
#######################################################
#                                                     #
#                        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_5
# Molecule2: number of CA atoms   99 (  800),  selected   99 , name T0285.pdb
# PARAMETERS: T0285TS393_5.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      S       7           #
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      -       -           -
LGA    P      36      -       -           -
LGA    N      37      P       8          4.103
LGA    W      38      A       9          3.521
LGA    S      39      K      10           #
LGA    -       -      R      11           -
LGA    L      40      L      12          3.136
LGA    -       -      L      13           -
LGA    -       -      F      14           -
LGA    -       -      Q      15           -
LGA    R      41      M      16          3.168
LGA    F      42      V      17           #
LGA    V      43      G      18           -
LGA    Y      44      N      19           -
LGA    I      45      A      20          3.729
LGA    V      46      I      21          5.075
LGA    D      47      N      22          3.120
LGA    R      48      R      23          1.946
LGA    -       -      N      24           -
LGA    -       -      T      25           -
LGA    -       -      Q      26           -
LGA    N      49      Q      27          2.244
LGA    N      50      L      28          4.215
LGA    Q      51      T      29           #
LGA    D      52      Q      30           #
LGA    L      53      D      31          4.604
LGA    L      54      L      32          3.636
LGA    K      55      R      33          5.146
LGA    -       -      A      34           -
LGA    R      56      M      35          3.654
LGA    P      57      P      36           #
LGA    L      58      N      37           -
LGA    P      59      W      38           #
LGA    P      60      S      39          1.608
LGA    G      61      L      40          0.495
LGA    -       -      R      41           -
LGA    I      62      F      42          4.248
LGA    M      63      V      43          2.453
LGA    V      64      Y      44          2.789
LGA    L      65      I      45           #
LGA    A      66      V      46          4.153
LGA    P      67      D      47          1.976
LGA    R      68      R      48          3.620
LGA    L      69      N      49          1.812
LGA    T      70      N      50           -
LGA    A      71      -       -           -
LGA    K      72      -       -           -
LGA    H      73      -       -           -
LGA    P      74      -       -           -
LGA    Y      75      -       -           -
LGA    D      76      -       -           -
LGA    K      77      -       -           -
LGA    V      78      Q      51           #
LGA    Q      79      D      52           -
LGA    D      80      L      53           -
LGA    R      81      -       -           -
LGA    N      82      -       -           -
LGA    R      83      -       -           -
LGA    K      84      L      54           #
LGA    L      85      K      55          2.754
LGA    Y      86      R      56          4.510
LGA    G      87      P      57          3.474
LGA    R      88      L      58          3.446
LGA    H      89      P      59          3.836
LGA    I      90      P      60          4.693
LGA    T      91      G      61          2.482
LGA    L      92      I      62           #
LGA    N      93      M      63           #
LGA    D      94      -       -           -
LGA    G      95      -       -           -
LGA    N      96      V      64           #
LGA    S      97      L      65          5.126
LGA    V      98      A      66          4.126
LGA    K      99      P      67           #
LGA    -       -      R      68           -
LGA    -       -      L      69           -
LGA    -       -      T      70           -
LGA    -       -      A      71           -
LGA    -       -      K      72           -
LGA    -       -      H      73           -
LGA    -       -      P      74           -
LGA    V     100      Y      75           #
LGA    V     101      D      76          1.329
LGA    T     102      K      77          4.916
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    I     103      R      88           #
LGA    S     104      H      89           -
LGA    A     105      I      90           -
LGA    G     106      T      91           -
LGA    R     107      L      92           -
LGA    D     108      N      93           -
LGA    E     109      D      94           -
LGA    G     110      G      95           -
LGA    P     111      N      96           -
LGA    D     112      S      97           -
LGA    R     113      V      98           -
LGA    D     114      K      99           -
LGA    I     115      V     100           -
LGA    I     116      V     101           -
LGA    W     117      T     102           -
LGA    E     118      I     103           -
LGA    M     119      S     104           -
LGA    F     120      A     105           -
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     34    3.58    11.76     20.745     0.924

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.990342 * X  +   0.069836 * Y  +   0.119775 * Z  +  15.855698
  Y_new =  -0.049517 * X  +   0.985063 * Y  +  -0.164923 * Z  +   6.922435
  Z_new =  -0.129503 * X  +   0.157399 * Y  +   0.979007 * Z  +  79.398315 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.159410   -2.982183  [ DEG:     9.1335   -170.8665 ]
  Theta =   0.129868    3.011725  [ DEG:     7.4409    172.5591 ]
  Phi   =  -0.049959    3.091634  [ DEG:    -2.8624    177.1376 ]
 
# 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_5                                  
REMARK     2: T0285.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0285TS393_5.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   34   3.58   11.76  20.745
REMARK  ---------------------------------------------------------- 
MOLECULE T0285TS393_5
PFRMAT TS
TARGET T0285
MODEL 5
PARENT N/A
ATOM      1  CA  ALA     1      -5.442  -4.695  63.229  1.00 25.00           C
ATOM      2  CA  TYR     2      -4.914  -1.817  65.660  1.00 25.00           C
ATOM      3  CA  LEU     3      -1.205  -1.930  64.775  1.00 25.00           C
ATOM      4  CA  PRO     4       1.599  -1.935  62.215  1.00 25.00           C
ATOM      5  CA  ASP     5       4.246  -4.009  64.043  1.00 25.00           C
ATOM      6  CA  ASP     6       7.017  -1.671  63.124  1.00 25.00           C
ATOM      7  CA  SER     7       8.007   0.463  66.050  1.00 25.00           C
ATOM      8  CA  PRO     8       9.032   3.385  68.231  1.00 25.00           C
ATOM      9  CA  ALA     9       7.037   5.987  70.208  1.00 25.00           C
ATOM     10  CA  LYS    10       6.806   3.586  73.183  1.00 25.00           C
ATOM     11  CA  ARG    11      10.585   2.986  73.024  1.00 25.00           C
ATOM     12  CA  LEU    12      11.207   6.765  72.956  1.00 25.00           C
ATOM     13  CA  LEU    13       8.915   7.221  75.990  1.00 25.00           C
ATOM     14  CA  PHE    14      10.793   4.453  77.855  1.00 25.00           C
ATOM     15  CA  GLN    15      14.135   6.127  77.024  1.00 25.00           C
ATOM     16  CA  MET    16      12.799   9.482  78.298  1.00 25.00           C
ATOM     17  CA  VAL    17      11.624   7.812  81.538  1.00 25.00           C
ATOM     18  CA  GLY    18      15.071   6.206  81.989  1.00 25.00           C
ATOM     19  CA  ASN    19      16.753   9.604  81.445  1.00 25.00           C
ATOM     20  CA  ALA    20      14.425  11.199  84.033  1.00 25.00           C
ATOM     21  CA  ILE    21      15.255   8.416  86.530  1.00 25.00           C
ATOM     22  CA  ASN    22      18.998   8.956  85.925  1.00 25.00           C
ATOM     23  CA  ARG    23      18.571  12.720  86.490  1.00 25.00           C
ATOM     24  CA  ASN    24      16.680  12.042  89.750  1.00 25.00           C
ATOM     25  CA  THR    25      19.467   9.682  90.904  1.00 25.00           C
ATOM     26  CA  GLN    26      22.094  12.349  90.095  1.00 25.00           C
ATOM     27  CA  GLN    27      20.098  14.951  92.072  1.00 25.00           C
ATOM     28  CA  LEU    28      19.868  12.550  95.047  1.00 25.00           C
ATOM     29  CA  THR    29      23.647  11.951  94.888  1.00 25.00           C
ATOM     30  CA  GLN    30      24.268  15.729  94.820  1.00 25.00           C
ATOM     31  CA  ASP    31      21.977  16.185  97.854  1.00 25.00           C
ATOM     32  CA  LEU    32      23.854  13.417  99.719  1.00 25.00           C
ATOM     33  CA  ARG    33      27.197  15.093  98.889  1.00 25.00           C
ATOM     34  CA  ALA    34      28.605  13.342  95.821  1.00 25.00           C
ATOM     35  CA  MET    35      28.704  15.279  92.536  1.00 25.00           C
ATOM     36  CA  PRO    36      27.276  17.449  89.780  1.00 25.00           C
ATOM     37  CA  ASN    37      25.669  19.219  86.823  1.00 25.00           C
ATOM     38  CA  TRP    38      22.246  17.715  87.292  1.00 25.00           C
ATOM     39  CA  SER    39      22.903  15.887  84.041  1.00 25.00           C
ATOM     40  CA  LEU    40      22.008  12.460  82.735  1.00 25.00           C
ATOM     41  CA  ARG    41      21.003  11.157  79.267  1.00 25.00           C
ATOM     42  CA  PHE    42      20.665   7.461  78.210  1.00 25.00           C
ATOM     43  CA  VAL    43      18.468   4.349  78.725  1.00 25.00           C
ATOM     44  CA  TYR    44      19.839   3.453  75.260  1.00 25.00           C
ATOM     45  CA  ILE    45      17.803   6.019  73.369  1.00 25.00           C
ATOM     46  CA  VAL    46      17.855   3.483  70.527  1.00 25.00           C
ATOM     47  CA  ASP    47      19.553   5.518  67.766  1.00 25.00           C
ATOM     48  CA  ARG    48      22.864   3.660  67.648  1.00 25.00           C
ATOM     49  CA  ASN    49      26.647   3.077  67.325  1.00 25.00           C
ATOM     50  CA  ASN    50      27.425   5.274  70.349  1.00 25.00           C
ATOM     51  CA  GLN    51      30.810   4.643  72.027  1.00 25.00           C
ATOM     52  CA  ASP    52      31.920   8.211  71.184  1.00 25.00           C
ATOM     53  CA  LEU    53      28.666   9.596  72.654  1.00 25.00           C
ATOM     54  CA  LEU    54      29.204   7.541  75.842  1.00 25.00           C
ATOM     55  CA  LYS    55      32.355   7.342  77.956  1.00 25.00           C
ATOM     56  CA  ARG    56      33.012  11.039  78.090  1.00 25.00           C
ATOM     57  CA  PRO    57      32.028  14.639  77.578  1.00 25.00           C
ATOM     58  CA  LEU    58      28.738  15.195  79.407  1.00 25.00           C
ATOM     59  CA  PRO    59      29.683  12.935  82.318  1.00 25.00           C
ATOM     60  CA  PRO    60      30.478   9.719  84.089  1.00 25.00           C
ATOM     61  CA  GLY    61      27.762   6.995  84.054  1.00 25.00           C
ATOM     62  CA  ILE    62      24.345   8.177  82.794  1.00 25.00           C
ATOM     63  CA  MET    63      21.668   5.417  82.961  1.00 25.00           C
ATOM     64  CA  VAL    64      18.783   3.268  84.106  1.00 25.00           C
ATOM     65  CA  LEU    65      16.025   0.606  84.560  1.00 25.00           C
ATOM     66  CA  ALA    66      13.470   0.496  81.702  1.00 25.00           C
ATOM     67  CA  PRO    67      15.493  -1.655  79.393  1.00 25.00           C
ATOM     68  CA  ARG    68      16.202  -5.435  79.399  1.00 25.00           C
ATOM     69  CA  LEU    69      12.852  -7.051  80.189  1.00 25.00           C
ATOM     70  CA  THR    70      10.116  -9.668  80.562  1.00 25.00           C
ATOM     71  CA  ALA    71       9.704  -8.399  84.063  1.00 25.00           C
ATOM     72  CA  LYS    72      10.775 -11.816  85.293  1.00 25.00           C
ATOM     73  CA  HIS    73      13.815 -10.486  87.209  1.00 25.00           C
ATOM     74  CA  PRO    74      15.508 -11.095  83.837  1.00 25.00           C
ATOM     75  CA  TYR    75      15.502 -11.853  80.051  1.00 25.00           C
ATOM     76  CA  ASP    76      17.663 -13.998  77.727  1.00 25.00           C
ATOM     77  CA  LYS    77      19.979 -11.017  77.087  1.00 25.00           C
ATOM     78  CA  VAL    78      20.277 -10.407  80.856  1.00 25.00           C
ATOM     79  CA  GLN    79      21.120 -14.101  81.412  1.00 25.00           C
ATOM     80  CA  ASP    80      23.792 -13.928  78.674  1.00 25.00           C
ATOM     81  CA  ARG    81      26.575 -11.393  79.275  1.00 25.00           C
ATOM     82  CA  ASN    82      29.571 -13.150  80.833  1.00 25.00           C
ATOM     83  CA  ARG    83      28.996 -12.931  84.566  1.00 25.00           C
ATOM     84  CA  LYS    84      28.234  -9.198  84.828  1.00 25.00           C
ATOM     85  CA  LEU    85      25.852  -6.252  84.906  1.00 25.00           C
ATOM     86  CA  TYR    86      24.316  -6.382  88.402  1.00 25.00           C
ATOM     87  CA  GLY    87      20.924  -5.570  86.766  1.00 25.00           C
ATOM     88  CA  ARG    88      20.881  -1.926  85.561  1.00 25.00           C
ATOM     89  CA  HIS    89      19.099  -0.464  88.600  1.00 25.00           C
ATOM     90  CA  ILE    90      17.091   2.714  89.397  1.00 25.00           C
ATOM     91  CA  THR    91      15.145   5.619  90.897  1.00 25.00           C
ATOM     92  CA  LEU    92      11.660   7.159  90.811  1.00 25.00           C
ATOM     93  CA  ASN    93      10.458   5.869  94.150  1.00 25.00           C
ATOM     94  CA  ASP    94       7.910   6.166  96.904  1.00 25.00           C
ATOM     95  CA  GLY    95       4.918   6.339  94.585  1.00 25.00           C
ATOM     96  CA  ASN    96       4.071   5.657  90.974  1.00 25.00           C
ATOM     97  CA  SER    97       6.779   2.954  90.605  1.00 25.00           C
ATOM     98  CA  VAL    98      10.112   2.872  88.704  1.00 25.00           C
ATOM     99  CA  LYS    99      10.502   5.452  85.936  1.00 25.00           C
ATOM    100  CA  VAL   100      10.052   9.219  86.476  1.00 25.00           C
ATOM    101  CA  VAL   101       7.824  11.827  84.817  1.00 25.00           C
ATOM    102  CA  THR   102      10.126  13.398  82.269  1.00 25.00           C
ATOM    103  CA  ILE   103      13.081  14.309  79.970  1.00 25.00           C
ATOM    104  CA  SER   104      10.639  15.383  77.268  1.00 25.00           C
ATOM    105  CA  ALA   105      13.017  18.201  76.317  1.00 25.00           C
ATOM    106  CA  GLY   106      10.996  20.900  74.449  1.00 25.00           C
ATOM    107  CA  ARG   107      13.359  22.038  71.684  1.00 25.00           C
ATOM    108  CA  ASP   108      14.957  25.468  71.536  1.00 25.00           C
ATOM    109  CA  GLU   109      15.188  27.351  68.257  1.00 25.00           C
ATOM    110  CA  GLY   110      13.462  26.353  65.031  1.00 25.00           C
ATOM    111  CA  PRO   111       9.973  27.118  66.271  1.00 25.00           C
ATOM    112  CA  ASP   112       9.967  24.375  68.919  1.00 25.00           C
ATOM    113  CA  ARG   113       7.837  24.037  72.019  1.00 25.00           C
ATOM    114  CA  ASP   114       4.057  23.908  72.618  1.00 25.00           C
ATOM    115  CA  ILE   115       3.428  24.155  68.848  1.00 25.00           C
ATOM    116  CA  ILE   116       5.917  21.313  68.221  1.00 25.00           C
ATOM    117  CA  TRP   117       4.171  19.168  70.870  1.00 25.00           C
ATOM    118  CA  GLU   118       0.778  19.870  69.238  1.00 25.00           C
ATOM    119  CA  MET   119       2.192  18.886  65.818  1.00 25.00           C
ATOM    120  CA  PHE   120       3.584  15.640  67.299  1.00 25.00           C
ATOM    121  CA  LEU   121       0.176  14.866  68.866  1.00 25.00           C
ATOM    122  CA  GLU   122      -1.542  15.496  65.502  1.00 25.00           C
ATOM    123  CA  ASN   123       0.951  13.165  63.765  1.00 25.00           C
ATOM    124  CA  LEU   124       2.031  14.590  60.353  1.00 25.00           C
ATOM    125  CA  GLU   125       0.410  15.750  57.110  1.00 25.00           C
TER
END
