
#######################################################
#                                                     #
#                        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  125 (  125),  selected  125 , name T0285TS393_1
# Molecule2: number of CA atoms   99 (  800),  selected   99 , name T0285.pdb
# PARAMETERS: T0285TS393_1.T0285.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A       1      -       -           -
LGA    Y       2      -       -           -
LGA    L       3      -       -           -
LGA    P       4      -       -           -
LGA    D       5      -       -           -
LGA    D       6      -       -           -
LGA    S       7      -       -           -
LGA    P       8      -       -           -
LGA    A       9      -       -           -
LGA    K      10      -       -           -
LGA    R      11      -       -           -
LGA    L      12      -       -           -
LGA    L      13      -       -           -
LGA    F      14      -       -           -
LGA    Q      15      -       -           -
LGA    M      16      -       -           -
LGA    V      17      -       -           -
LGA    G      18      -       -           -
LGA    N      19      -       -           -
LGA    A      20      -       -           -
LGA    I      21      -       -           -
LGA    N      22      -       -           -
LGA    R      23      -       -           -
LGA    N      24      -       -           -
LGA    T      25      -       -           -
LGA    Q      26      -       -           -
LGA    Q      27      -       -           -
LGA    L      28      -       -           -
LGA    T      29      -       -           -
LGA    Q      30      -       -           -
LGA    D      31      -       -           -
LGA    L      32      -       -           -
LGA    R      33      -       -           -
LGA    A      34      -       -           -
LGA    M      35      S       7          5.003
LGA    P      36      P       8          2.614
LGA    N      37      A       9          4.771
LGA    W      38      K      10          3.087
LGA    -       -      R      11           -
LGA    -       -      L      12           -
LGA    S      39      L      13          1.512
LGA    -       -      F      14           -
LGA    -       -      Q      15           -
LGA    L      40      M      16          3.747
LGA    R      41      V      17          4.110
LGA    -       -      G      18           -
LGA    -       -      N      19           -
LGA    F      42      A      20          3.949
LGA    V      43      I      21           -
LGA    Y      44      N      22           -
LGA    I      45      R      23           -
LGA    V      46      N      24          3.581
LGA    D      47      T      25          4.104
LGA    R      48      Q      26          1.785
LGA    N      49      Q      27          4.164
LGA    N      50      L      28           #
LGA    Q      51      T      29           #
LGA    D      52      Q      30           #
LGA    L      53      D      31          3.062
LGA    L      54      L      32          3.017
LGA    -       -      R      33           -
LGA    -       -      A      34           -
LGA    K      55      M      35          2.265
LGA    R      56      P      36           #
LGA    P      57      N      37           -
LGA    L      58      W      38           -
LGA    P      59      S      39          3.399
LGA    P      60      L      40          2.651
LGA    -       -      R      41           -
LGA    -       -      F      42           -
LGA    G      61      V      43          1.235
LGA    I      62      Y      44          3.198
LGA    M      63      I      45          2.968
LGA    V      64      V      46          1.530
LGA    L      65      D      47          3.326
LGA    A      66      R      48          1.675
LGA    P      67      N      49          3.262
LGA    -       -      N      50           -
LGA    -       -      Q      51           -
LGA    R      68      D      52           #
LGA    L      69      L      53           -
LGA    T      70      -       -           -
LGA    A      71      -       -           -
LGA    K      72      -       -           -
LGA    H      73      -       -           -
LGA    P      74      -       -           -
LGA    Y      75      -       -           -
LGA    D      76      -       -           -
LGA    K      77      -       -           -
LGA    V      78      -       -           -
LGA    Q      79      -       -           -
LGA    D      80      -       -           -
LGA    R      81      -       -           -
LGA    N      82      -       -           -
LGA    R      83      -       -           -
LGA    K      84      L      54           #
LGA    L      85      K      55          4.536
LGA    Y      86      R      56          3.710
LGA    G      87      P      57          2.928
LGA    R      88      L      58          2.047
LGA    H      89      P      59           -
LGA    -       -      P      60           -
LGA    -       -      G      61           -
LGA    -       -      I      62           -
LGA    I      90      M      63          4.204
LGA    -       -      V      64           -
LGA    -       -      L      65           -
LGA    T      91      A      66          1.051
LGA    L      92      P      67          3.989
LGA    N      93      R      68          3.831
LGA    D      94      -       -           -
LGA    G      95      -       -           -
LGA    N      96      -       -           -
LGA    S      97      -       -           -
LGA    V      98      -       -           -
LGA    K      99      L      69          4.365
LGA    V     100      T      70          2.062
LGA    V     101      A      71          2.065
LGA    -       -      K      72           -
LGA    -       -      H      73           -
LGA    T     102      P      74          3.509
LGA    -       -      Y      75           -
LGA    -       -      D      76           -
LGA    -       -      K      77           -
LGA    -       -      V      78           -
LGA    -       -      Q      79           -
LGA    -       -      D      80           -
LGA    -       -      R      81           -
LGA    -       -      N      82           -
LGA    -       -      R      83           -
LGA    -       -      K      84           -
LGA    -       -      L      85           -
LGA    -       -      Y      86           -
LGA    -       -      G      87           -
LGA    -       -      R      88           -
LGA    -       -      H      89           -
LGA    I     103      I      90          4.366
LGA    S     104      T      91           #
LGA    A     105      L      92           -
LGA    G     106      N      93           -
LGA    R     107      D      94           -
LGA    D     108      G      95           -
LGA    E     109      N      96           -
LGA    G     110      S      97           -
LGA    P     111      V      98           -
LGA    D     112      K      99           -
LGA    R     113      V     100           -
LGA    D     114      V     101           -
LGA    I     115      T     102           -
LGA    I     116      I     103           -
LGA    W     117      S     104           -
LGA    E     118      A     105           -
LGA    M     119      -       -           -
LGA    F     120      -       -           -
LGA    L     121      -       -           -
LGA    E     122      -       -           -
LGA    N     123      -       -           -
LGA    L     124      -       -           -
LGA    E     125      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  125   99    5.0     37    3.32    10.81     20.237     1.081

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.688493 * X  +  -0.585370 * Y  +  -0.428158 * Z  +  15.536469
  Y_new =   0.644379 * X  +   0.764650 * Y  +  -0.009231 * Z  +   2.788712
  Z_new =   0.332795 * X  +  -0.269540 * Y  +   0.903657 * Z  +  75.351295 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.289876    2.851717  [ DEG:   -16.6087    163.3913 ]
  Theta =  -0.339266   -2.802327  [ DEG:   -19.4385   -160.5615 ]
  Phi   =   0.752313   -2.389280  [ DEG:    43.1044   -136.8956 ]
 
# 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: T0285TS393_1                                  
REMARK     2: T0285.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0285TS393_1.T0285.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  125   99   5.0   37   3.32   10.81  20.237
REMARK  ---------------------------------------------------------- 
MOLECULE T0285TS393_1
PFRMAT TS
TARGET T0285
MODEL 1
PARENT N/A
ATOM      1  CA  ALA     1       8.898 -20.092  58.527  1.00 25.00           C
ATOM      2  CA  TYR     2       8.878 -19.396  62.329  1.00 25.00           C
ATOM      3  CA  LEU     3       8.135 -16.159  64.158  1.00 25.00           C
ATOM      4  CA  PRO     4       7.657 -14.048  61.042  1.00 25.00           C
ATOM      5  CA  ASP     5       9.947 -12.026  58.833  1.00 25.00           C
ATOM      6  CA  ASP     6      11.863  -8.788  58.362  1.00 25.00           C
ATOM      7  CA  SER     7      13.463  -6.825  61.270  1.00 25.00           C
ATOM      8  CA  PRO     8      14.512  -3.685  63.203  1.00 25.00           C
ATOM      9  CA  ALA     9      11.029  -2.417  64.165  1.00 25.00           C
ATOM     10  CA  LYS    10      11.253  -4.266  67.512  1.00 25.00           C
ATOM     11  CA  ARG    11      14.698  -2.723  68.161  1.00 25.00           C
ATOM     12  CA  LEU    12      13.317   0.758  67.363  1.00 25.00           C
ATOM     13  CA  LEU    13      10.392   0.175  69.764  1.00 25.00           C
ATOM     14  CA  PHE    14      12.827  -0.935  72.503  1.00 25.00           C
ATOM     15  CA  GLN    15      14.947   2.202  71.923  1.00 25.00           C
ATOM     16  CA  MET    16      11.813   4.391  72.160  1.00 25.00           C
ATOM     17  CA  VAL    17      10.823   2.662  75.430  1.00 25.00           C
ATOM     18  CA  GLY    18      14.339   3.241  76.831  1.00 25.00           C
ATOM     19  CA  ASN    19      14.148   6.937  75.848  1.00 25.00           C
ATOM     20  CA  ALA    20      10.736   7.243  77.562  1.00 25.00           C
ATOM     21  CA  ILE    21      12.152   5.609  80.724  1.00 25.00           C
ATOM     22  CA  ASN    22      15.111   8.040  80.685  1.00 25.00           C
ATOM     23  CA  ARG    23      12.708  10.998  80.311  1.00 25.00           C
ATOM     24  CA  ASN    24      10.622   9.708  83.253  1.00 25.00           C
ATOM     25  CA  THR    25      13.789   9.367  85.380  1.00 25.00           C
ATOM     26  CA  GLN    26      14.814  12.943  84.472  1.00 25.00           C
ATOM     27  CA  GLN    27      11.330  14.211  85.435  1.00 25.00           C
ATOM     28  CA  LEU    28      11.555  12.362  88.781  1.00 25.00           C
ATOM     29  CA  THR    29      14.999  13.905  89.430  1.00 25.00           C
ATOM     30  CA  GLN    30      13.618  17.387  88.632  1.00 25.00           C
ATOM     31  CA  ASP    31      10.693  16.804  91.034  1.00 25.00           C
ATOM     32  CA  LEU    32      13.129  15.693  93.772  1.00 25.00           C
ATOM     33  CA  ARG    33      15.248  18.830  93.193  1.00 25.00           C
ATOM     34  CA  ALA    34      18.187  16.577  92.494  1.00 25.00           C
ATOM     35  CA  MET    35      19.913  15.946  89.152  1.00 25.00           C
ATOM     36  CA  PRO    36      19.374  18.878  86.800  1.00 25.00           C
ATOM     37  CA  ASN    37      18.482  18.970  83.080  1.00 25.00           C
ATOM     38  CA  TRP    38      20.278  15.729  83.594  1.00 25.00           C
ATOM     39  CA  SER    39      19.931  13.536  80.568  1.00 25.00           C
ATOM     40  CA  LEU    40      19.685  10.049  79.110  1.00 25.00           C
ATOM     41  CA  ARG    41      19.090   7.538  76.318  1.00 25.00           C
ATOM     42  CA  PHE    42      19.159   4.833  73.629  1.00 25.00           C
ATOM     43  CA  VAL    43      19.525   1.350  75.072  1.00 25.00           C
ATOM     44  CA  TYR    44      17.076  -1.560  75.079  1.00 25.00           C
ATOM     45  CA  ILE    45      18.616  -2.926  71.922  1.00 25.00           C
ATOM     46  CA  VAL    46      21.212  -1.501  69.562  1.00 25.00           C
ATOM     47  CA  ASP    47      23.080   0.362  66.862  1.00 25.00           C
ATOM     48  CA  ARG    48      26.113  -1.498  68.302  1.00 25.00           C
ATOM     49  CA  ASN    49      29.642  -0.041  67.737  1.00 25.00           C
ATOM     50  CA  ASN    50      29.373   1.651  71.177  1.00 25.00           C
ATOM     51  CA  GLN    51      32.025   3.728  72.999  1.00 25.00           C
ATOM     52  CA  ASP    52      31.536   6.590  70.502  1.00 25.00           C
ATOM     53  CA  LEU    53      27.746   6.435  71.028  1.00 25.00           C
ATOM     54  CA  LEU    54      28.245   6.541  74.824  1.00 25.00           C
ATOM     55  CA  LYS    55      30.816   8.505  76.878  1.00 25.00           C
ATOM     56  CA  ARG    56      28.955  11.511  75.532  1.00 25.00           C
ATOM     57  CA  PRO    57      28.193  14.224  78.096  1.00 25.00           C
ATOM     58  CA  LEU    58      25.218  12.123  79.277  1.00 25.00           C
ATOM     59  CA  PRO    59      26.981  11.648  82.608  1.00 25.00           C
ATOM     60  CA  PRO    60      26.554   8.853  85.207  1.00 25.00           C
ATOM     61  CA  GLY    61      23.826   6.612  83.751  1.00 25.00           C
ATOM     62  CA  ILE    62      22.022   5.738  80.523  1.00 25.00           C
ATOM     63  CA  MET    63      19.160   4.176  82.389  1.00 25.00           C
ATOM     64  CA  VAL    64      17.203   1.395  80.770  1.00 25.00           C
ATOM     65  CA  LEU    65      14.425  -1.137  80.170  1.00 25.00           C
ATOM     66  CA  ALA    66      14.072  -4.710  78.910  1.00 25.00           C
ATOM     67  CA  PRO    67      17.560  -6.060  79.260  1.00 25.00           C
ATOM     68  CA  ARG    68      19.940  -7.030  82.120  1.00 25.00           C
ATOM     69  CA  LEU    69      17.553  -9.259  84.120  1.00 25.00           C
ATOM     70  CA  THR    70      16.452 -10.887  87.428  1.00 25.00           C
ATOM     71  CA  ALA    71      12.914 -10.816  86.109  1.00 25.00           C
ATOM     72  CA  LYS    72      12.352 -13.904  83.864  1.00 25.00           C
ATOM     73  CA  HIS    73      12.797 -14.179  80.064  1.00 25.00           C
ATOM     74  CA  PRO    74      16.103 -13.685  78.368  1.00 25.00           C
ATOM     75  CA  TYR    75      19.539 -15.324  77.821  1.00 25.00           C
ATOM     76  CA  ASP    76      23.128 -13.994  77.686  1.00 25.00           C
ATOM     77  CA  LYS    77      22.545 -12.020  80.914  1.00 25.00           C
ATOM     78  CA  VAL    78      21.147 -15.157  82.609  1.00 25.00           C
ATOM     79  CA  GLN    79      24.204 -17.163  81.472  1.00 25.00           C
ATOM     80  CA  ASP    80      26.529 -14.451  82.853  1.00 25.00           C
ATOM     81  CA  ARG    81      30.272 -14.833  83.402  1.00 25.00           C
ATOM     82  CA  ASN    82      31.895 -11.395  83.283  1.00 25.00           C
ATOM     83  CA  ARG    83      32.009  -8.467  85.618  1.00 25.00           C
ATOM     84  CA  LYS    84      29.202  -9.690  87.846  1.00 25.00           C
ATOM     85  CA  LEU    85      26.585  -8.089  85.551  1.00 25.00           C
ATOM     86  CA  TYR    86      23.671  -6.015  86.895  1.00 25.00           C
ATOM     87  CA  GLY    87      20.342  -4.653  88.298  1.00 25.00           C
ATOM     88  CA  ARG    88      18.912  -1.261  87.306  1.00 25.00           C
ATOM     89  CA  HIS    89      16.237  -2.308  84.810  1.00 25.00           C
ATOM     90  CA  ILE    90      13.410   0.203  84.908  1.00 25.00           C
ATOM     91  CA  THR    91      10.219   2.259  85.320  1.00 25.00           C
ATOM     92  CA  LEU    92       7.110   4.313  86.007  1.00 25.00           C
ATOM     93  CA  ASN    93       3.594   3.672  87.361  1.00 25.00           C
ATOM     94  CA  ASP    94      -0.188   4.360  87.584  1.00 25.00           C
ATOM     95  CA  GLY    95      -2.072   2.927  84.561  1.00 25.00           C
ATOM     96  CA  ASN    96       0.235   0.640  82.562  1.00 25.00           C
ATOM     97  CA  SER    97       3.850  -0.316  83.445  1.00 25.00           C
ATOM     98  CA  VAL    98       7.492  -1.115  82.690  1.00 25.00           C
ATOM     99  CA  LYS    99       9.751   0.894  80.369  1.00 25.00           C
ATOM    100  CA  VAL   100       7.530   3.685  79.137  1.00 25.00           C
ATOM    101  CA  VAL   101       6.200   5.192  75.955  1.00 25.00           C
ATOM    102  CA  THR   102       7.132   8.467  74.290  1.00 25.00           C
ATOM    103  CA  ILE   103      10.483   9.601  72.985  1.00 25.00           C
ATOM    104  CA  SER   104       9.092  12.669  71.133  1.00 25.00           C
ATOM    105  CA  ALA   105      10.011  11.970  67.472  1.00 25.00           C
ATOM    106  CA  GLY   106      11.221  15.336  66.180  1.00 25.00           C
ATOM    107  CA  ARG   107      14.166  16.422  63.982  1.00 25.00           C
ATOM    108  CA  ASP   108      14.501  18.367  60.722  1.00 25.00           C
ATOM    109  CA  GLU   109      18.075  18.965  59.661  1.00 25.00           C
ATOM    110  CA  GLY   110      18.336  15.280  58.563  1.00 25.00           C
ATOM    111  CA  PRO   111      18.483  14.445  54.861  1.00 25.00           C
ATOM    112  CA  ASP   112      16.457  11.239  55.203  1.00 25.00           C
ATOM    113  CA  ARG   113      13.773  12.542  57.643  1.00 25.00           C
ATOM    114  CA  ASP   114      10.645  13.926  55.920  1.00 25.00           C
ATOM    115  CA  ILE   115       9.847  10.451  54.521  1.00 25.00           C
ATOM    116  CA  ILE   116      10.262   8.925  58.010  1.00 25.00           C
ATOM    117  CA  TRP   117       7.925  11.581  59.476  1.00 25.00           C
ATOM    118  CA  GLU   118       5.332  10.836  56.758  1.00 25.00           C
ATOM    119  CA  MET   119       5.578   7.090  57.515  1.00 25.00           C
ATOM    120  CA  PHE   120       5.095   7.788  61.249  1.00 25.00           C
ATOM    121  CA  LEU   121       2.027   9.943  60.475  1.00 25.00           C
ATOM    122  CA  GLU   122       0.585   7.149  58.289  1.00 25.00           C
ATOM    123  CA  ASN   123       1.164   4.616  61.102  1.00 25.00           C
ATOM    124  CA  LEU   124       1.570   1.733  58.644  1.00 25.00           C
ATOM    125  CA  GLU   125      -1.039   2.711  56.093  1.00 25.00           C
TER
END
