    Y      18      V      23           -
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      R      24          5.219
LGA    I      40      Q      25          4.433
LGA    S      41      I      26           #
LGA    A      42      E      27          3.012
LGA    -       -      E      28           -
LGA    -       -      F      29           -
LGA    I      43      L      30           #
LGA    G      44      E      31          3.980
LGA    -       -      E      32           -
LGA    -       -      K      33           -
LGA    A      45      G      34          1.421
LGA    V      46      I      35          2.522
LGA    R      47      H      36          1.538
LGA    S      48      A      37          2.473
LGA    A      49      A      38          2.974
LGA    V      50      H      39          3.063
LGA    I      51      I      40          1.331
LGA    G      52      S      41          1.996
LGA    Y      53      A      42          3.499
LGA    Y      54      I      43          3.382
LGA    -       -      G      44           -
LGA    -       -      A      45           -
LGA    -       -      V      46           -
LGA    -       -      R      47           -
LGA    -       -      S      48           -
LGA    -       -      A      49           -
LGA    -       -      V      50           -
LGA    -       -      I      51           -
LGA    -       -      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    -       -      E      71           -
LGA    D      55      I      72           #
LGA    Q      56      L      73           #
LGA    E      57      -       -           -
LGA    K      58      -       -           -
LGA    K      59      -       -           -
LGA    E      60      -       -           -
LGA    Y      61      S      74           #
LGA    V      62      L      75           #
LGA    K      63      S      76          4.283
LGA    K      64      G      77          2.675
LGA    E      65      N      78          2.442
LGA    L      66      V      79          3.042
LGA    M      67      S      80          2.758
LGA    E      68      M      81          2.335
LGA    -       -      K      82           -
LGA    -       -      D      83           -
LGA    -       -      S      84           -
LGA    P      69      K      85          1.798
LGA    L      70      P      86          4.611
LGA    E      71      F      87           -
LGA    I      72      -       -           -
LGA    L      73      -       -           -
LGA    S      74      -       -           -
LGA    L      75      -       -           -
LGA    S      76      C      88          3.467
LGA    G      77      H      89           #
LGA    N      78      I      90          3.884
LGA    V      79      H      91          3.525
LGA    S      80      V      92          1.975
LGA    M      81      L      93          3.733
LGA    K      82      -       -           -
LGA    D      83      -       -           -
LGA    S      84      -       -           -
LGA    K      85      -       -           -
LGA    P      86      L      94          4.618
LGA    F      87      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           -
LGA    -       -      S     107           -
LGA    C      88      A     108           #
LGA    H      89      -       -           -
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      -       -           -
LGA    S     107      E     109          3.599
LGA    A     108      V     110          4.224
LGA    E     109      F     111          1.460
LGA    V     110      -       -           -
LGA    F     111      A     112          2.157
LGA    A     112      C     113          1.642
LGA    C     113      E     114          1.170
LGA    E     114      V     115          0.638
LGA    V     115      F     116          3.716
LGA    F     116      V     117          1.526
LGA    V     117      L     118          3.825
LGA    L     118      P     119          2.078
LGA    P     119      -       -           -
LGA    L     120      L     120          1.879
LGA    S     121      S     121          2.971
LGA    G     122      G     122           -
LGA    E     123      E     123           -
LGA    A     124      A     124           -
LGA    P     125      P     125           -
LGA    E     126      E     126           -
LGA    R     127      R     127           -
LGA    A     128      A     128           -
LGA    F     129      F     129           -
LGA    D     130      D     130           -
LGA    E     131      E     131           -
LGA    Q     132      Q     132           -
LGA    T     133      T     133           -
LGA    G     134      G     134           -
LGA    L     135      L     135           -
LGA    F     136      F     136           -
LGA    L     137      L     137           -
LGA    W     138      W     138           -
LGA    L     139      L     139           -
LGA    E     140      E     140           -
LGA    H     141      -       -           -
LGA    H     142      -       -           -
LGA    H     143      -       -           -
LGA    H     144      -       -           -
LGA    H     145      -       -           -
LGA    H     146      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  146  140    5.0     47    3.18     8.51     19.079     1.434

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.623219 * X  +  -0.692027 * Y  +  -0.364276 * Z  +  58.096992
  Y_new =   0.640844 * X  +   0.718884 * Y  +  -0.269305 * Z  +  14.380505
  Z_new =   0.448239 * X  +  -0.065608 * Y  +   0.891503 * Z  +  14.308736 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.073460    3.068133  [ DEG:    -4.2090    175.7910 ]
  Theta =  -0.464794   -2.676799  [ DEG:   -26.6307   -153.3693 ]
  Phi   =   0.799340   -2.342252  [ DEG:    45.7988   -134.2012 ]
 
# 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_5                                  
REMARK     2: T0312.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0312TS393_5.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   47   3.18    8.51  19.079
REMARK  ---------------------------------------------------------- 
MOLECULE T0312TS393_5
PFRMAT TS
TARGET T0312
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1      57.033  30.476  21.855  1.00 25.00           C
ATOM      2  CA  LYS     2      56.114  26.802  21.502  1.00 25.00           C
ATOM      3  CA  VAL     3      56.924  23.180  21.036  1.00 25.00           C
ATOM      4  CA  PHE     4      57.346  23.361  17.311  1.00 25.00           C
ATOM      5  CA  GLU     5      58.388  22.840  13.708  1.00 25.00           C
ATOM      6  CA  PHE     6      58.471  20.359  10.828  1.00 25.00           C
ATOM      7  CA  GLU     7      57.866  20.760   7.082  1.00 25.00           C
ATOM      8  CA  VAL     8      59.866  23.964   7.362  1.00 25.00           C
ATOM      9  CA  GLY     9      63.649  23.939   6.979  1.00 25.00           C
ATOM     10  CA  LYS    10      65.988  21.756   8.974  1.00 25.00           C
ATOM     11  CA  GLY    11      66.618  18.592  10.955  1.00 25.00           C
ATOM     12  CA  PHE    12      64.046  15.885  10.399  1.00 25.00           C
ATOM     13  CA  LEU    13      61.038  14.247   8.667  1.00 25.00           C
ATOM     14  CA  LEU    14      60.996  11.204  11.041  1.00 25.00           C
ATOM     15  CA  ARG    15      59.255   7.784  11.249  1.00 25.00           C
ATOM     16  CA  LEU    16      59.168   5.374   8.270  1.00 25.00           C
ATOM     17  CA  ASP    17      60.474   2.479   6.216  1.00 25.00           C
ATOM     18  CA  TYR    18      60.565  -1.330   6.231  1.00 25.00           C
ATOM     19  CA  GLY    19      60.284  -4.369   3.920  1.00 25.00           C
ATOM     20  CA  LYS    20      59.689  -3.313   0.320  1.00 25.00           C
ATOM     21  CA  ASP    21      58.531  -1.419  -2.800  1.00 25.00           C
ATOM     22  CA  LEU    22      58.032   1.756  -0.716  1.00 25.00           C
ATOM     23  CA  VAL    23      61.542   1.367   0.764  1.00 25.00           C
ATOM     24  CA  ARG    24      63.002   0.937  -2.751  1.00 25.00           C
ATOM     25  CA  GLN    25      61.164   4.084  -3.927  1.00 25.00           C
ATOM     26  CA  ILE    26      62.521   6.031  -0.921  1.00 25.00           C
ATOM     27  CA  GLU    27      66.068   4.817  -1.705  1.00 25.00           C
ATOM     28  CA  GLU    28      65.658   5.901  -5.355  1.00 25.00           C
ATOM     29  CA  PHE    29      64.432   9.347  -4.219  1.00 25.00           C
ATOM     30  CA  LEU    30      67.448   9.676  -1.880  1.00 25.00           C
ATOM     31  CA  GLU    31      69.805   8.724  -4.745  1.00 25.00           C
ATOM     32  CA  GLU    32      68.150  11.337  -7.005  1.00 25.00           C
ATOM     33  CA  LYS    33      68.393  15.169  -6.985  1.00 25.00           C
ATOM     34  CA  GLY    34      69.829  14.639  -3.488  1.00 25.00           C
ATOM     35  CA  ILE    35      68.047  14.365  -0.142  1.00 25.00           C
ATOM     36  CA  HIS    36      68.103  17.623   1.728  1.00 25.00           C
ATOM     37  CA  ALA    37      66.197  16.430   4.749  1.00 25.00           C
ATOM     38  CA  ALA    38      66.659  13.001   6.334  1.00 25.00           C
ATOM     39  CA  HIS    39      63.462  11.020   5.751  1.00 25.00           C
ATOM     40  CA  ILE    40      64.511   8.463   8.293  1.00 25.00           C
ATOM     41  CA  SER    41      64.175   5.369  10.554  1.00 25.00           C
ATOM     42  CA  ALA    42      65.879   6.162  13.890  1.00 25.00           C
ATOM     43  CA  ILE    43      67.370   7.792  17.042  1.00 25.00           C
ATOM     44  CA  GLY    44      70.024  10.057  18.484  1.00 25.00           C
ATOM     45  CA  ALA    45      72.168  12.738  20.248  1.00 25.00           C
ATOM     46  CA  VAL    46      70.182  12.182  23.481  1.00 25.00           C
ATOM     47  CA  ARG    47      70.290   8.449  23.792  1.00 25.00           C
ATOM     48  CA  SER    48      66.810   7.119  22.836  1.00 25.00           C
ATOM     49  CA  ALA    49      63.295   8.535  22.527  1.00 25.00           C
ATOM     50  CA  VAL    50      59.518   8.992  22.590  1.00 25.00           C
ATOM     51  CA  ILE    51      57.585  11.897  21.225  1.00 25.00           C
ATOM     52  CA  GLY    52      54.196  10.343  21.886  1.00 25.00           C
ATOM     53  CA  TYR    53      51.168  12.650  21.454  1.00 25.00           C
ATOM     54  CA  TYR    54      47.907  13.842  19.859  1.00 25.00           C
ATOM     55  CA  ASP    55      44.774  13.051  21.973  1.00 25.00           C
ATOM     56  CA  GLN    56      41.157  13.869  22.855  1.00 25.00           C
ATOM     57  CA  GLU    57      40.321  16.325  25.640  1.00 25.00           C
ATOM     58  CA  LYS    58      42.424  15.910  28.757  1.00 25.00           C
ATOM     59  CA  LYS    59      43.032  12.251  29.664  1.00 25.00           C
ATOM     60  CA  GLU    60      44.815   9.059  28.668  1.00 25.00           C
ATOM     61  CA  TYR    61      47.592   8.617  26.081  1.00 25.00           C
ATOM     62  CA  VAL    62      49.555   5.303  26.126  1.00 25.00           C
ATOM     63  CA  LYS    63      53.335   5.404  25.460  1.00 25.00           C
ATOM     64  CA  LYS    64      56.892   4.456  24.466  1.00 25.00           C
ATOM     65  CA  GLU    65      60.715   4.154  24.221  1.00 25.00           C
ATOM     66  CA  LEU    66      62.794   3.726  21.064  1.00 25.00           C
ATOM     67  CA  MET    67      65.649   1.547  22.338  1.00 25.00           C
ATOM     68  CA  GLU    68      68.360   1.619  19.711  1.00 25.00           C
ATOM     69  CA  PRO    69      71.437   3.556  18.743  1.00 25.00           C
ATOM     70  CA  LEU    70      72.655   5.995  16.110  1.00 25.00           C
ATOM     71  CA  GLU    71      71.393   8.117  13.259  1.00 25.00           C
ATOM     72  CA  ILE    72      69.947  11.653  13.689  1.00 25.00           C
ATOM     73  CA  LEU    73      66.456  11.055  12.211  1.00 25.00           C
ATOM     74  CA  SER    74      63.592  10.624  14.678  1.00 25.00           C
ATOM     75  CA  LEU    75      62.197   8.357  17.434  1.00 25.00           C
ATOM     76  CA  SER    76      59.491   6.042  16.078  1.00 25.00           C
ATOM     77  CA  GLY    77      56.662   7.632  18.008  1.00 25.00           C
ATOM     78  CA  ASN    78      53.339   6.040  16.880  1.00 25.00           C
ATOM     79  CA  VAL    79      51.407   6.312  20.138  1.00 25.00           C
ATOM     80  CA  SER    80      47.877   5.543  18.938  1.00 25.00           C
ATOM     81  CA  MET    81      46.602   1.911  19.150  1.00 25.00           C
ATOM     82  CA  LYS    82      44.008  -0.727  18.233  1.00 25.00           C
ATOM     83  CA  ASP    83      41.175   0.086  15.855  1.00 25.00           C
ATOM     84  CA  SER    84      43.322   2.621  14.028  1.00 25.00           C
ATOM     85  CA  LYS    85      45.920   5.382  13.972  1.00 25.00           C
ATOM     86  CA  PRO    86      48.780   7.721  13.167  1.00 25.00           C
ATOM     87  CA  PHE    87      50.898  10.405  14.855  1.00 25.00           C
ATOM     88  CA  CYS    88      54.178   9.431  13.256  1.00 25.00           C
ATOM     89  CA  HIS    89      57.192  11.353  14.693  1.00 25.00           C
ATOM     90  CA  ILE    90      59.900  12.881  16.859  1.00 25.00           C
ATOM     91  CA  HIS    91      63.078  13.895  18.766  1.00 25.00           C
ATOM     92  CA  VAL    92      65.039  15.298  15.771  1.00 25.00           C
ATOM     93  CA  LEU    93      68.217  14.769  17.731  1.00 25.00           C
ATOM     94  CA  LEU    94      69.555  17.846  15.879  1.00 25.00           C
ATOM     95  CA  GLY    95      72.528  15.906  14.610  1.00 25.00           C
ATOM     96  CA  LYS    96      75.507  17.077  16.633  1.00 25.00           C
ATOM     97  CA  ASP    97      73.789  20.202  18.006  1.00 25.00           C
ATOM     98  CA  GLY    98      72.052  17.902  20.537  1.00 25.00           C
ATOM     99  CA  GLU    99      68.879  19.580  21.874  1.00 25.00           C
ATOM    100  CA  VAL   100      66.093  19.391  19.286  1.00 25.00           C
ATOM    101  CA  TYR   101      63.337  21.074  17.246  1.00 25.00           C
ATOM    102  CA  GLY   102      62.521  19.692  13.733  1.00 25.00           C
ATOM    103  CA  GLY   103      60.164  16.687  13.623  1.00 25.00           C
ATOM    104  CA  HIS   104      57.141  15.401  11.670  1.00 25.00           C
ATOM    105  CA  LEU   105      56.404  12.448   9.389  1.00 25.00           C
ATOM    106  CA  PHE   106      55.188   9.285   7.662  1.00 25.00           C
ATOM    107  CA  SER   107      51.520   9.376   8.547  1.00 25.00           C
ATOM    108  CA  ALA   108      48.704  10.742   6.463  1.00 25.00           C
ATOM    109  CA  GLU   109      50.041  13.810   4.554  1.00 25.00           C
ATOM    110  CA  VAL   110      53.245  15.067   6.069  1.00 25.00           C
ATOM    111  CA  PHE   111      52.635  16.973   9.300  1.00 25.00           C
ATOM    112  CA  ALA   112      52.272  14.254  11.958  1.00 25.00           C
ATOM    113  CA  CYS   113      53.403  16.857  14.387  1.00 25.00           C
ATOM    114  CA  GLU   114      56.137  16.412  16.957  1.00 25.00           C
ATOM    115  CA  VAL   115      59.086  18.389  18.258  1.00 25.00           C
ATOM    116  CA  PHE   116      59.565  16.585  21.608  1.00 25.00           C
ATOM    117  CA  VAL   117      62.842  18.041  22.843  1.00 25.00           C
ATOM    118  CA  LEU   118      65.718  15.828  23.982  1.00 25.00           C
ATOM    119  CA  PRO   119      68.028  16.955  26.712  1.00 25.00           C
ATOM    120  CA  LEU   120      67.907  13.412  27.952  1.00 25.00           C
ATOM    121  CA  SER   121      68.130  13.271  31.744  1.00 25.00           C
ATOM    122  CA  GLY   122      64.838  11.384  31.981  1.00 25.00           C
ATOM    123  CA  GLU   123      62.940  13.331  29.305  1.00 25.00           C
ATOM    124  CA  ALA   124      60.408  13.717  26.570  1.00 25.00           C
ATOM    125  CA  PRO   125      59.765  17.399  27.217  1.00 25.00           C
ATOM    126  CA  GLU   126      56.411  18.491  25.694  1.00 25.00           C
ATOM    127  CA  ARG   127      53.176  19.147  23.719  1.00 25.00           C
ATOM    128  CA  ALA   128      51.375  18.462  20.441  1.00 25.00           C
ATOM    129  CA  PHE   129      48.820  18.834  17.652  1.00 25.00           C
ATOM    130  CA  ASP   130      47.275  21.574  19.738  1.00 25.00           C
ATOM    131  CA  GLU   131      44.129  23.687  19.540  1.00 25.00           C
ATOM    132  CA  GLN   132      40.643  22.527  18.562  1.00 25.00           C
ATOM    133  CA  THR   133      41.264  20.955  15.169  1.00 25.00           C
ATOM    134  CA  GLY   134      43.185  24.141  14.430  1.00 25.00           C
ATOM    135  CA  LEU   135      42.669  27.566  12.754  1.00 25.00           C
ATOM    136  CA  PHE   136      43.444  30.593  10.586  1.00 25.00           C
ATOM    137  CA  LEU   137      42.055  33.669   8.809  1.00 25.00           C
ATOM    138  CA  TRP   138      45.542  35.135   8.910  1.00 25.00           C
ATOM    139  CA  LEU   139      47.194  38.163   7.242  1.00 25.00           C
ATOM    140  CA  GLU   140      49.180  41.394   7.528  1.00 25.00           C
ATOM    141  CA  HIS   141      46.764  44.116   6.454  1.00 25.00           C
ATOM    142  CA  HIS   142      44.121  42.986   8.849  1.00 25.00           C
ATOM    143  CA  HIS   143      46.468  43.817  11.706  1.00 25.00           C
ATOM    144  CA  HIS   144      44.069  45.559  14.030  1.00 25.00           C
ATOM    145  CA  HIS   145      47.253  47.261  15.410  1.00 25.00           C
ATOM    146  CA  HIS   146      49.095  44.872  17.742  1.00 25.00           C
TER
END
