
#######################################################
#                                                     #
#                        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   43 (  172),  selected   43 , name T0366AL509_1
# Molecule2: number of CA atoms   84 (  589),  selected   84 , name T0366.pdb
# PARAMETERS: T0366AL509_1.T0366.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      L      11           -
LGA    R      12      R      12          1.805
LGA    T      13      T      13          0.603
LGA    V      14      V      14          1.209
LGA    E      15      E      15          1.528
LGA    M      16      M      16          1.803
LGA    K      17      K      17          1.697
LGA    K      18      K      18          1.606
LGA    G      19      -       -           -
LGA    P      20      -       -           -
LGA    T      21      -       -           -
LGA    D      22      S      23          3.684
LGA    S      23      L      24          3.763
LGA    L      24      G      25          3.589
LGA    G      25      I      26          2.491
LGA    I      26      S      27          3.001
LGA    -       -      I      28           -
LGA    -       -      A      29           -
LGA    -       -      G      30           -
LGA    -       -      G      31           -
LGA    -       -      V      32           -
LGA    -       -      G      33           -
LGA    -       -      S      34           -
LGA    -       -      P      35           -
LGA    -       -      L      36           -
LGA    -       -      G      37           -
LGA    -       -      D      38           -
LGA    -       -      V      39           -
LGA    -       -      P      40           -
LGA    -       -      I      41           -
LGA    -       -      F      42           -
LGA    -       -      I      43           -
LGA    -       -      A      44           -
LGA    -       -      M      45           -
LGA    -       -      M      46           -
LGA    -       -      H      47           -
LGA    -       -      P      48           -
LGA    -       -      T      49           -
LGA    -       -      G      50           -
LGA    -       -      V      51           -
LGA    -       -      A      52           -
LGA    -       -      A      53           -
LGA    -       -      Q      54           -
LGA    -       -      T      55           -
LGA    -       -      Q      56           -
LGA    -       -      K      57           -
LGA    -       -      L      58           -
LGA    -       -      R      59           -
LGA    -       -      V      60           -
LGA    G      69      G      61          1.582
LGA    T      70      D      62          1.196
LGA    -       -      R      63           -
LGA    -       -      I      64           -
LGA    -       -      V      65           -
LGA    -       -      T      66           -
LGA    -       -      I      67           -
LGA    -       -      C      68           -
LGA    -       -      G      69           -
LGA    -       -      T      70           -
LGA    -       -      S      71           -
LGA    -       -      T      72           -
LGA    E      73      E      73          2.008
LGA    G      74      G      74          1.765
LGA    M      75      M      75          0.561
LGA    T      76      T      76          0.472
LGA    H      77      H      77          0.483
LGA    T      78      T      78          0.560
LGA    Q      79      Q      79          0.058
LGA    A      80      A      80          0.392
LGA    V      81      V      81          0.829
LGA    N      82      N      82          0.942
LGA    L      83      L      83          0.852
LGA    L      84      L      84          0.973
LGA    K      85      K      85          1.903
LGA    N      86      N      86          2.178
LGA    A      87      A      87          1.096
LGA    S      88      S      88          1.082
LGA    G      89      G      89          3.491
LGA    S      90      S      90          2.835
LGA    I      91      I      91          1.282
LGA    E      92      E      92          0.599
LGA    M      93      M      93          0.585
LGA    Q      94      Q      94          1.219
LGA    V      95      V      95          0.481
LGA    V      96      V      96          1.109
LGA    A      97      A      97          1.144
LGA    G      98      G      98          4.504

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   43   84    5.0     40    1.91    85.00     43.139     1.994

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.159574 * X  +  -0.071087 * Y  +  -0.984623 * Z  +   6.663598
  Y_new =   0.969704 * X  +   0.175587 * Y  +  -0.169833 * Z  +  20.423342
  Z_new =   0.184960 * X  +  -0.981894 * Y  +   0.040914 * Z  +  11.823877 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.529152    1.612441  [ DEG:   -87.6140     92.3860 ]
  Theta =  -0.186031   -2.955562  [ DEG:   -10.6588   -169.3412 ]
  Phi   =   1.733894   -1.407698  [ DEG:    99.3448    -80.6552 ]
 
# 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: T0366AL509_1                                  
REMARK     2: T0366.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0366AL509_1.T0366.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   43   84   5.0   40   1.91   85.00  43.139
REMARK  ---------------------------------------------------------- 
MOLECULE T0366AL509_1
REMARK Aligment from pdb entry: 1ihj_A
ATOM      1  N   ARG    12      14.520  30.396  10.412  1.00  0.00              
ATOM      2  CA  ARG    12      13.747  30.929   9.301  1.00  0.00              
ATOM      3  C   ARG    12      12.319  30.406   9.363  1.00  0.00              
ATOM      4  O   ARG    12      12.001  29.556  10.193  1.00  0.00              
ATOM      5  N   THR    13      11.457  30.931   8.500  1.00  0.00              
ATOM      6  CA  THR    13      10.054  30.536   8.503  1.00  0.00              
ATOM      7  C   THR    13       9.697  29.704   7.291  1.00  0.00              
ATOM      8  O   THR    13      10.122  30.001   6.177  1.00  0.00              
ATOM      9  N   VAL    14       8.902  28.664   7.513  1.00  0.00              
ATOM     10  CA  VAL    14       8.468  27.803   6.424  1.00  0.00              
ATOM     11  C   VAL    14       6.978  27.536   6.560  1.00  0.00              
ATOM     12  O   VAL    14       6.513  27.101   7.607  1.00  0.00              
ATOM     13  N   GLU    15       6.229  27.812   5.500  1.00  0.00              
ATOM     14  CA  GLU    15       4.799  27.560   5.515  1.00  0.00              
ATOM     15  C   GLU    15       4.519  26.354   4.628  1.00  0.00              
ATOM     16  O   GLU    15       4.976  26.293   3.488  1.00  0.00              
ATOM     17  N   MET    16       3.796  25.384   5.171  1.00  0.00              
ATOM     18  CA  MET    16       3.433  24.192   4.424  1.00  0.00              
ATOM     19  C   MET    16       1.919  24.192   4.236  1.00  0.00              
ATOM     20  O   MET    16       1.165  24.546   5.146  1.00  0.00              
ATOM     21  N   LYS    17       1.492  23.800   3.046  1.00  0.00              
ATOM     22  CA  LYS    17       0.079  23.730   2.705  1.00  0.00              
ATOM     23  C   LYS    17      -0.134  22.298   2.231  1.00  0.00              
ATOM     24  O   LYS    17       0.459  21.884   1.235  1.00  0.00              
ATOM     25  N   LYS    18      -0.956  21.532   2.941  1.00  0.00              
ATOM     26  CA  LYS    18      -1.179  20.148   2.543  1.00  0.00              
ATOM     27  C   LYS    18      -2.371  19.962   1.620  1.00  0.00              
ATOM     28  O   LYS    18      -2.859  18.847   1.453  1.00  0.00              
ATOM     29  N   GLY    19      -2.836  21.053   1.022  1.00  0.00              
ATOM     30  CA  GLY    19      -3.960  20.969   0.095  1.00  0.00              
ATOM     31  C   GLY    19      -3.646  19.929  -0.976  1.00  0.00              
ATOM     32  O   GLY    19      -2.625  20.018  -1.661  1.00  0.00              
ATOM     33  N   PRO    20      -4.517  18.933  -1.100  1.00  0.00              
ATOM     34  CA  PRO    20      -4.324  17.894  -2.096  1.00  0.00              
ATOM     35  C   PRO    20      -3.412  16.764  -1.664  1.00  0.00              
ATOM     36  O   PRO    20      -3.121  15.857  -2.450  1.00  0.00              
ATOM     37  N   THR    21      -2.964  16.812  -0.411  1.00  0.00              
ATOM     38  CA  THR    21      -2.073  15.789   0.136  1.00  0.00              
ATOM     39  C   THR    21      -2.642  15.239   1.443  1.00  0.00              
ATOM     40  O   THR    21      -3.361  15.934   2.150  1.00  0.00              
ATOM     41  N   ASP    22      -2.305  13.992   1.758  1.00  0.00              
ATOM     42  CA  ASP    22      -2.790  13.324   2.963  1.00  0.00              
ATOM     43  C   ASP    22      -2.308  13.916   4.284  1.00  0.00              
ATOM     44  O   ASP    22      -2.998  13.839   5.304  1.00  0.00              
ATOM     45  N   SER    23      -1.118  14.495   4.274  1.00  0.00              
ATOM     46  CA  SER    23      -0.572  15.076   5.493  1.00  0.00              
ATOM     47  C   SER    23       0.548  16.019   5.118  1.00  0.00              
ATOM     48  O   SER    23       0.892  16.142   3.945  1.00  0.00              
ATOM     49  N   LEU    24       1.129  16.681   6.112  1.00  0.00              
ATOM     50  CA  LEU    24       2.209  17.609   5.829  1.00  0.00              
ATOM     51  C   LEU    24       3.493  16.862   5.486  1.00  0.00              
ATOM     52  O   LEU    24       4.335  17.374   4.748  1.00  0.00              
ATOM     53  N   GLY    25       3.630  15.652   6.023  1.00  0.00              
ATOM     54  CA  GLY    25       4.789  14.829   5.714  1.00  0.00              
ATOM     55  C   GLY    25       5.986  14.923   6.639  1.00  0.00              
ATOM     56  O   GLY    25       7.116  14.663   6.218  1.00  0.00              
ATOM     57  N   ILE    26       5.764  15.303   7.891  1.00  0.00              
ATOM     58  CA  ILE    26       6.880  15.385   8.817  1.00  0.00              
ATOM     59  C   ILE    26       6.697  14.451   9.996  1.00  0.00              
ATOM     60  O   ILE    26       5.591  14.291  10.515  1.00  0.00              
ATOM     61  N   GLY    69      16.644  16.830  10.820  1.00  0.00              
ATOM     62  CA  GLY    69      17.590  17.373  11.780  1.00  0.00              
ATOM     63  C   GLY    69      17.245  18.797  12.190  1.00  0.00              
ATOM     64  O   GLY    69      17.775  19.312  13.174  1.00  0.00              
ATOM     65  N   THR    70      16.366  19.449  11.431  1.00  0.00              
ATOM     66  CA  THR    70      15.961  20.818  11.769  1.00  0.00              
ATOM     67  C   THR    70      15.145  20.792  13.052  1.00  0.00              
ATOM     68  O   THR    70      14.463  19.811  13.326  1.00  0.00              
ATOM     69  N   GLU    73       9.128  24.669  21.915  1.00  0.00              
ATOM     70  CA  GLU    73      10.472  24.293  22.344  1.00  0.00              
ATOM     71  C   GLU    73      10.487  23.200  23.407  1.00  0.00              
ATOM     72  O   GLU    73      11.343  22.319  23.381  1.00  0.00              
ATOM     73  N   GLY    74       9.539  23.249  24.337  1.00  0.00              
ATOM     74  CA  GLY    74       9.491  22.255  25.407  1.00  0.00              
ATOM     75  C   GLY    74       8.274  21.341  25.339  1.00  0.00              
ATOM     76  O   GLY    74       7.945  20.658  26.309  1.00  0.00              
ATOM     77  N   MET    75       7.614  21.316  24.187  1.00  0.00              
ATOM     78  CA  MET    75       6.431  20.486  24.021  1.00  0.00              
ATOM     79  C   MET    75       6.761  19.009  23.853  1.00  0.00              
ATOM     80  O   MET    75       7.875  18.636  23.470  1.00  0.00              
ATOM     81  N   THR    76       5.783  18.170  24.169  1.00  0.00              
ATOM     82  CA  THR    76       5.917  16.734  24.000  1.00  0.00              
ATOM     83  C   THR    76       5.650  16.522  22.511  1.00  0.00              
ATOM     84  O   THR    76       5.096  17.407  21.855  1.00  0.00              
ATOM     85  N   HIS    77       6.035  15.371  21.972  1.00  0.00              
ATOM     86  CA  HIS    77       5.793  15.109  20.557  1.00  0.00              
ATOM     87  C   HIS    77       4.294  15.108  20.270  1.00  0.00              
ATOM     88  O   HIS    77       3.838  15.713  19.302  1.00  0.00              
ATOM     89  N   THR    78       3.526  14.438  21.122  1.00  0.00              
ATOM     90  CA  THR    78       2.084  14.368  20.922  1.00  0.00              
ATOM     91  C   THR    78       1.425  15.740  20.902  1.00  0.00              
ATOM     92  O   THR    78       0.497  15.976  20.126  1.00  0.00              
ATOM     93  N   GLN    79       1.896  16.644  21.758  1.00  0.00              
ATOM     94  CA  GLN    79       1.340  17.990  21.821  1.00  0.00              
ATOM     95  C   GLN    79       1.528  18.723  20.495  1.00  0.00              
ATOM     96  O   GLN    79       0.650  19.467  20.056  1.00  0.00              
ATOM     97  N   ALA    80       2.679  18.524  19.860  1.00  0.00              
ATOM     98  CA  ALA    80       2.937  19.180  18.584  1.00  0.00              
ATOM     99  C   ALA    80       2.051  18.554  17.513  1.00  0.00              
ATOM    100  O   ALA    80       1.498  19.261  16.666  1.00  0.00              
ATOM    101  N   VAL    81       1.916  17.232  17.551  1.00  0.00              
ATOM    102  CA  VAL    81       1.073  16.541  16.576  1.00  0.00              
ATOM    103  C   VAL    81      -0.373  17.019  16.709  1.00  0.00              
ATOM    104  O   VAL    81      -1.041  17.269  15.704  1.00  0.00              
ATOM    105  N   ASN    82      -0.855  17.152  17.942  1.00  0.00              
ATOM    106  CA  ASN    82      -2.224  17.620  18.148  1.00  0.00              
ATOM    107  C   ASN    82      -2.389  19.020  17.562  1.00  0.00              
ATOM    108  O   ASN    82      -3.392  19.312  16.910  1.00  0.00              
ATOM    109  N   LEU    83      -1.403  19.881  17.794  1.00  0.00              
ATOM    110  CA  LEU    83      -1.441  21.245  17.273  1.00  0.00              
ATOM    111  C   LEU    83      -1.542  21.241  15.751  1.00  0.00              
ATOM    112  O   LEU    83      -2.311  22.006  15.165  1.00  0.00              
ATOM    113  N   LEU    84      -0.755  20.384  15.111  1.00  0.00              
ATOM    114  CA  LEU    84      -0.775  20.293  13.659  1.00  0.00              
ATOM    115  C   LEU    84      -2.130  19.811  13.146  1.00  0.00              
ATOM    116  O   LEU    84      -2.655  20.349  12.172  1.00  0.00              
ATOM    117  N   LYS    85      -2.695  18.802  13.803  1.00  0.00              
ATOM    118  CA  LYS    85      -3.984  18.259  13.382  1.00  0.00              
ATOM    119  C   LYS    85      -5.126  19.242  13.592  1.00  0.00              
ATOM    120  O   LYS    85      -6.166  19.151  12.938  1.00  0.00              
ATOM    121  N   ASN    86      -4.924  20.193  14.495  1.00  0.00              
ATOM    122  CA  ASN    86      -5.935  21.200  14.778  1.00  0.00              
ATOM    123  C   ASN    86      -5.906  22.314  13.743  1.00  0.00              
ATOM    124  O   ASN    86      -6.834  23.118  13.661  1.00  0.00              
ATOM    125  N   ALA    87      -4.840  22.358  12.952  1.00  0.00              
ATOM    126  CA  ALA    87      -4.707  23.375  11.922  1.00  0.00              
ATOM    127  C   ALA    87      -5.548  22.992  10.707  1.00  0.00              
ATOM    128  O   ALA    87      -5.934  21.836  10.544  1.00  0.00              
ATOM    129  N   SER    88      -5.841  23.967   9.856  1.00  0.00              
ATOM    130  CA  SER    88      -6.631  23.696   8.664  1.00  0.00              
ATOM    131  C   SER    88      -5.751  22.976   7.647  1.00  0.00              
ATOM    132  O   SER    88      -5.398  21.811   7.832  1.00  0.00              
ATOM    133  N   GLY    89      -5.386  23.680   6.582  1.00  0.00              
ATOM    134  CA  GLY    89      -4.547  23.106   5.542  1.00  0.00              
ATOM    135  C   GLY    89      -3.130  23.661   5.594  1.00  0.00              
ATOM    136  O   GLY    89      -2.254  23.188   4.875  1.00  0.00              
ATOM    137  N   SER    90      -2.902  24.660   6.441  1.00  0.00              
ATOM    138  CA  SER    90      -1.574  25.254   6.533  1.00  0.00              
ATOM    139  C   SER    90      -0.999  25.389   7.933  1.00  0.00              
ATOM    140  O   SER    90      -1.714  25.571   8.921  1.00  0.00              
ATOM    141  N   ILE    91       0.321  25.295   8.002  1.00  0.00              
ATOM    142  CA  ILE    91       1.034  25.452   9.258  1.00  0.00              
ATOM    143  C   ILE    91       2.274  26.277   8.947  1.00  0.00              
ATOM    144  O   ILE    91       2.936  26.055   7.928  1.00  0.00              
ATOM    145  N   GLU    92       2.562  27.257   9.799  1.00  0.00              
ATOM    146  CA  GLU    92       3.741  28.082   9.610  1.00  0.00              
ATOM    147  C   GLU    92       4.720  27.624  10.673  1.00  0.00              
ATOM    148  O   GLU    92       4.409  27.644  11.862  1.00  0.00              
ATOM    149  N   MET    93       5.899  27.210  10.233  1.00  0.00              
ATOM    150  CA  MET    93       6.913  26.703  11.141  1.00  0.00              
ATOM    151  C   MET    93       8.114  27.621  11.273  1.00  0.00              
ATOM    152  O   MET    93       8.643  28.095  10.271  1.00  0.00              
ATOM    153  N   GLN    94       8.524  27.875  12.514  1.00  0.00              
ATOM    154  CA  GLN    94       9.713  28.677  12.790  1.00  0.00              
ATOM    155  C   GLN    94      10.722  27.544  12.921  1.00  0.00              
ATOM    156  O   GLN    94      10.613  26.719  13.832  1.00  0.00              
ATOM    157  N   VAL    95      11.681  27.511  12.006  1.00  0.00              
ATOM    158  CA  VAL    95      12.674  26.442  11.936  1.00  0.00              
ATOM    159  C   VAL    95      14.095  26.919  12.219  1.00  0.00              
ATOM    160  O   VAL    95      14.494  27.987  11.770  1.00  0.00              
ATOM    161  N   VAL    96      14.849  26.128  12.980  1.00  0.00              
ATOM    162  CA  VAL    96      16.250  26.449  13.241  1.00  0.00              
ATOM    163  C   VAL    96      16.999  25.351  12.501  1.00  0.00              
ATOM    164  O   VAL    96      16.816  24.166  12.790  1.00  0.00              
ATOM    165  N   ALA    97      17.831  25.744  11.540  1.00  0.00              
ATOM    166  CA  ALA    97      18.549  24.784  10.709  1.00  0.00              
ATOM    167  C   ALA    97      20.057  24.984  10.590  1.00  0.00              
ATOM    168  O   ALA    97      20.604  25.992  11.037  1.00  0.00              
ATOM    169  N   GLY    98      20.698  24.003   9.954  1.00  0.00              
ATOM    170  CA  GLY    98      22.137  23.987   9.709  1.00  0.00              
ATOM    171  C   GLY    98      22.932  23.704  10.975  1.00  0.00              
ATOM    172  O   GLY    98      23.785  22.795  10.929  1.00  0.00              
END
