
#######################################################
#                                                     #
#                        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  149 (  149),  selected  149 , name T0331TS168_3
# Molecule2: number of CA atoms  139 ( 1101),  selected  139 , name T0331.pdb
# PARAMETERS: T0331TS168_3.T0331.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    E       2      E       2           -
LGA    L       3      L       3           -
LGA    K       4      K       4           -
LGA    D       5      D       5           -
LGA    I       6      I       6           -
LGA    M       7      -       -           -
LGA    H       8      -       -           -
LGA    I       9      -       -           -
LGA    L      10      -       -           -
LGA    E      11      -       -           -
LGA    D      12      -       -           -
LGA    M      13      -       -           -
LGA    K      14      -       -           -
LGA    V      15      -       -           -
LGA    G      16      -       -           -
LGA    V      17      -       -           -
LGA    F      18      -       -           -
LGA    A      19      -       -           -
LGA    T      20      -       -           -
LGA    L      21      -       -           -
LGA    D      22      M       7           #
LGA    -       -      H       8           -
LGA    -       -      I       9           -
LGA    E      23      L      10          4.390
LGA    Y      24      E      11          2.373
LGA    G      25      D      12           #
LGA    N      26      M      13          1.969
LGA    P      27      K      14          1.927
LGA    H      28      V      15          3.354
LGA    -       -      G      16           -
LGA    -       -      V      17           -
LGA    -       -      F      18           -
LGA    -       -      A      19           -
LGA    -       -      T      20           -
LGA    -       -      L      21           -
LGA    -       -      D      22           -
LGA    -       -      E      23           -
LGA    -       -      Y      24           -
LGA    -       -      G      25           -
LGA    -       -      N      26           -
LGA    -       -      P      27           -
LGA    -       -      H      28           -
LGA    -       -      A      29           -
LGA    -       -      R      30           -
LGA    -       -      H      31           -
LGA    A      29      A      32          0.223
LGA    R      30      H      33           -
LGA    H      31      I      34           -
LGA    A      32      T      35           -
LGA    H      33      A      36           -
LGA    I      34      A      37           -
LGA    T      35      N      38           -
LGA    A      36      E      39           -
LGA    A      37      E      40           -
LGA    N      38      G      41           -
LGA    E      39      -       -           -
LGA    E      40      -       -           -
LGA    G      41      -       -           -
LGA    I      42      -       -           -
LGA    F      43      -       -           -
LGA    F      44      I      42           #
LGA    M      45      F      43          5.008
LGA    T      46      F      44          3.179
LGA    S      47      -       -           -
LGA    P      48      -       -           -
LGA    E      49      -       -           -
LGA    T      50      -       -           -
LGA    H      51      -       -           -
LGA    F      52      -       -           -
LGA    Y      53      -       -           -
LGA    D      54      -       -           -
LGA    Q      55      -       -           -
LGA    L      56      M      45          3.766
LGA    M      57      T      46          4.735
LGA    G      58      S      47          2.046
LGA    D      59      P      48          1.764
LGA    Q      60      E      49           -
LGA    -       -      T      50           -
LGA    -       -      H      51           -
LGA    R      61      F      52           #
LGA    V      62      Y      53          2.974
LGA    A      63      D      54           #
LGA    -       -      Q      55           -
LGA    -       -      L      56           -
LGA    -       -      M      57           -
LGA    -       -      G      58           -
LGA    -       -      D      59           -
LGA    -       -      Q      60           -
LGA    -       -      R      61           -
LGA    -       -      V      62           -
LGA    -       -      A      63           -
LGA    -       -      M      64           -
LGA    -       -      T      65           -
LGA    -       -      A      66           -
LGA    -       -      I      67           -
LGA    -       -      S      68           -
LGA    -       -      E      69           -
LGA    -       -      E      70           -
LGA    -       -      G      71           -
LGA    -       -      Y      72           -
LGA    -       -      L      73           -
LGA    -       -      I      74           -
LGA    -       -      Q      75           -
LGA    -       -      V      76           -
LGA    -       -      V      77           -
LGA    -       -      R      78           -
LGA    -       -      V      79           -
LGA    -       -      E      80           -
LGA    -       -      G      81           -
LGA    M      64      T      82           #
LGA    T      65      A      83          2.029
LGA    A      66      R      84           #
LGA    I      67      -       -           -
LGA    S      68      -       -           -
LGA    E      69      -       -           -
LGA    E      70      -       -           -
LGA    G      71      -       -           -
LGA    Y      72      -       -           -
LGA    L      73      -       -           -
LGA    I      74      -       -           -
LGA    Q      75      -       -           -
LGA    V      76      P      85          2.443
LGA    V      77      V      86          4.195
LGA    R      78      E      87           -
LGA    -       -      N      88           -
LGA    -       -      D      89           -
LGA    -       -      Y      90           -
LGA    V      79      L      91           #
LGA    E      80      K      92           -
LGA    G      81      -       -           -
LGA    T      82      -       -           -
LGA    A      83      -       -           -
LGA    R      84      -       -           -
LGA    P      85      -       -           -
LGA    V      86      -       -           -
LGA    E      87      -       -           -
LGA    N      88      -       -           -
LGA    D      89      -       -           -
LGA    Y      90      -       -           -
LGA    L      91      -       -           -
LGA    K      92      -       -           -
LGA    T      93      T      93          4.526
LGA    V      94      -       -           -
LGA    F      95      V      94           #
LGA    A      96      F      95          2.791
LGA    D      97      A      96          1.322
LGA    N      98      D      97          3.873
LGA    -       -      N      98           -
LGA    P      99      P      99          4.109
LGA    Y     100      Y     100          4.435
LGA    Y     101      Y     101          4.073
LGA    Q     102      Q     102          3.450
LGA    H     103      H     103          1.546
LGA    I     104      I     104          1.418
LGA    Y     105      Y     105          2.397
LGA    K     106      K     106          2.615
LGA    D     107      T     112           -
LGA    E     108      M     113           -
LGA    S     109      -       -           -
LGA    S     110      -       -           -
LGA    D     111      -       -           -
LGA    T     112      Q     114           #
LGA    M     113      V     115           #
LGA    Q     114      F     116           #
LGA    V     115      -       -           -
LGA    F     116      -       -           -
LGA    Q     117      Q     117          4.805
LGA    I     118      -       -           -
LGA    Y     119      -       -           -
LGA    A     120      -       -           -
LGA    G     121      -       -           -
LGA    H     122      -       -           -
LGA    G     123      I     118          2.320
LGA    F     124      Y     119          0.336
LGA    Y     125      A     120           #
LGA    H     126      G     121           -
LGA    S     127      H     122           -
LGA    L     128      G     123           -
LGA    T     129      F     124           -
LGA    Q     130      Y     125           -
LGA    G     131      H     126           -
LGA    H     132      S     127           -
LGA    K     133      L     128           -
LGA    Y     134      T     129           -
LGA    I     135      Q     130           -
LGA    -       -      G     131           -
LGA    -       -      H     132           -
LGA    -       -      K     133           -
LGA    -       -      Y     134           -
LGA    -       -      I     135           -
LGA    F     136      F     136           #
LGA    S     137      S     137          2.707
LGA    -       -      I     138           -
LGA    -       -      G     139           -
LGA    -       -      E     145           -
LGA    I     138      V     146          1.322
LGA    G     139      R     147          3.164
LGA    Q     140      A     148          3.610
LGA    G     141      L     149           #
LGA    E     142      -       -           -
LGA    H     143      -       -           -
LGA    S     144      -       -           -
LGA    E     145      -       -           -
LGA    V     146      -       -           -
LGA    R     147      -       -           -
LGA    A     148      -       -           -
LGA    L     149      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  149  139    5.0     35    3.15    37.14     14.821     1.077

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.920462 * X  +  -0.046717 * Y  +  -0.388031 * Z  +  19.075348
  Y_new =   0.333539 * X  +   0.611406 * Y  +   0.717589 * Z  +  41.057507
  Z_new =   0.203721 * X  +  -0.789937 * Y  +   0.578358 * Z  +  24.491760 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.938813    2.202780  [ DEG:   -53.7900    126.2100 ]
  Theta =  -0.205157   -2.936436  [ DEG:   -11.7546   -168.2454 ]
  Phi   =   0.347644   -2.793949  [ DEG:    19.9185   -160.0815 ]
 
# 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: T0331TS168_3                                  
REMARK     2: T0331.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0331TS168_3.T0331.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  149  139   5.0   35   3.15   37.14  14.821
REMARK  ---------------------------------------------------------- 
MOLECULE T0331TS168_3
PFRMAT TS
TARGET T0331
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      46.701  35.417  12.152  1.00 25.00           C
ATOM      2  CA  GLU     2      44.048  37.813  13.479  1.00 25.00           C
ATOM      3  CA  LEU     3      40.598  36.257  13.215  1.00 25.00           C
ATOM      4  CA  LYS     4      39.262  39.671  14.096  1.00 25.00           C
ATOM      5  CA  ASP     5      37.031  42.713  14.750  1.00 25.00           C
ATOM      6  CA  ILE     6      34.517  40.500  16.607  1.00 25.00           C
ATOM      7  CA  MET     7      37.344  39.023  18.727  1.00 25.00           C
ATOM      8  CA  HIS     8      38.599  42.546  19.551  1.00 25.00           C
ATOM      9  CA  ILE     9      35.059  43.598  20.564  1.00 25.00           C
ATOM     10  CA  LEU    10      34.756  40.507  22.805  1.00 25.00           C
ATOM     11  CA  GLU    11      38.124  41.326  24.433  1.00 25.00           C
ATOM     12  CA  ASP    12      36.979  44.930  25.044  1.00 25.00           C
ATOM     13  CA  MET    13      34.529  47.614  23.959  1.00 25.00           C
ATOM     14  CA  LYS    14      33.399  48.487  20.376  1.00 25.00           C
ATOM     15  CA  VAL    15      30.597  46.051  19.425  1.00 25.00           C
ATOM     16  CA  GLY    16      30.077  42.812  21.282  1.00 25.00           C
ATOM     17  CA  VAL    17      29.063  43.550  24.884  1.00 25.00           C
ATOM     18  CA  PHE    18      27.393  40.142  24.764  1.00 25.00           C
ATOM     19  CA  ALA    19      23.998  39.994  26.523  1.00 25.00           C
ATOM     20  CA  THR    20      20.936  37.988  27.295  1.00 25.00           C
ATOM     21  CA  LEU    21      17.839  36.023  28.093  1.00 25.00           C
ATOM     22  CA  ASP    22      17.225  33.526  25.312  1.00 25.00           C
ATOM     23  CA  GLU    23      13.466  33.456  24.751  1.00 25.00           C
ATOM     24  CA  TYR    24      13.677  29.731  23.955  1.00 25.00           C
ATOM     25  CA  GLY    25      17.030  28.049  24.471  1.00 25.00           C
ATOM     26  CA  ASN    26      15.007  26.779  27.432  1.00 25.00           C
ATOM     27  CA  PRO    27      14.671  29.464  30.055  1.00 25.00           C
ATOM     28  CA  HIS    28      16.667  29.764  33.258  1.00 25.00           C
ATOM     29  CA  ALA    29      19.930  31.523  34.219  1.00 25.00           C
ATOM     30  CA  ARG    30      21.953  28.745  32.528  1.00 25.00           C
ATOM     31  CA  HIS    31      19.817  29.081  29.367  1.00 25.00           C
ATOM     32  CA  ALA    32      20.366  32.871  29.368  1.00 25.00           C
ATOM     33  CA  HIS    33      24.142  32.349  29.740  1.00 25.00           C
ATOM     34  CA  ILE    34      24.112  29.870  26.822  1.00 25.00           C
ATOM     35  CA  THR    35      22.176  32.382  24.676  1.00 25.00           C
ATOM     36  CA  ALA    36      24.709  35.118  25.552  1.00 25.00           C
ATOM     37  CA  ALA    37      27.595  32.785  24.606  1.00 25.00           C
ATOM     38  CA  ASN    38      29.099  30.645  27.328  1.00 25.00           C
ATOM     39  CA  GLU    39      28.659  30.048  31.095  1.00 25.00           C
ATOM     40  CA  GLU    40      30.047  33.645  31.267  1.00 25.00           C
ATOM     41  CA  GLY    41      29.987  36.169  28.370  1.00 25.00           C
ATOM     42  CA  ILE    42      27.914  38.692  30.378  1.00 25.00           C
ATOM     43  CA  PHE    43      24.475  37.226  30.947  1.00 25.00           C
ATOM     44  CA  PHE    44      21.113  37.233  32.741  1.00 25.00           C
ATOM     45  CA  MET    45      17.337  37.758  33.094  1.00 25.00           C
ATOM     46  CA  THR    46      15.120  34.953  31.810  1.00 25.00           C
ATOM     47  CA  SER    47      12.099  33.689  29.804  1.00 25.00           C
ATOM     48  CA  PRO    48       8.578  32.216  29.737  1.00 25.00           C
ATOM     49  CA  GLU    49       9.118  28.523  30.456  1.00 25.00           C
ATOM     50  CA  THR    50      10.867  28.572  33.781  1.00 25.00           C
ATOM     51  CA  HIS    51       9.267  31.754  35.008  1.00 25.00           C
ATOM     52  CA  PHE    52      10.483  35.322  34.334  1.00 25.00           C
ATOM     53  CA  TYR    53       9.874  36.248  38.000  1.00 25.00           C
ATOM     54  CA  ASP    54      11.830  33.157  39.131  1.00 25.00           C
ATOM     55  CA  GLN    55      14.720  34.103  36.803  1.00 25.00           C
ATOM     56  CA  LEU    56      14.721  37.664  38.212  1.00 25.00           C
ATOM     57  CA  MET    57      16.394  37.073  41.578  1.00 25.00           C
ATOM     58  CA  GLY    58      18.839  39.391  43.345  1.00 25.00           C
ATOM     59  CA  ASP    59      20.879  42.066  41.672  1.00 25.00           C
ATOM     60  CA  GLN    60      18.796  41.169  38.565  1.00 25.00           C
ATOM     61  CA  ARG    61      20.623  37.823  38.927  1.00 25.00           C
ATOM     62  CA  VAL    62      23.445  39.209  36.709  1.00 25.00           C
ATOM     63  CA  ALA    63      22.288  42.149  34.641  1.00 25.00           C
ATOM     64  CA  MET    64      23.306  42.572  30.942  1.00 25.00           C
ATOM     65  CA  THR    65      24.382  44.940  28.123  1.00 25.00           C
ATOM     66  CA  ALA    66      26.129  47.524  26.045  1.00 25.00           C
ATOM     67  CA  ILE    67      28.764  49.766  24.364  1.00 25.00           C
ATOM     68  CA  SER    68      29.650  50.552  27.978  1.00 25.00           C
ATOM     69  CA  GLU    69      30.298  51.046  31.694  1.00 25.00           C
ATOM     70  CA  GLU    70      33.742  49.674  31.152  1.00 25.00           C
ATOM     71  CA  GLY    71      33.908  46.120  29.860  1.00 25.00           C
ATOM     72  CA  TYR    72      30.407  44.564  29.829  1.00 25.00           C
ATOM     73  CA  LEU    73      28.757  43.354  33.058  1.00 25.00           C
ATOM     74  CA  ILE    74      26.430  46.404  32.622  1.00 25.00           C
ATOM     75  CA  GLN    75      22.746  47.369  32.464  1.00 25.00           C
ATOM     76  CA  VAL    76      19.753  46.664  30.220  1.00 25.00           C
ATOM     77  CA  VAL    77      18.194  43.690  31.960  1.00 25.00           C
ATOM     78  CA  ARG    78      17.330  41.571  28.901  1.00 25.00           C
ATOM     79  CA  VAL    79      13.959  39.957  29.522  1.00 25.00           C
ATOM     80  CA  GLU    80      11.046  38.192  27.790  1.00 25.00           C
ATOM     81  CA  GLY    81       9.858  39.661  24.433  1.00 25.00           C
ATOM     82  CA  THR    82       7.482  36.781  23.537  1.00 25.00           C
ATOM     83  CA  ALA    83       6.111  37.985  20.187  1.00 25.00           C
ATOM     84  CA  ARG    84       7.191  40.201  17.240  1.00 25.00           C
ATOM     85  CA  PRO    85       9.679  42.707  15.827  1.00 25.00           C
ATOM     86  CA  VAL    86      10.069  46.015  13.974  1.00 25.00           C
ATOM     87  CA  GLU    87       6.450  46.027  12.902  1.00 25.00           C
ATOM     88  CA  ASN    88       6.723  49.766  13.218  1.00 25.00           C
ATOM     89  CA  ASP    89       8.098  50.639  16.685  1.00 25.00           C
ATOM     90  CA  TYR    90       4.542  51.252  17.968  1.00 25.00           C
ATOM     91  CA  LEU    91       3.420  47.878  16.545  1.00 25.00           C
ATOM     92  CA  LYS    92       6.384  46.148  18.244  1.00 25.00           C
ATOM     93  CA  THR    93       5.495  47.834  21.567  1.00 25.00           C
ATOM     94  CA  VAL    94       1.857  46.690  21.202  1.00 25.00           C
ATOM     95  CA  PHE    95       3.029  43.113  20.495  1.00 25.00           C
ATOM     96  CA  ALA    96       5.277  43.210  23.595  1.00 25.00           C
ATOM     97  CA  ASP    97       3.906  45.639  26.160  1.00 25.00           C
ATOM     98  CA  ASN    98       2.887  42.806  28.432  1.00 25.00           C
ATOM     99  CA  PRO    99       2.989  39.030  27.720  1.00 25.00           C
ATOM    100  CA  TYR   100       5.578  38.858  30.549  1.00 25.00           C
ATOM    101  CA  TYR   101       7.931  41.834  30.035  1.00 25.00           C
ATOM    102  CA  GLN   102       5.868  43.922  32.497  1.00 25.00           C
ATOM    103  CA  HIS   103       6.017  41.084  35.064  1.00 25.00           C
ATOM    104  CA  ILE   104       9.813  40.848  34.619  1.00 25.00           C
ATOM    105  CA  TYR   105      10.285  44.507  35.548  1.00 25.00           C
ATOM    106  CA  LYS   106       7.336  45.582  37.744  1.00 25.00           C
ATOM    107  CA  ASP   107       3.841  45.553  39.264  1.00 25.00           C
ATOM    108  CA  GLU   108       3.908  49.171  40.343  1.00 25.00           C
ATOM    109  CA  SER   109       6.445  50.883  38.001  1.00 25.00           C
ATOM    110  CA  SER   110       8.691  52.894  40.311  1.00 25.00           C
ATOM    111  CA  ASP   111      11.795  51.378  38.710  1.00 25.00           C
ATOM    112  CA  THR   112      13.626  49.344  35.995  1.00 25.00           C
ATOM    113  CA  MET   113      13.758  48.112  32.392  1.00 25.00           C
ATOM    114  CA  GLN   114      12.778  44.705  31.062  1.00 25.00           C
ATOM    115  CA  VAL   115      11.883  44.691  27.379  1.00 25.00           C
ATOM    116  CA  PHE   116      15.416  45.960  26.847  1.00 25.00           C
ATOM    117  CA  GLN   117      15.774  43.232  24.252  1.00 25.00           C
ATOM    118  CA  ILE   118      15.857  39.692  22.838  1.00 25.00           C
ATOM    119  CA  TYR   119      15.168  36.536  20.881  1.00 25.00           C
ATOM    120  CA  ALA   120      18.600  34.937  20.172  1.00 25.00           C
ATOM    121  CA  GLY   121      21.088  36.286  17.649  1.00 25.00           C
ATOM    122  CA  HIS   122      20.414  39.664  19.352  1.00 25.00           C
ATOM    123  CA  GLY   123      20.814  40.352  23.114  1.00 25.00           C
ATOM    124  CA  PHE   124      20.800  44.121  23.253  1.00 25.00           C
ATOM    125  CA  TYR   125      19.570  47.547  24.445  1.00 25.00           C
ATOM    126  CA  HIS   126      17.844  50.876  24.039  1.00 25.00           C
ATOM    127  CA  SER   127      17.009  54.074  22.193  1.00 25.00           C
ATOM    128  CA  LEU   128      20.748  54.075  21.411  1.00 25.00           C
ATOM    129  CA  THR   129      20.889  57.338  19.400  1.00 25.00           C
ATOM    130  CA  GLN   130      18.359  58.316  16.698  1.00 25.00           C
ATOM    131  CA  GLY   131      18.988  55.119  14.728  1.00 25.00           C
ATOM    132  CA  HIS   132      19.370  51.665  16.315  1.00 25.00           C
ATOM    133  CA  LYS   133      16.642  49.012  16.971  1.00 25.00           C
ATOM    134  CA  TYR   134      16.752  45.584  18.652  1.00 25.00           C
ATOM    135  CA  ILE   135      16.407  41.995  17.381  1.00 25.00           C
ATOM    136  CA  PHE   136      18.765  40.803  14.645  1.00 25.00           C
ATOM    137  CA  SER   137      20.230  37.665  13.073  1.00 25.00           C
ATOM    138  CA  ILE   138      18.783  37.018   9.649  1.00 25.00           C
ATOM    139  CA  GLY   139      19.138  36.050   6.033  1.00 25.00           C
ATOM    140  CA  GLN   140      19.980  32.838   4.081  1.00 25.00           C
ATOM    141  CA  GLY   141      21.648  33.455   0.767  1.00 25.00           C
ATOM    142  CA  GLU   142      19.178  33.742  -2.106  1.00 25.00           C
ATOM    143  CA  HIS   143      19.489  36.752  -4.435  1.00 25.00           C
ATOM    144  CA  SER   144      18.855  40.412  -4.838  1.00 25.00           C
ATOM    145  CA  GLU   145      20.981  42.211  -2.283  1.00 25.00           C
ATOM    146  CA  VAL   146      23.282  43.127  -5.140  1.00 25.00           C
ATOM    147  CA  ARG   147      27.066  43.044  -4.516  1.00 25.00           C
ATOM    148  CA  ALA   148      30.764  43.042  -3.680  1.00 25.00           C
ATOM    149  CA  LEU   149      32.509  45.843  -1.847  1.00 25.00           C
TER
END
