
#######################################################
#                                                     #
#                        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  123 (  123),  selected  123 , name T0307TS168_2-D1
# Molecule2: number of CA atoms  123 (  939),  selected  123 , name T0307_D1.pdb
# PARAMETERS: T0307TS168_2-D1.T0307_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    I      10      -       -           -
LGA    M      11      -       -           -
LGA    T      12      -       -           -
LGA    F      13      -       -           -
LGA    S      14      -       -           -
LGA    G      15      -       -           -
LGA    Q      16      -       -           -
LGA    E      17      -       -           -
LGA    L      18      -       -           -
LGA    T      19      I      10          4.554
LGA    A      20      -       -           -
LGA    I      21      M      11          5.119
LGA    I      22      T      12          1.899
LGA    K      23      F      13           #
LGA    M      24      -       -           -
LGA    A      25      -       -           -
LGA    K      26      -       -           -
LGA    S      27      -       -           -
LGA    M      28      -       -           -
LGA    V      29      -       -           -
LGA    M      30      -       -           -
LGA    A      31      -       -           -
LGA    D      32      -       -           -
LGA    G      33      -       -           -
LGA    K      34      -       -           -
LGA    I      35      -       -           -
LGA    K      36      -       -           -
LGA    P      37      -       -           -
LGA    A      38      -       -           -
LGA    E      39      -       -           -
LGA    I      40      -       -           -
LGA    A      41      -       -           -
LGA    V      42      -       -           -
LGA    M      43      -       -           -
LGA    T      44      -       -           -
LGA    R      45      -       -           -
LGA    E      46      -       -           -
LGA    F      47      -       -           -
LGA    M      48      -       -           -
LGA    R      49      -       -           -
LGA    F      50      -       -           -
LGA    G      51      -       -           -
LGA    I      52      -       -           -
LGA    L      53      -       -           -
LGA    Q      54      -       -           -
LGA    D      55      -       -           -
LGA    Q      56      -       -           -
LGA    V      57      -       -           -
LGA    D      58      -       -           -
LGA    L      59      -       -           -
LGA    L      60      S      14          0.821
LGA    L      61      G      15          0.286
LGA    K      62      Q      16          0.274
LGA    A      63      E      17          0.625
LGA    S      64      L      18          0.739
LGA    D      65      T      19          0.419
LGA    S      66      A      20          0.316
LGA    I      67      I      21          0.873
LGA    E      68      I      22          1.152
LGA    A      69      K      23          0.488
LGA    S      70      M      24          0.794
LGA    Q      71      A      25          1.212
LGA    A      72      K      26          0.844
LGA    V      73      S      27          0.579
LGA    A      74      M      28          1.536
LGA    L      75      V      29          1.645
LGA    I      76      M      30          0.292
LGA    A      77      A      31          1.640
LGA    R      78      D      32          4.219
LGA    M      79      G      33          3.391
LGA    D      80      K      34          4.785
LGA    E      81      -       -           -
LGA    E      82      I      35           #
LGA    R      83      K      36           -
LGA    K      84      P      37           -
LGA    K      85      A      38           -
LGA    Y      86      E      39           -
LGA    V      87      I      40           -
LGA    A      88      A      41           -
LGA    S      89      V      42           -
LGA    Y      90      M      43           -
LGA    L      91      T      44           -
LGA    G      92      R      45           -
LGA    V      93      E      46           -
LGA    I      94      F      47           -
LGA    M      95      M      48           -
LGA    A      96      R      49           -
LGA    S      97      F      50           -
LGA    D      98      G      51           -
LGA    G      99      I      52           -
LGA    D     100      L      53           -
LGA    I     101      Q      54           -
LGA    -       -      D      55           -
LGA    -       -      Q      56           -
LGA    -       -      V      57           -
LGA    -       -      D      58           -
LGA    -       -      L      59           -
LGA    -       -      L      60           -
LGA    -       -      L      61           -
LGA    -       -      K      62           -
LGA    -       -      A      63           -
LGA    -       -      S      64           -
LGA    -       -      D      65           -
LGA    -       -      S      66           -
LGA    -       -      I      67           -
LGA    -       -      E      68           -
LGA    -       -      A      69           -
LGA    -       -      S      70           -
LGA    -       -      Q      71           -
LGA    -       -      A      72           -
LGA    -       -      V      73           -
LGA    -       -      A      74           -
LGA    -       -      L      75           -
LGA    -       -      I      76           -
LGA    -       -      A      77           -
LGA    -       -      R      78           -
LGA    -       -      M      79           -
LGA    -       -      D      80           -
LGA    -       -      E      81           -
LGA    -       -      E      82           -
LGA    -       -      R      83           -
LGA    -       -      K      84           -
LGA    -       -      K      85           -
LGA    -       -      Y      86           -
LGA    -       -      V      87           -
LGA    -       -      A      88           -
LGA    -       -      S      89           -
LGA    -       -      Y      90           -
LGA    -       -      L      91           -
LGA    -       -      G      92           -
LGA    -       -      V      93           -
LGA    -       -      I      94           -
LGA    -       -      M      95           -
LGA    -       -      A      96           -
LGA    -       -      S      97           -
LGA    -       -      D      98           -
LGA    -       -      G      99           -
LGA    -       -      D     100           -
LGA    -       -      I     101           -
LGA    -       -      D     102           -
LGA    D     102      D     103          5.606
LGA    D     103      N     104          1.038
LGA    N     104      E     105          2.297
LGA    E     105      L     106          2.019
LGA    L     106      A     107          1.029
LGA    A     107      L     108          1.374
LGA    L     108      W     109          1.135
LGA    W     109      T     110          1.531
LGA    T     110      L     111          1.865
LGA    L     111      I     112          1.040
LGA    I     112      S     113          0.977
LGA    S     113      T     114          2.312
LGA    T     114      L     115          2.175
LGA    L     115      C     116          1.263
LGA    C     116      G     117          3.372
LGA    G     117      L     118           -
LGA    L     118      -       -           -
LGA    P     119      -       -           -
LGA    T     120      -       -           -
LGA    M     121      -       -           -
LGA    T     122      -       -           -
LGA    V     123      -       -           -
LGA    M     124      -       -           -
LGA    E     125      -       -           -
LGA    A     126      P     119          1.595
LGA    I     127      T     120          3.775
LGA    N     128      -       -           -
LGA    N     129      -       -           -
LGA    M     130      -       -           -
LGA    K     131      M     121          1.540
LGA    N     132      T     122          2.371
LGA    -       -      V     123           -
LGA    -       -      M     124           -
LGA    -       -      E     125           -
LGA    -       -      A     126           -
LGA    -       -      I     127           -
LGA    -       -      N     128           -
LGA    -       -      N     129           -
LGA    -       -      M     130           -
LGA    -       -      K     131           -
LGA    -       -      N     132           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  123  123    5.0     43    2.26     6.98     26.061     1.821

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.675736 * X  +  -0.713782 * Y  +   0.184109 * Z  +  17.345398
  Y_new =  -0.666311 * X  +   0.484618 * Y  +  -0.566722 * Z  +   8.363753
  Z_new =   0.315293 * X  +  -0.505629 * Y  +  -0.803075 * Z  +  34.150272 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.579681    0.561912  [ DEG:  -147.8048     32.1952 ]
  Theta =  -0.320766   -2.820827  [ DEG:   -18.3785   -161.6215 ]
  Phi   =  -2.363217    0.778376  [ DEG:  -135.4024     44.5976 ]
 
# 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: T0307TS168_2-D1                               
REMARK     2: T0307_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0307TS168_2-D1.T0307_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  123  123   5.0   43   2.26    6.98  26.061
REMARK  ---------------------------------------------------------- 
MOLECULE T0307TS168_2-D1
PFRMAT TS
TARGET T0307
MODEL 2
PARENT N/A
ATOM     10  CA  ILE    10      -3.521   7.976  33.347  1.00 25.00           C
ATOM     11  CA  MET    11      -0.966   8.679  30.641  1.00 25.00           C
ATOM     12  CA  THR    12       0.025  11.769  28.712  1.00 25.00           C
ATOM     13  CA  PHE    13       3.687  10.630  28.551  1.00 25.00           C
ATOM     14  CA  SER    14       4.786  14.291  29.080  1.00 25.00           C
ATOM     15  CA  GLY    15       7.884  14.642  31.326  1.00 25.00           C
ATOM     16  CA  GLN    16       5.847  12.632  33.873  1.00 25.00           C
ATOM     17  CA  GLU    17       8.648  10.029  34.094  1.00 25.00           C
ATOM     18  CA  LEU    18      11.223  12.810  34.648  1.00 25.00           C
ATOM     19  CA  THR    19       9.039  14.314  37.412  1.00 25.00           C
ATOM     20  CA  ALA    20       8.734  10.878  39.075  1.00 25.00           C
ATOM     21  CA  ILE    21      12.534  10.434  38.912  1.00 25.00           C
ATOM     22  CA  ILE    22      13.031  13.891  40.483  1.00 25.00           C
ATOM     23  CA  LYS    23      10.569  13.001  43.278  1.00 25.00           C
ATOM     24  CA  MET    24      12.438   9.720  43.914  1.00 25.00           C
ATOM     25  CA  ALA    25      15.762  11.616  44.075  1.00 25.00           C
ATOM     26  CA  LYS    26      14.249  14.105  46.562  1.00 25.00           C
ATOM     27  CA  SER    27      12.962  11.211  48.713  1.00 25.00           C
ATOM     28  CA  MET    28      16.433   9.593  48.657  1.00 25.00           C
ATOM     29  CA  VAL    29      18.026  12.916  49.702  1.00 25.00           C
ATOM     30  CA  MET    30      15.513  13.247  52.572  1.00 25.00           C
ATOM     31  CA  ALA    31      16.467  13.742  56.252  1.00 25.00           C
ATOM     32  CA  ASP    32      16.617  15.264  59.712  1.00 25.00           C
ATOM     33  CA  GLY    33      16.661  17.075  63.063  1.00 25.00           C
ATOM     34  CA  LYS    34      17.176  19.236  66.181  1.00 25.00           C
ATOM     35  CA  ILE    35      17.276  21.352  69.334  1.00 25.00           C
ATOM     36  CA  LYS    36      17.138  24.096  72.018  1.00 25.00           C
ATOM     37  CA  PRO    37      16.508  27.637  73.299  1.00 25.00           C
ATOM     38  CA  ALA    38      13.449  27.483  71.000  1.00 25.00           C
ATOM     39  CA  GLU    39      15.093  29.977  68.604  1.00 25.00           C
ATOM     40  CA  ILE    40      18.297  27.879  68.579  1.00 25.00           C
ATOM     41  CA  ALA    41      16.256  24.726  67.828  1.00 25.00           C
ATOM     42  CA  VAL    42      14.476  26.532  64.957  1.00 25.00           C
ATOM     43  CA  MET    43      17.851  27.671  63.549  1.00 25.00           C
ATOM     44  CA  THR    44      19.174  24.083  63.752  1.00 25.00           C
ATOM     45  CA  ARG    45      16.055  22.804  61.933  1.00 25.00           C
ATOM     46  CA  GLU    46      16.531  25.449  59.206  1.00 25.00           C
ATOM     47  CA  PHE    47      20.200  24.423  58.815  1.00 25.00           C
ATOM     48  CA  MET    48      19.166  20.747  58.522  1.00 25.00           C
ATOM     49  CA  ARG    49      16.572  21.664  55.858  1.00 25.00           C
ATOM     50  CA  PHE    50      19.222  23.634  53.920  1.00 25.00           C
ATOM     51  CA  GLY    51      21.611  20.647  54.102  1.00 25.00           C
ATOM     52  CA  ILE    52      18.846  18.327  52.820  1.00 25.00           C
ATOM     53  CA  LEU    53      18.133  20.734  49.928  1.00 25.00           C
ATOM     54  CA  GLN    54      21.862  20.831  49.057  1.00 25.00           C
ATOM     55  CA  ASP    55      21.995  17.004  49.095  1.00 25.00           C
ATOM     56  CA  GLN    56      18.935  16.849  46.797  1.00 25.00           C
ATOM     57  CA  VAL    57      20.580  19.344  44.400  1.00 25.00           C
ATOM     58  CA  ASP    58      23.784  17.246  44.375  1.00 25.00           C
ATOM     59  CA  LEU    59      21.743  14.093  43.623  1.00 25.00           C
ATOM     60  CA  LEU    60      19.963  15.900  40.754  1.00 25.00           C
ATOM     61  CA  LEU    61      23.338  17.037  39.345  1.00 25.00           C
ATOM     62  CA  LYS    62      24.661  13.449  39.548  1.00 25.00           C
ATOM     63  CA  ALA    63      21.542  12.171  37.729  1.00 25.00           C
ATOM     64  CA  SER    64      22.018  14.816  35.003  1.00 25.00           C
ATOM     65  CA  ASP    65      25.687  13.789  34.611  1.00 25.00           C
ATOM     66  CA  SER    66      24.651  10.114  34.319  1.00 25.00           C
ATOM     67  CA  ILE    67      22.058  11.030  31.654  1.00 25.00           C
ATOM     68  CA  GLU    68      24.709  13.001  29.717  1.00 25.00           C
ATOM     69  CA  ALA    69      27.098  10.013  29.897  1.00 25.00           C
ATOM     70  CA  SER    70      24.333   7.693  28.616  1.00 25.00           C
ATOM     71  CA  GLN    71      23.620  10.101  25.724  1.00 25.00           C
ATOM     72  CA  ALA    72      27.348  10.197  24.853  1.00 25.00           C
ATOM     73  CA  VAL    73      27.481   6.371  24.892  1.00 25.00           C
ATOM     74  CA  ALA    74      24.422   6.216  22.592  1.00 25.00           C
ATOM     75  CA  LEU    75      26.067   8.710  20.196  1.00 25.00           C
ATOM     76  CA  ILE    76      29.271   6.611  20.171  1.00 25.00           C
ATOM     77  CA  ALA    77      27.229   3.459  19.420  1.00 25.00           C
ATOM     78  CA  ARG    78      25.449   5.267  16.549  1.00 25.00           C
ATOM     79  CA  MET    79      28.825   6.404  15.141  1.00 25.00           C
ATOM     80  CA  ASP    80      30.147   2.816  15.344  1.00 25.00           C
ATOM     81  CA  GLU    81      27.028   1.537  13.525  1.00 25.00           C
ATOM     82  CA  GLU    82      27.505   4.183  10.798  1.00 25.00           C
ATOM     83  CA  ARG    83      31.173   3.156  10.408  1.00 25.00           C
ATOM     84  CA  LYS    84      30.138  -0.519  10.115  1.00 25.00           C
ATOM     85  CA  LYS    85      27.544   0.397   7.450  1.00 25.00           C
ATOM     86  CA  TYR    86      30.196   2.368   5.513  1.00 25.00           C
ATOM     87  CA  VAL    87      32.584  -0.620   5.693  1.00 25.00           C
ATOM     88  CA  ALA    88      29.819  -2.939   4.412  1.00 25.00           C
ATOM     89  CA  SER    89      29.106  -0.532   1.519  1.00 25.00           C
ATOM     90  CA  TYR    90      32.835  -0.436   0.649  1.00 25.00           C
ATOM     91  CA  LEU    91      32.968  -4.263   0.688  1.00 25.00           C
ATOM     92  CA  GLY    92      29.909  -4.417  -1.612  1.00 25.00           C
ATOM     93  CA  VAL    93      31.554  -1.923  -4.007  1.00 25.00           C
ATOM     94  CA  ILE    94      34.757  -4.022  -4.033  1.00 25.00           C
ATOM     95  CA  MET    95      32.715  -7.174  -4.785  1.00 25.00           C
ATOM     96  CA  ALA    96      30.936  -5.367  -7.655  1.00 25.00           C
ATOM     97  CA  SER    97      27.816  -5.523  -5.490  1.00 25.00           C
ATOM     98  CA  ASP    98      26.024  -5.234  -2.201  1.00 25.00           C
ATOM     99  CA  GLY    99      24.788  -4.789   1.329  1.00 25.00           C
ATOM    100  CA  ASP   100      23.674  -4.525   4.958  1.00 25.00           C
ATOM    101  CA  ILE   101      22.807  -3.781   8.588  1.00 25.00           C
ATOM    102  CA  ASP   102      21.907  -3.138  12.178  1.00 25.00           C
ATOM    103  CA  ASP   103      21.013  -2.361  15.836  1.00 25.00           C
ATOM    104  CA  ASN   104      21.522   0.949  17.692  1.00 25.00           C
ATOM    105  CA  GLU   105      17.859   0.915  18.809  1.00 25.00           C
ATOM    106  CA  LEU   106      18.246  -2.686  20.053  1.00 25.00           C
ATOM    107  CA  ALA   107      21.400  -1.704  21.992  1.00 25.00           C
ATOM    108  CA  LEU   108      19.542   1.255  23.563  1.00 25.00           C
ATOM    109  CA  TRP   109      16.659  -1.058  24.567  1.00 25.00           C
ATOM    110  CA  THR   110      19.143  -3.515  26.136  1.00 25.00           C
ATOM    111  CA  LEU   111      20.789  -0.651  28.074  1.00 25.00           C
ATOM    112  CA  ILE   112      17.358   0.510  29.320  1.00 25.00           C
ATOM    113  CA  SER   113      16.529  -3.059  30.436  1.00 25.00           C
ATOM    114  CA  THR   114      19.872  -3.282  32.290  1.00 25.00           C
ATOM    115  CA  LEU   115      19.165   0.061  34.019  1.00 25.00           C
ATOM    116  CA  CYS   116      18.467  -0.932  37.650  1.00 25.00           C
ATOM    117  CA  GLY   117      19.457  -2.487  41.028  1.00 25.00           C
ATOM    118  CA  LEU   118      16.762  -0.231  42.408  1.00 25.00           C
ATOM    119  CA  PRO   119      15.981  -3.030  44.947  1.00 25.00           C
ATOM    120  CA  THR   120      13.367  -4.065  42.338  1.00 25.00           C
ATOM    121  CA  MET   121      14.291  -3.740  38.720  1.00 25.00           C
ATOM    122  CA  THR   122      10.550  -2.957  38.289  1.00 25.00           C
ATOM    123  CA  VAL   123       9.564  -5.477  35.579  1.00 25.00           C
ATOM    124  CA  MET   124       6.483  -3.376  34.711  1.00 25.00           C
ATOM    125  CA  GLU   125       8.662  -0.235  34.472  1.00 25.00           C
ATOM    126  CA  ALA   126      11.110  -2.078  32.174  1.00 25.00           C
ATOM    127  CA  ILE   127       8.204  -3.229  29.961  1.00 25.00           C
ATOM    128  CA  ASN   128       6.888   0.364  29.778  1.00 25.00           C
ATOM    129  CA  ASN   129      10.375   1.616  28.805  1.00 25.00           C
ATOM    130  CA  MET   130      10.602  -1.061  26.077  1.00 25.00           C
ATOM    131  CA  LYS   131       7.494   0.711  24.790  1.00 25.00           C
ATOM    132  CA  ASN   132       9.543   2.540  22.158  1.00 25.00           C
TER
END
