
#######################################################
#                                                     #
#                        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 T0331TS393_4
# Molecule2: number of CA atoms  139 ( 1101),  selected  139 , name T0331.pdb
# PARAMETERS: T0331TS393_4.T0331.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    E       2      E       2           -
LGA    L       3      -       -           -
LGA    K       4      -       -           -
LGA    D       5      -       -           -
LGA    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      -       -           -
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      32      -       -           -
LGA    H      33      -       -           -
LGA    I      34      -       -           -
LGA    T      35      -       -           -
LGA    A      36      -       -           -
LGA    A      37      -       -           -
LGA    N      38      -       -           -
LGA    E      39      -       -           -
LGA    E      40      -       -           -
LGA    G      41      -       -           -
LGA    I      42      -       -           -
LGA    F      43      -       -           -
LGA    F      44      -       -           -
LGA    M      45      -       -           -
LGA    T      46      L       3           #
LGA    S      47      K       4           -
LGA    -       -      D       5           -
LGA    -       -      I       6           -
LGA    -       -      M       7           -
LGA    -       -      H       8           -
LGA    -       -      I       9           -
LGA    P      48      L      10          2.539
LGA    E      49      E      11          1.886
LGA    -       -      D      12           -
LGA    T      50      M      13          2.648
LGA    H      51      K      14          2.743
LGA    -       -      V      15           -
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      32           -
LGA    -       -      H      33           -
LGA    F      52      I      34          2.201
LGA    Y      53      T      35          4.399
LGA    D      54      A      36           -
LGA    -       -      A      37           -
LGA    -       -      N      38           -
LGA    -       -      E      39           -
LGA    -       -      E      40           -
LGA    -       -      G      41           -
LGA    -       -      I      42           -
LGA    -       -      F      43           -
LGA    Q      55      F      44          4.537
LGA    L      56      M      45          3.592
LGA    M      57      T      46          4.277
LGA    G      58      S      47           -
LGA    D      59      P      48           -
LGA    -       -      E      49           -
LGA    -       -      T      50           -
LGA    -       -      H      51           -
LGA    Q      60      F      52          3.396
LGA    -       -      Y      53           -
LGA    -       -      D      54           -
LGA    -       -      Q      55           -
LGA    R      61      L      56          4.307
LGA    V      62      M      57           #
LGA    A      63      G      58           -
LGA    M      64      D      59          3.561
LGA    T      65      Q      60          4.009
LGA    A      66      -       -           -
LGA    I      67      -       -           -
LGA    S      68      -       -           -
LGA    E      69      -       -           -
LGA    E      70      -       -           -
LGA    G      71      -       -           -
LGA    Y      72      -       -           -
LGA    L      73      R      61          5.228
LGA    I      74      V      62          3.486
LGA    Q      75      A      63          3.792
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    V      76      T      82           #
LGA    V      77      -       -           -
LGA    R      78      A      83          5.830
LGA    V      79      R      84           -
LGA    E      80      P      85           -
LGA    G      81      V      86           -
LGA    T      82      E      87           -
LGA    A      83      N      88           -
LGA    R      84      D      89           -
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      Y      90          3.729
LGA    -       -      L      91           -
LGA    V      94      K      92          4.908
LGA    F      95      T      93          1.992
LGA    A      96      V      94          2.159
LGA    D      97      F      95          3.057
LGA    N      98      A      96          4.007
LGA    -       -      D      97           -
LGA    P      99      N      98           #
LGA    -       -      P      99           -
LGA    -       -      Y     100           -
LGA    Y     100      Y     101          5.031
LGA    Y     101      Q     102           -
LGA    Q     102      H     103           -
LGA    H     103      I     104          3.205
LGA    I     104      Y     105           -
LGA    Y     105      -       -           -
LGA    K     106      -       -           -
LGA    D     107      -       -           -
LGA    E     108      K     106          3.159
LGA    S     109      T     112          3.739
LGA    S     110      M     113          4.145
LGA    D     111      Q     114          2.387
LGA    T     112      V     115          2.515
LGA    M     113      F     116          0.602
LGA    Q     114      Q     117          1.560
LGA    V     115      I     118          2.872
LGA    F     116      Y     119          0.908
LGA    Q     117      A     120          2.339
LGA    I     118      G     121          1.937
LGA    Y     119      H     122          2.991
LGA    -       -      G     123           -
LGA    -       -      F     124           -
LGA    -       -      Y     125           -
LGA    -       -      H     126           -
LGA    -       -      S     127           -
LGA    -       -      L     128           -
LGA    -       -      T     129           -
LGA    -       -      Q     130           -
LGA    -       -      G     131           -
LGA    -       -      H     132           -
LGA    -       -      K     133           -
LGA    -       -      Y     134           -
LGA    A     120      I     135           #
LGA    G     121      F     136          1.574
LGA    H     122      S     137          3.372
LGA    G     123      I     138          2.125
LGA    F     124      G     139          2.330
LGA    Y     125      E     145           -
LGA    H     126      V     146           -
LGA    S     127      R     147           -
LGA    L     128      A     148           -
LGA    T     129      L     149           -
LGA    Q     130      -       -           -
LGA    G     131      -       -           -
LGA    H     132      -       -           -
LGA    K     133      -       -           -
LGA    Y     134      -       -           -
LGA    I     135      -       -           -
LGA    F     136      -       -           -
LGA    S     137      -       -           -
LGA    I     138      -       -           -
LGA    G     139      -       -           -
LGA    Q     140      -       -           -
LGA    G     141      -       -           -
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     41    3.36     7.32     16.208     1.186

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.090796 * X  +  -0.974209 * Y  +   0.206573 * Z  +  24.648409
  Y_new =   0.392168 * X  +   0.225646 * Y  +   0.891789 * Z  +  41.123051
  Z_new =  -0.915402 * X  +   0.000041 * Y  +   0.402541 * Z  +  27.406244 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.000101   -3.141492  [ DEG:     0.0058   -179.9942 ]
  Theta =   1.156505    1.985087  [ DEG:    66.2629    113.7371 ]
  Phi   =   1.343282   -1.798310  [ DEG:    76.9644   -103.0356 ]
 
# 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: T0331TS393_4                                  
REMARK     2: T0331.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0331TS393_4.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   41   3.36    7.32  16.208
REMARK  ---------------------------------------------------------- 
MOLECULE T0331TS393_4
PFRMAT TS
TARGET T0331
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1      46.729  32.098  41.891  1.00 25.00           C
ATOM      2  CA  GLU     2      45.585  35.700  41.645  1.00 25.00           C
ATOM      3  CA  LEU     3      42.254  35.457  39.811  1.00 25.00           C
ATOM      4  CA  LYS     4      42.932  37.527  36.662  1.00 25.00           C
ATOM      5  CA  ASP     5      42.467  34.307  34.642  1.00 25.00           C
ATOM      6  CA  ILE     6      39.418  35.819  32.887  1.00 25.00           C
ATOM      7  CA  MET     7      41.427  38.972  32.059  1.00 25.00           C
ATOM      8  CA  HIS     8      44.264  36.824  30.645  1.00 25.00           C
ATOM      9  CA  ILE     9      41.756  34.875  28.506  1.00 25.00           C
ATOM     10  CA  LEU    10      40.276  38.159  27.206  1.00 25.00           C
ATOM     11  CA  GLU    11      43.785  39.426  26.340  1.00 25.00           C
ATOM     12  CA  ASP    12      44.531  36.160  24.484  1.00 25.00           C
ATOM     13  CA  MET    13      42.887  36.753  21.111  1.00 25.00           C
ATOM     14  CA  LYS    14      40.627  33.747  21.893  1.00 25.00           C
ATOM     15  CA  VAL    15      37.892  36.412  21.933  1.00 25.00           C
ATOM     16  CA  GLY    16      37.422  39.779  20.236  1.00 25.00           C
ATOM     17  CA  VAL    17      33.903  40.988  20.756  1.00 25.00           C
ATOM     18  CA  PHE    18      33.369  38.533  23.562  1.00 25.00           C
ATOM     19  CA  ALA    19      29.569  38.595  23.756  1.00 25.00           C
ATOM     20  CA  THR    20      26.395  36.598  24.407  1.00 25.00           C
ATOM     21  CA  LEU    21      23.452  34.268  24.302  1.00 25.00           C
ATOM     22  CA  ASP    22      22.246  31.562  21.849  1.00 25.00           C
ATOM     23  CA  GLU    23      19.520  30.858  24.445  1.00 25.00           C
ATOM     24  CA  TYR    24      17.827  28.479  21.938  1.00 25.00           C
ATOM     25  CA  GLY    25      19.757  25.808  23.779  1.00 25.00           C
ATOM     26  CA  ASN    26      18.888  26.752  27.419  1.00 25.00           C
ATOM     27  CA  PRO    27      18.756  27.346  31.207  1.00 25.00           C
ATOM     28  CA  HIS    28      21.796  29.460  31.774  1.00 25.00           C
ATOM     29  CA  ALA    29      25.425  30.640  32.105  1.00 25.00           C
ATOM     30  CA  ARG    30      26.659  27.352  30.577  1.00 25.00           C
ATOM     31  CA  HIS    31      24.200  27.752  27.669  1.00 25.00           C
ATOM     32  CA  ALA    32      25.417  31.339  27.100  1.00 25.00           C
ATOM     33  CA  HIS    33      29.052  30.131  27.098  1.00 25.00           C
ATOM     34  CA  ILE    34      28.169  27.402  24.560  1.00 25.00           C
ATOM     35  CA  THR    35      26.439  29.996  22.337  1.00 25.00           C
ATOM     36  CA  ALA    36      29.519  32.262  22.540  1.00 25.00           C
ATOM     37  CA  ALA    37      31.777  29.319  21.586  1.00 25.00           C
ATOM     38  CA  ASN    38      29.907  26.458  19.821  1.00 25.00           C
ATOM     39  CA  GLU    39      29.839  28.471  16.595  1.00 25.00           C
ATOM     40  CA  GLU    40      31.204  31.954  17.284  1.00 25.00           C
ATOM     41  CA  GLY    41      33.273  33.765  19.829  1.00 25.00           C
ATOM     42  CA  ILE    42      31.159  36.864  19.316  1.00 25.00           C
ATOM     43  CA  PHE    43      27.482  35.816  19.544  1.00 25.00           C
ATOM     44  CA  PHE    44      23.715  35.575  18.942  1.00 25.00           C
ATOM     45  CA  MET    45      20.881  38.030  19.864  1.00 25.00           C
ATOM     46  CA  THR    46      18.680  35.037  20.717  1.00 25.00           C
ATOM     47  CA  SER    47      15.459  33.053  20.296  1.00 25.00           C
ATOM     48  CA  PRO    48      14.262  32.089  23.752  1.00 25.00           C
ATOM     49  CA  GLU    49      11.203  30.253  25.115  1.00 25.00           C
ATOM     50  CA  THR    50      13.707  28.593  27.424  1.00 25.00           C
ATOM     51  CA  HIS    51      13.137  30.627  30.609  1.00 25.00           C
ATOM     52  CA  PHE    52      13.720  34.413  30.632  1.00 25.00           C
ATOM     53  CA  TYR    53      14.654  34.270  34.344  1.00 25.00           C
ATOM     54  CA  ASP    54      17.101  31.409  33.644  1.00 25.00           C
ATOM     55  CA  GLN    55      18.672  33.421  30.788  1.00 25.00           C
ATOM     56  CA  LEU    56      19.034  36.458  33.093  1.00 25.00           C
ATOM     57  CA  MET    57      19.999  34.578  36.313  1.00 25.00           C
ATOM     58  CA  GLY    58      21.917  31.552  37.693  1.00 25.00           C
ATOM     59  CA  ASP    59      25.406  32.891  36.935  1.00 25.00           C
ATOM     60  CA  GLN    60      25.953  35.958  34.685  1.00 25.00           C
ATOM     61  CA  ARG    61      24.274  39.357  34.371  1.00 25.00           C
ATOM     62  CA  VAL    62      26.508  40.410  31.467  1.00 25.00           C
ATOM     63  CA  ALA    63      26.926  41.284  27.819  1.00 25.00           C
ATOM     64  CA  MET    64      29.156  44.116  28.899  1.00 25.00           C
ATOM     65  CA  THR    65      29.295  45.206  25.272  1.00 25.00           C
ATOM     66  CA  ALA    66      29.719  44.272  21.643  1.00 25.00           C
ATOM     67  CA  ILE    67      30.925  44.871  18.043  1.00 25.00           C
ATOM     68  CA  SER    68      34.370  46.111  19.191  1.00 25.00           C
ATOM     69  CA  GLU    69      38.076  45.907  20.027  1.00 25.00           C
ATOM     70  CA  GLU    70      37.737  47.874  23.297  1.00 25.00           C
ATOM     71  CA  GLY    71      37.743  44.705  25.415  1.00 25.00           C
ATOM     72  CA  TYR    72      34.521  42.823  25.985  1.00 25.00           C
ATOM     73  CA  LEU    73      35.090  39.742  28.229  1.00 25.00           C
ATOM     74  CA  ILE    74      31.386  38.941  28.477  1.00 25.00           C
ATOM     75  CA  GLN    75      28.726  36.240  28.832  1.00 25.00           C
ATOM     76  CA  VAL    76      24.974  35.903  29.649  1.00 25.00           C
ATOM     77  CA  VAL    77      22.643  38.592  28.287  1.00 25.00           C
ATOM     78  CA  ARG    78      21.134  38.809  24.820  1.00 25.00           C
ATOM     79  CA  VAL    79      18.920  35.887  25.779  1.00 25.00           C
ATOM     80  CA  GLU    80      16.098  37.943  24.300  1.00 25.00           C
ATOM     81  CA  GLY    81      14.655  40.619  22.052  1.00 25.00           C
ATOM     82  CA  THR    82      12.336  41.510  19.159  1.00 25.00           C
ATOM     83  CA  ALA    83       9.097  43.077  18.011  1.00 25.00           C
ATOM     84  CA  ARG    84      10.868  46.497  17.954  1.00 25.00           C
ATOM     85  CA  PRO    85      12.362  49.719  16.630  1.00 25.00           C
ATOM     86  CA  VAL    86       9.527  51.471  14.718  1.00 25.00           C
ATOM     87  CA  GLU    87      12.062  54.049  13.408  1.00 25.00           C
ATOM     88  CA  ASN    88      12.399  54.827  17.083  1.00 25.00           C
ATOM     89  CA  ASP    89      14.427  53.604  20.093  1.00 25.00           C
ATOM     90  CA  TYR    90      12.189  55.626  22.454  1.00 25.00           C
ATOM     91  CA  LEU    91       9.068  54.128  20.818  1.00 25.00           C
ATOM     92  CA  LYS    92      10.517  50.606  21.220  1.00 25.00           C
ATOM     93  CA  THR    93      11.264  51.308  24.910  1.00 25.00           C
ATOM     94  CA  VAL    94       7.683  52.566  25.421  1.00 25.00           C
ATOM     95  CA  PHE    95       6.309  49.408  23.748  1.00 25.00           C
ATOM     96  CA  ALA    96       8.495  47.227  26.012  1.00 25.00           C
ATOM     97  CA  ASP    97       6.744  45.322  28.839  1.00 25.00           C
ATOM     98  CA  ASN    98       5.336  43.311  25.976  1.00 25.00           C
ATOM     99  CA  PRO    99       6.960  39.928  25.477  1.00 25.00           C
ATOM    100  CA  TYR   100       9.396  38.653  28.131  1.00 25.00           C
ATOM    101  CA  TYR   101      12.419  40.538  26.724  1.00 25.00           C
ATOM    102  CA  GLN   102      11.673  43.504  29.028  1.00 25.00           C
ATOM    103  CA  HIS   103      11.429  41.141  32.032  1.00 25.00           C
ATOM    104  CA  ILE   104      14.778  39.546  31.081  1.00 25.00           C
ATOM    105  CA  TYR   105      15.566  39.623  34.835  1.00 25.00           C
ATOM    106  CA  LYS   106      12.332  39.174  36.837  1.00 25.00           C
ATOM    107  CA  ASP   107       9.225  38.398  38.896  1.00 25.00           C
ATOM    108  CA  GLU   108       8.946  42.076  39.890  1.00 25.00           C
ATOM    109  CA  SER   109      12.138  41.321  41.926  1.00 25.00           C
ATOM    110  CA  SER   110      13.086  44.898  40.982  1.00 25.00           C
ATOM    111  CA  ASP   111      16.094  45.383  38.675  1.00 25.00           C
ATOM    112  CA  THR   112      17.832  44.041  35.569  1.00 25.00           C
ATOM    113  CA  MET   113      18.858  42.670  32.173  1.00 25.00           C
ATOM    114  CA  GLN   114      17.600  42.985  28.630  1.00 25.00           C
ATOM    115  CA  VAL   115      20.862  43.502  26.833  1.00 25.00           C
ATOM    116  CA  PHE   116      19.983  43.394  23.084  1.00 25.00           C
ATOM    117  CA  GLN   117      23.682  43.838  22.557  1.00 25.00           C
ATOM    118  CA  ILE   118      25.070  40.702  20.920  1.00 25.00           C
ATOM    119  CA  TYR   119      25.605  40.616  17.140  1.00 25.00           C
ATOM    120  CA  ALA   120      23.797  38.736  14.464  1.00 25.00           C
ATOM    121  CA  GLY   121      20.786  37.207  12.770  1.00 25.00           C
ATOM    122  CA  HIS   122      19.303  40.663  13.171  1.00 25.00           C
ATOM    123  CA  GLY   123      18.283  41.260  16.820  1.00 25.00           C
ATOM    124  CA  PHE   124      21.342  43.179  17.977  1.00 25.00           C
ATOM    125  CA  TYR   125      23.342  46.402  18.267  1.00 25.00           C
ATOM    126  CA  HIS   126      23.549  49.643  20.140  1.00 25.00           C
ATOM    127  CA  SER   127      25.110  52.989  19.451  1.00 25.00           C
ATOM    128  CA  LEU   128      27.639  53.108  22.288  1.00 25.00           C
ATOM    129  CA  THR   129      27.834  56.496  23.999  1.00 25.00           C
ATOM    130  CA  GLN   130      25.889  59.766  23.723  1.00 25.00           C
ATOM    131  CA  GLY   131      23.418  58.178  21.396  1.00 25.00           C
ATOM    132  CA  HIS   132      22.856  55.305  23.808  1.00 25.00           C
ATOM    133  CA  LYS   133      22.711  53.514  27.203  1.00 25.00           C
ATOM    134  CA  TYR   134      23.374  50.001  25.782  1.00 25.00           C
ATOM    135  CA  ILE   135      24.875  47.486  28.207  1.00 25.00           C
ATOM    136  CA  PHE   136      26.614  47.944  31.556  1.00 25.00           C
ATOM    137  CA  SER   137      28.226  47.709  34.960  1.00 25.00           C
ATOM    138  CA  ILE   138      28.607  49.756  38.134  1.00 25.00           C
ATOM    139  CA  GLY   139      29.189  52.084  41.083  1.00 25.00           C
ATOM    140  CA  GLN   140      32.106  51.792  43.486  1.00 25.00           C
ATOM    141  CA  GLY   141      31.684  54.219  46.371  1.00 25.00           C
ATOM    142  CA  GLU   142      33.710  57.430  46.996  1.00 25.00           C
ATOM    143  CA  HIS   143      35.305  59.091  43.969  1.00 25.00           C
ATOM    144  CA  SER   144      38.803  57.588  43.731  1.00 25.00           C
ATOM    145  CA  GLU   145      41.765  55.323  44.382  1.00 25.00           C
ATOM    146  CA  VAL   146      44.876  57.201  45.597  1.00 25.00           C
ATOM    147  CA  ARG   147      46.108  58.027  42.094  1.00 25.00           C
ATOM    148  CA  ALA   148      46.492  55.354  39.429  1.00 25.00           C
ATOM    149  CA  LEU   149      48.235  52.466  37.618  1.00 25.00           C
TER
END
