
#######################################################
#                                                     #
#                        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   45 (  180),  selected   45 , name T0363AL333_5
# Molecule2: number of CA atoms   80 (  645),  selected   80 , name T0363.pdb
# PARAMETERS: T0363AL333_5.T0363.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      L      10           -
LGA    -       -      N      11           -
LGA    -       -      Q      12           -
LGA    -       -      I      13           -
LGA    -       -      N      14           -
LGA    -       -      I      15           -
LGA    -       -      E      16           -
LGA    -       -      I      17           -
LGA    -       -      A      18           -
LGA    -       -      Y      19           -
LGA    -       -      A      20           -
LGA    -       -      F      21           -
LGA    -       -      P      22           -
LGA    I      42      E      23           #
LGA    T      43      R      24          2.925
LGA    -       -      Y      25           -
LGA    Q      44      Y      26          2.411
LGA    S      45      L      27          1.427
LGA    G      46      K      28          3.605
LGA    I      47      S      29           #
LGA    L      48      F      30           -
LGA    -       -      Q      31           -
LGA    -       -      V      32           -
LGA    -       -      D      33           -
LGA    -       -      E      34           -
LGA    -       -      G      35           -
LGA    -       -      I      36           -
LGA    S      49      T      37           #
LGA    Q      50      V      38          1.751
LGA    -       -      Q      39           -
LGA    F      51      T      40          1.886
LGA    -       -      A      41           -
LGA    -       -      I      42           -
LGA    P      52      T      43           #
LGA    E      53      Q      44           -
LGA    I      54      S      45          4.608
LGA    D      55      G      46          2.497
LGA    L      56      I      47          3.410
LGA    S      57      L      48          3.523
LGA    T      58      S      49           -
LGA    -       -      Q      50           -
LGA    -       -      F      51           -
LGA    -       -      P      52           -
LGA    -       -      E      53           -
LGA    N      59      I      54          4.841
LGA    K      60      D      55          3.078
LGA    I      61      L      56          3.054
LGA    G      62      S      57          3.287
LGA    I      63      T      58          3.605
LGA    F      64      N      59          2.243
LGA    S      65      K      60          2.051
LGA    L      74      I      61          1.563
LGA    K      75      G      62          3.747
LGA    E      76      I      63          4.527
LGA    G      77      -       -           -
LGA    D      78      F      64          4.974
LGA    R      79      S      65           -
LGA    I      80      R      66           -
LGA    E      81      P      67           -
LGA    I      82      I      68           -
LGA    Y      83      K      69           -
LGA    R      84      L      70           -
LGA    P      85      T      71           -
LGA    P      90      D      72           -
LGA    K      91      V      73           -
LGA    E      92      L      74           -
LGA    I      93      K      75           -
LGA    R      94      E      76           -
LGA    R      95      G      77           -
LGA    E      96      D      78           -
LGA    G      97      R      79           -
LGA    -       -      I      80           -
LGA    -       -      E      81           -
LGA    -       -      I      82           -
LGA    -       -      Y      83           -
LGA    -       -      R      84           -
LGA    -       -      P      85           -
LGA    -       -      L      86           -
LGA    -       -      L      87           -
LGA    -       -      A      88           -
LGA    -       -      D      89           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   45   80    5.0     21    3.27     0.00     16.089     0.623

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.610050 * X  +   0.359930 * Y  +   0.705896 * Z  +  50.594231
  Y_new =   0.792019 * X  +   0.250763 * Y  +   0.556618 * Z  +  12.022046
  Z_new =   0.023331 * X  +   0.898648 * Y  +  -0.438049 * Z  +   3.957827 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.024357   -1.117236  [ DEG:   115.9871    -64.0129 ]
  Theta =  -0.023333   -3.118259  [ DEG:    -1.3369   -178.6631 ]
  Phi   =   2.227130   -0.914462  [ DEG:   127.6052    -52.3948 ]
 
# 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: T0363AL333_5                                  
REMARK     2: T0363.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL333_5.T0363.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   45   80   5.0   21   3.27    0.00  16.089
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL333_5
REMARK Aligment from pdb entry: 1a62
ATOM      1  N   MET     1      34.574  22.439 -12.446  1.00  0.00              
ATOM      2  CA  MET     1      34.108  22.241 -11.079  1.00  0.00              
ATOM      3  C   MET     1      32.825  21.434 -11.103  1.00  0.00              
ATOM      4  O   MET     1      32.038  21.534 -12.041  1.00  0.00              
ATOM      5  N   ILE    42      32.627  20.622 -10.071  1.00  0.00              
ATOM      6  CA  ILE    42      31.410  19.852  -9.941  1.00  0.00              
ATOM      7  C   ILE    42      30.943  20.079  -8.500  1.00  0.00              
ATOM      8  O   ILE    42      31.762  20.167  -7.571  1.00  0.00              
ATOM      9  N   THR    43      29.638  20.202  -8.321  1.00  0.00              
ATOM     10  CA  THR    43      29.093  20.470  -7.005  1.00  0.00              
ATOM     11  C   THR    43      28.153  19.396  -6.519  1.00  0.00              
ATOM     12  O   THR    43      27.662  18.571  -7.299  1.00  0.00              
ATOM     13  N   GLN    44      27.890  19.431  -5.216  1.00  0.00              
ATOM     14  CA  GLN    44      26.980  18.485  -4.598  1.00  0.00              
ATOM     15  C   GLN    44      26.414  19.085  -3.314  1.00  0.00              
ATOM     16  O   GLN    44      26.886  20.122  -2.845  1.00  0.00              
ATOM     17  N   SER    45      25.397  18.449  -2.750  1.00  0.00              
ATOM     18  CA  SER    45      24.819  18.955  -1.517  1.00  0.00              
ATOM     19  C   SER    45      24.064  17.856  -0.798  1.00  0.00              
ATOM     20  O   SER    45      23.791  16.796  -1.357  1.00  0.00              
ATOM     21  N   GLY    46      23.737  18.099   0.460  1.00  0.00              
ATOM     22  CA  GLY    46      23.011  17.089   1.203  1.00  0.00              
ATOM     23  C   GLY    46      22.968  17.381   2.681  1.00  0.00              
ATOM     24  O   GLY    46      23.502  18.389   3.144  1.00  0.00              
ATOM     25  N   ILE    47      22.315  16.494   3.419  1.00  0.00              
ATOM     26  CA  ILE    47      22.199  16.639   4.861  1.00  0.00              
ATOM     27  C   ILE    47      23.303  15.815   5.486  1.00  0.00              
ATOM     28  O   ILE    47      23.454  14.632   5.191  1.00  0.00              
ATOM     29  N   LEU    48      24.074  16.456   6.351  1.00  0.00              
ATOM     30  CA  LEU    48      25.187  15.788   6.984  1.00  0.00              
ATOM     31  C   LEU    48      24.804  14.930   8.169  1.00  0.00              
ATOM     32  O   LEU    48      23.953  15.307   8.986  1.00  0.00              
ATOM     33  N   SER    49      25.430  13.759   8.242  1.00  0.00              
ATOM     34  CA  SER    49      25.266  12.846   9.367  1.00  0.00              
ATOM     35  C   SER    49      26.680  12.416   9.714  1.00  0.00              
ATOM     36  O   SER    49      27.367  11.817   8.895  1.00  0.00              
ATOM     37  N   GLN    50      27.128  12.757  10.913  1.00  0.00              
ATOM     38  CA  GLN    50      28.457  12.374  11.366  1.00  0.00              
ATOM     39  C   GLN    50      28.322  11.004  12.023  1.00  0.00              
ATOM     40  O   GLN    50      27.512  10.818  12.933  1.00  0.00              
ATOM     41  N   PHE    51      29.100  10.036  11.557  1.00  0.00              
ATOM     42  CA  PHE    51      29.043   8.697  12.112  1.00  0.00              
ATOM     43  C   PHE    51      30.012   8.516  13.272  1.00  0.00              
ATOM     44  O   PHE    51      30.731   9.441  13.646  1.00  0.00              
ATOM     45  N   PRO    52      30.013   7.314  13.835  1.00  0.00              
ATOM     46  CA  PRO    52      30.864   6.974  14.974  1.00  0.00              
ATOM     47  C   PRO    52      32.342   7.310  14.799  1.00  0.00              
ATOM     48  O   PRO    52      32.938   7.987  15.643  1.00  0.00              
ATOM     49  N   GLU    53      32.932   6.830  13.713  1.00  0.00              
ATOM     50  CA  GLU    53      34.344   7.064  13.447  1.00  0.00              
ATOM     51  C   GLU    53      34.741   8.542  13.380  1.00  0.00              
ATOM     52  O   GLU    53      35.927   8.866  13.392  1.00  0.00              
ATOM     53  N   ILE    54      27.893  11.738  -0.253  1.00  0.00              
ATOM     54  CA  ILE    54      29.135  12.506  -0.352  1.00  0.00              
ATOM     55  C   ILE    54      29.902  12.425   0.965  1.00  0.00              
ATOM     56  O   ILE    54      29.390  12.783   2.022  1.00  0.00              
ATOM     57  N   ASP    55      31.134  11.935   0.883  1.00  0.00              
ATOM     58  CA  ASP    55      31.994  11.794   2.052  1.00  0.00              
ATOM     59  C   ASP    55      32.483  13.126   2.582  1.00  0.00              
ATOM     60  O   ASP    55      32.937  13.975   1.814  1.00  0.00              
ATOM     61  N   LEU    56      32.407  13.300   3.902  1.00  0.00              
ATOM     62  CA  LEU    56      32.869  14.508   4.562  1.00  0.00              
ATOM     63  C   LEU    56      33.894  14.107   5.609  1.00  0.00              
ATOM     64  O   LEU    56      33.598  13.318   6.498  1.00  0.00              
ATOM     65  N   SER    57      35.092  14.664   5.515  1.00  0.00              
ATOM     66  CA  SER    57      36.174  14.319   6.428  1.00  0.00              
ATOM     67  C   SER    57      36.082  14.925   7.811  1.00  0.00              
ATOM     68  O   SER    57      35.402  15.931   8.030  1.00  0.00              
ATOM     69  N   THR    58      36.746  14.288   8.788  1.00  0.00              
ATOM     70  CA  THR    58      36.749  14.788  10.163  1.00  0.00              
ATOM     71  C   THR    58      37.355  16.188  10.202  1.00  0.00              
ATOM     72  O   THR    58      36.956  17.016  11.019  1.00  0.00              
ATOM     73  N   ASN    59      38.315  16.448   9.313  1.00  0.00              
ATOM     74  CA  ASN    59      38.956  17.756   9.277  1.00  0.00              
ATOM     75  C   ASN    59      38.003  18.842   8.777  1.00  0.00              
ATOM     76  O   ASN    59      38.052  19.971   9.264  1.00  0.00              
ATOM     77  N   LYS    60      37.132  18.502   7.827  1.00  0.00              
ATOM     78  CA  LYS    60      36.165  19.473   7.309  1.00  0.00              
ATOM     79  C   LYS    60      35.101  19.769   8.370  1.00  0.00              
ATOM     80  O   LYS    60      34.640  20.900   8.520  1.00  0.00              
ATOM     81  N   ILE    61      34.735  18.733   9.114  1.00  0.00              
ATOM     82  CA  ILE    61      33.741  18.871  10.169  1.00  0.00              
ATOM     83  C   ILE    61      34.282  19.801  11.256  1.00  0.00              
ATOM     84  O   ILE    61      33.577  20.681  11.746  1.00  0.00              
ATOM     85  N   GLY    62      35.551  19.613  11.616  1.00  0.00              
ATOM     86  CA  GLY    62      36.177  20.449  12.636  1.00  0.00              
ATOM     87  C   GLY    62      36.404  21.866  12.131  1.00  0.00              
ATOM     88  O   GLY    62      36.158  22.837  12.841  1.00  0.00              
ATOM     89  N   ILE    63      36.873  21.973  10.895  1.00  0.00              
ATOM     90  CA  ILE    63      37.151  23.273  10.306  1.00  0.00              
ATOM     91  C   ILE    63      35.945  24.195  10.392  1.00  0.00              
ATOM     92  O   ILE    63      36.087  25.373  10.711  1.00  0.00              
ATOM     93  N   PHE    64      34.760  23.649  10.121  1.00  0.00              
ATOM     94  CA  PHE    64      33.544  24.458  10.154  1.00  0.00              
ATOM     95  C   PHE    64      32.571  24.070  11.268  1.00  0.00              
ATOM     96  O   PHE    64      31.390  24.434  11.223  1.00  0.00              
ATOM     97  N   SER    65      33.072  23.352  12.272  1.00  0.00              
ATOM     98  CA  SER    65      32.247  22.919  13.398  1.00  0.00              
ATOM     99  C   SER    65      30.925  22.425  12.866  1.00  0.00              
ATOM    100  O   SER    65      29.861  22.916  13.244  1.00  0.00              
ATOM    101  N   LEU    74      31.002  21.450  11.970  1.00  0.00              
ATOM    102  CA  LEU    74      29.810  20.886  11.366  1.00  0.00              
ATOM    103  C   LEU    74      29.052  20.012  12.353  1.00  0.00              
ATOM    104  O   LEU    74      29.637  19.399  13.252  1.00  0.00              
ATOM    105  N   LYS    75      27.734  19.972  12.171  1.00  0.00              
ATOM    106  CA  LYS    75      26.839  19.211  13.027  1.00  0.00              
ATOM    107  C   LYS    75      25.900  18.308  12.226  1.00  0.00              
ATOM    108  O   LYS    75      25.481  18.651  11.115  1.00  0.00              
ATOM    109  N   GLU    76      25.577  17.149  12.784  1.00  0.00              
ATOM    110  CA  GLU    76      24.659  16.243  12.116  1.00  0.00              
ATOM    111  C   GLU    76      23.374  17.051  11.951  1.00  0.00              
ATOM    112  O   GLU    76      22.972  17.790  12.861  1.00  0.00              
ATOM    113  N   GLY    77      22.742  16.928  10.790  1.00  0.00              
ATOM    114  CA  GLY    77      21.516  17.669  10.557  1.00  0.00              
ATOM    115  C   GLY    77      21.790  18.945   9.792  1.00  0.00              
ATOM    116  O   GLY    77      20.865  19.626   9.336  1.00  0.00              
ATOM    117  N   ASP    78      23.063  19.285   9.662  1.00  0.00              
ATOM    118  CA  ASP    78      23.448  20.474   8.930  1.00  0.00              
ATOM    119  C   ASP    78      23.266  20.204   7.440  1.00  0.00              
ATOM    120  O   ASP    78      23.473  19.079   6.972  1.00  0.00              
ATOM    121  N   ARG    79      22.871  21.232   6.700  1.00  0.00              
ATOM    122  CA  ARG    79      22.724  21.108   5.259  1.00  0.00              
ATOM    123  C   ARG    79      24.008  21.681   4.692  1.00  0.00              
ATOM    124  O   ARG    79      24.412  22.790   5.044  1.00  0.00              
ATOM    125  N   ILE    80      24.659  20.912   3.826  1.00  0.00              
ATOM    126  CA  ILE    80      25.916  21.351   3.247  1.00  0.00              
ATOM    127  C   ILE    80      25.892  21.322   1.728  1.00  0.00              
ATOM    128  O   ILE    80      25.254  20.460   1.129  1.00  0.00              
ATOM    129  N   GLU    81      26.579  22.273   1.109  1.00  0.00              
ATOM    130  CA  GLU    81      26.683  22.346  -0.341  1.00  0.00              
ATOM    131  C   GLU    81      28.084  22.842  -0.655  1.00  0.00              
ATOM    132  O   GLU    81      28.681  23.606   0.116  1.00  0.00              
ATOM    133  N   ILE    82      31.831  22.205  -3.490  1.00  0.00              
ATOM    134  CA  ILE    82      32.534  21.521  -4.562  1.00  0.00              
ATOM    135  C   ILE    82      32.850  20.107  -4.124  1.00  0.00              
ATOM    136  O   ILE    82      33.213  19.862  -2.980  1.00  0.00              
ATOM    137  N   TYR    83      32.724  19.174  -5.051  1.00  0.00              
ATOM    138  CA  TYR    83      33.013  17.792  -4.744  1.00  0.00              
ATOM    139  C   TYR    83      34.010  17.285  -5.766  1.00  0.00              
ATOM    140  O   TYR    83      34.253  17.937  -6.780  1.00  0.00              
ATOM    141  N   ARG    84      34.620  16.146  -5.489  1.00  0.00              
ATOM    142  CA  ARG    84      35.562  15.559  -6.434  1.00  0.00              
ATOM    143  C   ARG    84      35.191  14.099  -6.615  1.00  0.00              
ATOM    144  O   ARG    84      34.641  13.465  -5.706  1.00  0.00              
ATOM    145  N   PRO    85      35.464  13.539  -7.801  1.00  0.00              
ATOM    146  CA  PRO    85      35.123  12.136  -8.027  1.00  0.00              
ATOM    147  C   PRO    85      36.086  11.220  -7.296  1.00  0.00              
ATOM    148  O   PRO    85      37.227  11.594  -7.018  1.00  0.00              
ATOM    149  N   PRO    90      35.631  10.008  -6.949  1.00  0.00              
ATOM    150  CA  PRO    90      36.499   9.061  -6.240  1.00  0.00              
ATOM    151  C   PRO    90      37.672   8.664  -7.128  1.00  0.00              
ATOM    152  O   PRO    90      37.533   8.601  -8.347  1.00  0.00              
ATOM    153  N   LYS    91      38.827   8.413  -6.521  1.00  0.00              
ATOM    154  CA  LYS    91      40.012   8.012  -7.279  1.00  0.00              
ATOM    155  C   LYS    91      40.024   6.494  -7.415  1.00  0.00              
ATOM    156  O   LYS    91      39.101   5.824  -6.955  1.00  0.00              
ATOM    157  N   GLU    92      41.055   5.950  -8.049  1.00  0.00              
ATOM    158  CA  GLU    92      41.148   4.509  -8.227  1.00  0.00              
ATOM    159  C   GLU    92      41.170   3.788  -6.884  1.00  0.00              
ATOM    160  O   GLU    92      42.091   3.964  -6.081  1.00  0.00              
ATOM    161  N   ILE    93      40.149   2.971  -6.653  1.00  0.00              
ATOM    162  CA  ILE    93      40.047   2.240  -5.408  1.00  0.00              
ATOM    163  C   ILE    93      39.060   2.936  -4.493  1.00  0.00              
ATOM    164  O   ILE    93      38.525   2.333  -3.568  1.00  0.00              
ATOM    165  N   ARG    94      38.830   4.216  -4.762  1.00  0.00              
ATOM    166  CA  ARG    94      37.895   5.019  -3.979  1.00  0.00              
ATOM    167  C   ARG    94      36.459   4.624  -4.310  1.00  0.00              
ATOM    168  O   ARG    94      36.163   4.152  -5.411  1.00  0.00              
ATOM    169  N   ARG    95      35.563   4.849  -3.357  1.00  0.00              
ATOM    170  CA  ARG    95      34.159   4.501  -3.528  1.00  0.00              
ATOM    171  C   ARG    95      33.185   5.681  -3.634  1.00  0.00              
ATOM    172  O   ARG    95      32.249   5.655  -4.435  1.00  0.00              
ATOM    173  N   GLU    96      33.406   6.716  -2.831  1.00  0.00              
ATOM    174  CA  GLU    96      32.501   7.857  -2.820  1.00  0.00              
ATOM    175  C   GLU    96      33.024   9.159  -3.370  1.00  0.00              
ATOM    176  O   GLU    96      34.227   9.400  -3.423  1.00  0.00              
ATOM    177  N   GLY    97      32.087  10.002  -3.776  1.00  0.00              
ATOM    178  CA  GLY    97      32.440  11.329  -4.230  1.00  0.00              
ATOM    179  C   GLY    97      32.776  11.966  -2.881  1.00  0.00              
ATOM    180  O   GLY    97      32.198  11.586  -1.858  1.00  0.00              
END
