
#######################################################
#                                                     #
#                        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  141 (  141),  selected  141 , name T0357TS393_1
# Molecule2: number of CA atoms  132 ( 2030),  selected  132 , name T0357.pdb
# PARAMETERS: T0357TS393_1.T0357.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      V       2           -
LGA    V       2      K       3           -
LGA    -       -      F       4           -
LGA    -       -      A       5           -
LGA    -       -      C       6           -
LGA    -       -      R       7           -
LGA    -       -      A       8           -
LGA    -       -      I       9           -
LGA    -       -      T      10           -
LGA    -       -      R      11           -
LGA    -       -      G      12           -
LGA    -       -      R      13           -
LGA    -       -      A      14           -
LGA    K       3      E      15          4.880
LGA    F       4      -       -           -
LGA    A       5      G      16          3.559
LGA    C       6      E      17          2.248
LGA    R       7      A      18          3.104
LGA    A       8      L      19          0.789
LGA    I       9      V      20          4.247
LGA    T      10      -       -           -
LGA    R      11      -       -           -
LGA    G      12      -       -           -
LGA    R      13      -       -           -
LGA    A      14      -       -           -
LGA    E      15      -       -           -
LGA    G      16      -       -           -
LGA    E      17      -       -           -
LGA    A      18      T      21           #
LGA    L      19      K      22           -
LGA    -       -      E      23           -
LGA    -       -      Y      24           -
LGA    V      20      I      25          3.926
LGA    T      21      S      26          1.750
LGA    K      22      F      27           -
LGA    E      23      L      28           -
LGA    Y      24      G      29           -
LGA    I      25      G      30           -
LGA    -       -      I      31           -
LGA    -       -      D      32           -
LGA    -       -      K      33           -
LGA    -       -      E      34           -
LGA    -       -      T      35           -
LGA    -       -      G      36           -
LGA    -       -      I      37           -
LGA    -       -      V      38           -
LGA    -       -      K      39           -
LGA    S      26      E      40           #
LGA    F      27      D      41          1.015
LGA    L      28      -       -           -
LGA    G      29      -       -           -
LGA    G      30      C      42          4.733
LGA    I      31      E      43          0.809
LGA    D      32      I      44           #
LGA    K      33      K      45           -
LGA    E      34      G      46           -
LGA    T      35      E      47           -
LGA    G      36      S      48           -
LGA    -       -      V      49           -
LGA    -       -      A      50           -
LGA    -       -      G      51           -
LGA    -       -      R      52           -
LGA    -       -      I      53           -
LGA    I      37      L      54          4.639
LGA    V      38      V      55          4.530
LGA    K      39      F      56          4.333
LGA    E      40      P      57          3.697
LGA    D      41      -       -           -
LGA    C      42      -       -           -
LGA    E      43      -       -           -
LGA    I      44      -       -           -
LGA    K      45      -       -           -
LGA    G      46      -       -           -
LGA    E      47      -       -           -
LGA    S      48      -       -           -
LGA    V      49      -       -           -
LGA    A      50      -       -           -
LGA    G      51      -       -           -
LGA    R      52      -       -           -
LGA    I      53      -       -           -
LGA    L      54      -       -           -
LGA    V      55      G      58          1.856
LGA    F      56      G      59          2.415
LGA    P      57      K      60          3.293
LGA    G      58      G      61          3.092
LGA    G      59      S      62          5.388
LGA    K      60      T      63           -
LGA    G      61      V      64           -
LGA    S      62      G      65           -
LGA    T      63      S      66           -
LGA    V      64      Y      67           -
LGA    G      65      V      68           -
LGA    S      66      -       -           -
LGA    Y      67      L      69           #
LGA    V      68      L      70           -
LGA    L      69      N      71           -
LGA    L      70      -       -           -
LGA    N      71      L      72          3.109
LGA    L      72      R      73           -
LGA    R      73      -       -           -
LGA    K      74      -       -           -
LGA    N      75      K      74          2.893
LGA    G      76      N      75           #
LGA    V      77      G      76          1.034
LGA    A      78      V      77          3.172
LGA    P      79      A      78          3.828
LGA    K      80      P      79          3.022
LGA    A      81      -       -           -
LGA    I      82      -       -           -
LGA    I      83      -       -           -
LGA    N      84      -       -           -
LGA    K      85      -       -           -
LGA    K      86      -       -           -
LGA    T      87      -       -           -
LGA    E      88      -       -           -
LGA    T      89      -       -           -
LGA    I      90      -       -           -
LGA    I      91      -       -           -
LGA    A      92      -       -           -
LGA    V      93      -       -           -
LGA    G      94      -       -           -
LGA    A      95      -       -           -
LGA    A      96      -       -           -
LGA    M      97      -       -           -
LGA    A      98      -       -           -
LGA    E      99      K      80          1.979
LGA    I     100      A      81          2.031
LGA    P     101      I      82          5.277
LGA    L     102      I      83           #
LGA    -       -      N      84           -
LGA    -       -      K      85           -
LGA    -       -      K      86           -
LGA    V     103      T      87          3.109
LGA    E     104      E      88          1.381
LGA    V     105      T      89          2.385
LGA    R     106      I      90          2.371
LGA    D     107      I      91           #
LGA    E     108      -       -           -
LGA    K     109      -       -           -
LGA    F     110      A      92          3.613
LGA    F     111      V      93           -
LGA    E     112      G      94           -
LGA    -       -      A      95           -
LGA    -       -      A      96           -
LGA    -       -      M      97           -
LGA    -       -      A      98           -
LGA    -       -      E      99           -
LGA    -       -      I     100           -
LGA    -       -      P     101           -
LGA    A     113      L     102          2.960
LGA    V     114      V     103          3.358
LGA    K     115      E     104          2.100
LGA    T     116      V     105           #
LGA    G     117      R     106           -
LGA    D     118      D     107           -
LGA    -       -      E     108           -
LGA    -       -      K     109           -
LGA    -       -      F     110           -
LGA    R     119      F     111           #
LGA    V     120      E     112           -
LGA    V     121      A     113           -
LGA    V     122      -       -           -
LGA    N     123      -       -           -
LGA    A     124      -       -           -
LGA    D     125      -       -           -
LGA    E     126      -       -           -
LGA    G     127      -       -           -
LGA    Y     128      -       -           -
LGA    V     129      -       -           -
LGA    E     130      V     114          4.586
LGA    L     131      K     115          2.568
LGA    I     132      T     116          1.738
LGA    E     133      G     117          4.700
LGA    L     134      D     118           -
LGA    E     135      R     119           -
LGA    H     136      V     120           -
LGA    H     137      V     121           -
LGA    H     138      V     122           -
LGA    H     139      N     123           -
LGA    H     140      A     124           -
LGA    H     141      D     125           -
LGA    -       -      E     126           -
LGA    -       -      G     127           -
LGA    -       -      Y     128           -
LGA    -       -      V     129           -
LGA    -       -      E     130           -
LGA    -       -      L     131           -
LGA    -       -      I     132           -
LGA    -       -      E     133           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  141  132    5.0     41    3.30     9.76     17.154     1.204

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.446750 * X  +  -0.542177 * Y  +   0.711660 * Z  +  -1.828077
  Y_new =   0.849034 * X  +  -0.507711 * Y  +   0.146189 * Z  +  -0.857311
  Z_new =   0.282057 * X  +   0.669533 * Y  +   0.687146 * Z  +  -4.044171 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.772416   -2.369176  [ DEG:    44.2562   -135.7438 ]
  Theta =  -0.285938   -2.855655  [ DEG:   -16.3830   -163.6170 ]
  Phi   =   2.055172   -1.086420  [ DEG:   117.7527    -62.2473 ]
 
# 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: T0357TS393_1                                  
REMARK     2: T0357.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0357TS393_1.T0357.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  141  132   5.0   41   3.30    9.76  17.154
REMARK  ---------------------------------------------------------- 
MOLECULE T0357TS393_1
PFRMAT TS
TARGET T0357
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1      11.267   0.638 -21.913  1.00 25.00           C
ATOM      2  CA  VAL     2       9.528   0.199 -18.588  1.00 25.00           C
ATOM      3  CA  LYS     3       9.071  -1.230 -15.078  1.00 25.00           C
ATOM      4  CA  PHE     4       5.841  -3.234 -15.083  1.00 25.00           C
ATOM      5  CA  ALA     5       2.530  -2.247 -13.607  1.00 25.00           C
ATOM      6  CA  CYS     6       3.483   0.901 -11.770  1.00 25.00           C
ATOM      7  CA  ARG     7       0.467  -0.210  -9.733  1.00 25.00           C
ATOM      8  CA  ALA     8      -3.215   0.480  -9.063  1.00 25.00           C
ATOM      9  CA  ILE     9      -6.476   0.684 -10.914  1.00 25.00           C
ATOM     10  CA  THR    10      -8.411  -1.599 -13.329  1.00 25.00           C
ATOM     11  CA  ARG    11      -6.767  -3.528 -16.201  1.00 25.00           C
ATOM     12  CA  GLY    12      -6.836  -7.370 -15.992  1.00 25.00           C
ATOM     13  CA  ARG    13      -3.122  -7.629 -16.621  1.00 25.00           C
ATOM     14  CA  ALA    14       0.020  -6.652 -14.604  1.00 25.00           C
ATOM     15  CA  GLU    15      -2.232  -4.065 -12.886  1.00 25.00           C
ATOM     16  CA  GLY    16      -3.055  -6.688 -10.339  1.00 25.00           C
ATOM     17  CA  GLU    17      -6.202  -4.524  -9.879  1.00 25.00           C
ATOM     18  CA  ALA    18      -5.206  -4.014  -6.246  1.00 25.00           C
ATOM     19  CA  LEU    19      -4.898  -4.416  -2.474  1.00 25.00           C
ATOM     20  CA  VAL    20      -6.607  -3.400   0.701  1.00 25.00           C
ATOM     21  CA  THR    21      -8.818  -2.490   3.636  1.00 25.00           C
ATOM     22  CA  LYS    22     -12.649  -2.455   3.637  1.00 25.00           C
ATOM     23  CA  GLU    23     -16.452  -2.540   3.269  1.00 25.00           C
ATOM     24  CA  TYR    24     -17.358   1.186   2.814  1.00 25.00           C
ATOM     25  CA  ILE    25     -15.777   0.626  -0.610  1.00 25.00           C
ATOM     26  CA  SER    26     -15.016  -1.163  -3.882  1.00 25.00           C
ATOM     27  CA  PHE    27     -14.999  -4.916  -4.361  1.00 25.00           C
ATOM     28  CA  LEU    28     -18.563  -4.609  -3.026  1.00 25.00           C
ATOM     29  CA  GLY    29     -19.686  -2.817  -6.170  1.00 25.00           C
ATOM     30  CA  GLY    30     -17.546  -3.158  -9.316  1.00 25.00           C
ATOM     31  CA  ILE    31     -14.121  -1.471  -8.804  1.00 25.00           C
ATOM     32  CA  ASP    32     -16.106   1.809  -8.999  1.00 25.00           C
ATOM     33  CA  LYS    33     -15.095   3.905  -5.977  1.00 25.00           C
ATOM     34  CA  GLU    34     -11.551   2.678  -6.813  1.00 25.00           C
ATOM     35  CA  THR    35      -8.172   1.048  -6.185  1.00 25.00           C
ATOM     36  CA  GLY    36      -8.143  -0.501  -2.703  1.00 25.00           C
ATOM     37  CA  ILE    37      -4.613   0.745  -2.211  1.00 25.00           C
ATOM     38  CA  VAL    38      -3.904   3.189   0.563  1.00 25.00           C
ATOM     39  CA  LYS    39      -4.615   6.855   1.201  1.00 25.00           C
ATOM     40  CA  GLU    40      -7.368   9.423   1.441  1.00 25.00           C
ATOM     41  CA  ASP    41      -6.907  11.951  -1.417  1.00 25.00           C
ATOM     42  CA  CYS    42      -3.100  11.496  -1.603  1.00 25.00           C
ATOM     43  CA  GLU    43      -3.200  15.232  -2.313  1.00 25.00           C
ATOM     44  CA  ILE    44      -0.261  14.355  -4.612  1.00 25.00           C
ATOM     45  CA  LYS    45       0.785  17.983  -4.095  1.00 25.00           C
ATOM     46  CA  GLY    46       3.237  17.566  -6.936  1.00 25.00           C
ATOM     47  CA  GLU    47       5.569  15.722  -4.485  1.00 25.00           C
ATOM     48  CA  SER    48       5.515  11.961  -5.013  1.00 25.00           C
ATOM     49  CA  VAL    49       5.680   8.177  -4.625  1.00 25.00           C
ATOM     50  CA  ALA    50       2.865   8.861  -2.082  1.00 25.00           C
ATOM     51  CA  GLY    51       0.170   8.049  -4.651  1.00 25.00           C
ATOM     52  CA  ARG    52      -3.367   6.745  -4.294  1.00 25.00           C
ATOM     53  CA  ILE    53      -6.645   5.253  -3.112  1.00 25.00           C
ATOM     54  CA  LEU    54      -8.847   3.932  -0.323  1.00 25.00           C
ATOM     55  CA  VAL    55      -8.162   2.781   3.213  1.00 25.00           C
ATOM     56  CA  PHE    56      -7.860   1.817   6.892  1.00 25.00           C
ATOM     57  CA  PRO    57      -8.448  -1.202   9.082  1.00 25.00           C
ATOM     58  CA  GLY    58      -9.000  -4.937   8.318  1.00 25.00           C
ATOM     59  CA  GLY    59      -8.367  -7.266   5.395  1.00 25.00           C
ATOM     60  CA  LYS    60      -6.816  -9.986   3.170  1.00 25.00           C
ATOM     61  CA  GLY    61      -9.367 -12.344   1.523  1.00 25.00           C
ATOM     62  CA  SER    62     -11.250 -10.604  -1.242  1.00 25.00           C
ATOM     63  CA  THR    63      -9.023  -7.510  -0.860  1.00 25.00           C
ATOM     64  CA  VAL    64      -9.113  -5.978  -4.303  1.00 25.00           C
ATOM     65  CA  GLY    65      -9.747  -9.317  -6.070  1.00 25.00           C
ATOM     66  CA  SER    66      -6.312  -9.106  -7.752  1.00 25.00           C
ATOM     67  CA  TYR    67      -4.672  -8.388  -4.367  1.00 25.00           C
ATOM     68  CA  VAL    68      -6.475 -11.394  -2.825  1.00 25.00           C
ATOM     69  CA  LEU    69      -5.289 -13.616  -5.711  1.00 25.00           C
ATOM     70  CA  LEU    70      -1.697 -12.384  -5.214  1.00 25.00           C
ATOM     71  CA  ASN    71      -1.930 -13.137  -1.467  1.00 25.00           C
ATOM     72  CA  LEU    72      -3.241 -16.653  -2.229  1.00 25.00           C
ATOM     73  CA  ARG    73      -0.352 -17.225  -4.678  1.00 25.00           C
ATOM     74  CA  LYS    74       2.156 -16.057  -2.030  1.00 25.00           C
ATOM     75  CA  ASN    75       4.825 -17.837  -4.041  1.00 25.00           C
ATOM     76  CA  GLY    76       7.554 -15.176  -4.301  1.00 25.00           C
ATOM     77  CA  VAL    77       4.776 -13.287  -6.154  1.00 25.00           C
ATOM     78  CA  ALA    78       3.445 -10.646  -8.587  1.00 25.00           C
ATOM     79  CA  PRO    79       2.565  -7.077  -7.596  1.00 25.00           C
ATOM     80  CA  LYS    80      -0.279  -4.554  -7.215  1.00 25.00           C
ATOM     81  CA  ALA    81      -0.689  -2.186  -4.193  1.00 25.00           C
ATOM     82  CA  ILE    82      -0.152  -4.067  -0.912  1.00 25.00           C
ATOM     83  CA  ILE    83      -1.955  -1.704   1.493  1.00 25.00           C
ATOM     84  CA  ASN    84      -3.928  -0.243   4.398  1.00 25.00           C
ATOM     85  CA  LYS    85      -3.816  -2.341   7.568  1.00 25.00           C
ATOM     86  CA  LYS    86      -2.759  -5.582   9.188  1.00 25.00           C
ATOM     87  CA  THR    87      -3.084  -7.399   5.912  1.00 25.00           C
ATOM     88  CA  GLU    88      -3.330 -10.632   7.991  1.00 25.00           C
ATOM     89  CA  THR    89       0.386 -10.064   7.845  1.00 25.00           C
ATOM     90  CA  ILE    90       0.663 -12.758   5.136  1.00 25.00           C
ATOM     91  CA  ILE    91      -0.695 -10.306   2.525  1.00 25.00           C
ATOM     92  CA  ALA    92       1.850  -7.671   3.642  1.00 25.00           C
ATOM     93  CA  VAL    93       4.673 -10.244   3.366  1.00 25.00           C
ATOM     94  CA  GLY    94       3.498 -11.192  -0.154  1.00 25.00           C
ATOM     95  CA  ALA    95       3.433  -7.496  -1.155  1.00 25.00           C
ATOM     96  CA  ALA    96       6.981  -7.038   0.214  1.00 25.00           C
ATOM     97  CA  MET    97       8.163 -10.099  -1.760  1.00 25.00           C
ATOM     98  CA  ALA    98       6.555  -8.701  -4.942  1.00 25.00           C
ATOM     99  CA  GLU    99       6.609  -4.946  -4.365  1.00 25.00           C
ATOM    100  CA  ILE   100       4.621  -2.698  -2.003  1.00 25.00           C
ATOM    101  CA  PRO   101       4.701  -2.816   1.730  1.00 25.00           C
ATOM    102  CA  LEU   102       2.862  -2.149   4.964  1.00 25.00           C
ATOM    103  CA  VAL   103       0.180   0.285   6.050  1.00 25.00           C
ATOM    104  CA  GLU   104      -1.102   1.478   9.462  1.00 25.00           C
ATOM    105  CA  VAL   105       0.598   0.526  12.717  1.00 25.00           C
ATOM    106  CA  ARG   106       1.425  -2.808  11.082  1.00 25.00           C
ATOM    107  CA  ASP   107       4.994  -3.484  12.011  1.00 25.00           C
ATOM    108  CA  GLU   108       7.848  -2.729   9.687  1.00 25.00           C
ATOM    109  CA  LYS   109       7.908   1.046  10.137  1.00 25.00           C
ATOM    110  CA  PHE   110       4.262   0.878   8.975  1.00 25.00           C
ATOM    111  CA  PHE   111       3.978   4.688   9.236  1.00 25.00           C
ATOM    112  CA  GLU   112       7.194   5.091   7.195  1.00 25.00           C
ATOM    113  CA  ALA   113       5.832   2.700   4.531  1.00 25.00           C
ATOM    114  CA  VAL   114       2.561   4.687   4.385  1.00 25.00           C
ATOM    115  CA  LYS   115       4.530   7.947   3.987  1.00 25.00           C
ATOM    116  CA  THR   116       8.029   7.262   2.672  1.00 25.00           C
ATOM    117  CA  GLY   117       7.358   5.156  -0.437  1.00 25.00           C
ATOM    118  CA  ASP   118       3.874   3.953  -1.114  1.00 25.00           C
ATOM    119  CA  ARG   119       0.247   4.856  -0.466  1.00 25.00           C
ATOM    120  CA  VAL   120      -0.308   2.802  -3.664  1.00 25.00           C
ATOM    121  CA  VAL   121       2.656   0.643  -4.826  1.00 25.00           C
ATOM    122  CA  VAL   122       4.205  -1.684  -7.403  1.00 25.00           C
ATOM    123  CA  ASN   123       5.728  -3.965 -10.035  1.00 25.00           C
ATOM    124  CA  ALA   124       8.960  -2.940  -8.377  1.00 25.00           C
ATOM    125  CA  ASP   125      11.874  -0.581  -7.779  1.00 25.00           C
ATOM    126  CA  GLU   126      11.912   1.291  -4.469  1.00 25.00           C
ATOM    127  CA  GLY   127       8.168   0.740  -4.678  1.00 25.00           C
ATOM    128  CA  TYR   128       6.100   3.426  -6.381  1.00 25.00           C
ATOM    129  CA  VAL   129       2.829   4.382  -8.171  1.00 25.00           C
ATOM    130  CA  GLU   130      -0.917   4.933  -8.523  1.00 25.00           C
ATOM    131  CA  LEU   131      -4.542   5.481  -9.573  1.00 25.00           C
ATOM    132  CA  ILE   132      -4.802   5.120 -13.331  1.00 25.00           C
ATOM    133  CA  GLU   133      -5.844   7.010 -16.496  1.00 25.00           C
ATOM    134  CA  LEU   134      -6.605   9.178 -19.528  1.00 25.00           C
ATOM    135  CA  GLU   135      -7.526  11.645 -22.259  1.00 25.00           C
ATOM    136  CA  HIS   136      -5.272  14.429 -23.342  1.00 25.00           C
ATOM    137  CA  HIS   137      -4.604  12.151 -26.297  1.00 25.00           C
ATOM    138  CA  HIS   138      -1.059  12.950 -27.284  1.00 25.00           C
ATOM    139  CA  HIS   139      -1.331  11.099 -30.667  1.00 25.00           C
ATOM    140  CA  HIS   140       0.782  13.899 -32.054  1.00 25.00           C
ATOM    141  CA  HIS   141      -0.751  16.248 -34.598  1.00 25.00           C
TER
END
