
#######################################################
#                                                     #
#                        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   47 (  188),  selected   47 , name T0379AL586_1-D2
# Molecule2: number of CA atoms   64 (  528),  selected   64 , name T0379_D2.pdb
# PARAMETERS: T0379AL586_1-D2.T0379_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    N      17      N      17          3.134
LGA    R      18      R      18          2.694
LGA    E      19      E      19          1.581
LGA    E      20      E      20          2.495
LGA    S      21      S      21          2.493
LGA    I      22      I      22          1.317
LGA    R      23      R      23          1.206
LGA    R      24      R      24          1.584
LGA    F      25      F      25          1.053
LGA    K      26      K      26          0.965
LGA    I      28      A      27          4.575
LGA    G      29      I      28          2.556
LGA    A      31      G      29           #
LGA    I      33      -       -           -
LGA    E      35      V      30          4.444
LGA    M      36      A      31          4.352
LGA    D      38      D      32          2.270
LGA    P      39      I      33          2.562
LGA    -       -      E      34           -
LGA    Y      40      E      35          0.795
LGA    Q      42      M      36          1.592
LGA    K      43      L      37          0.899
LGA    -       -      D      38           -
LGA    -       -      P      39           -
LGA    -       -      K      43           -
LGA    -       -      G      44           -
LGA    -       -      L      45           -
LGA    L      45      F      46          1.810
LGA    F      46      L      47          4.825
LGA    -       -      D      48           -
LGA    L      47      L      49          5.589
LGA    -       -      E      50           -
LGA    -       -      S      51           -
LGA    -       -      G      52           -
LGA    -       -      R      53           -
LGA    -       -      K      54           -
LGA    -       -      S      55           -
LGA    -       -      E      56           -
LGA    -       -      E      57           -
LGA    -       -      E      58           -
LGA    -       -      F      59           -
LGA    D      48      R      60          2.834
LGA    S      51      T      61           -
LGA    G      52      E      62           #
LGA    R      53      L      63          1.656
LGA    -       -      S      64           -
LGA    -       -      R      65           -
LGA    K      54      Y      66          2.486
LGA    S      55      I      67          2.023
LGA    E      56      G      68          2.670
LGA    F      59      K      69           #
LGA    E      62      E      70          5.285
LGA    L      63      L      71          4.380
LGA    Y      66      T      72          1.809
LGA    -       -      Y      73           -
LGA    G      68      Q      74          2.203
LGA    K      69      Q      75          2.690
LGA    -       -      V      76           -
LGA    E      70      Y      77          0.964
LGA    T      72      D      78          2.169
LGA    Y      73      A      79          3.308
LGA    -       -      L      80           -
LGA    Q      74      L      81          2.309
LGA    V      76      G      82          3.336
LGA    Y      77      F      83          4.607
LGA    A      79      -       -           -
LGA    L      80      -       -           -
LGA    G      82      -       -           -
LGA    F      83      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   47   64    5.0     38    2.92    36.84     37.197     1.258

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.243785 * X  +  -0.419280 * Y  +  -0.874513 * Z  +  80.240585
  Y_new =   0.969724 * X  +  -0.118660 * Y  +  -0.213436 * Z  +   0.332736
  Z_new =  -0.014280 * X  +  -0.900069 * Y  +   0.435513 * Z  +  31.653006 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.120138    2.021454  [ DEG:   -64.1792    115.8208 ]
  Theta =   0.014281    3.127312  [ DEG:     0.8182    179.1818 ]
  Phi   =   1.817089   -1.324504  [ DEG:   104.1115    -75.8885 ]
 
# 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: T0379AL586_1-D2                               
REMARK     2: T0379_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0379AL586_1-D2.T0379_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   47   64   5.0   38   2.92   36.84  37.197
REMARK  ---------------------------------------------------------- 
MOLECULE T0379AL586_1-D2
REMARK Aligment from pdb entry: 1o08_A
ATOM     45  N   ASN    17      65.724   5.817  13.330  1.00  0.00              
ATOM     46  CA  ASN    17      65.570   6.568  14.568  1.00  0.00              
ATOM     47  C   ASN    17      64.881   5.803  15.685  1.00  0.00              
ATOM     48  O   ASN    17      64.902   6.270  16.814  1.00  0.00              
ATOM     49  N   ARG    18      64.318   4.642  15.401  1.00  0.00              
ATOM     50  CA  ARG    18      63.862   3.789  16.494  1.00  0.00              
ATOM     51  C   ARG    18      65.032   3.454  17.402  1.00  0.00              
ATOM     52  O   ARG    18      64.894   3.361  18.640  1.00  0.00              
ATOM     53  N   GLU    19      66.232   3.299  16.830  1.00  0.00              
ATOM     54  CA  GLU    19      67.428   2.982  17.626  1.00  0.00              
ATOM     55  C   GLU    19      67.709   4.142  18.568  1.00  0.00              
ATOM     56  O   GLU    19      68.126   3.946  19.722  1.00  0.00              
ATOM     57  N   GLU    20      67.526   5.362  18.074  1.00  0.00              
ATOM     58  CA  GLU    20      67.827   6.531  18.919  1.00  0.00              
ATOM     59  C   GLU    20      66.769   6.686  19.997  1.00  0.00              
ATOM     60  O   GLU    20      67.068   7.016  21.168  1.00  0.00              
ATOM     61  N   SER    21      65.480   6.432  19.722  1.00  0.00              
ATOM     62  CA  SER    21      64.473   6.467  20.783  1.00  0.00              
ATOM     63  C   SER    21      64.791   5.436  21.855  1.00  0.00              
ATOM     64  O   SER    21      64.672   5.695  23.056  1.00  0.00              
ATOM     65  N   ILE    22      65.192   4.238  21.459  1.00  0.00              
ATOM     66  CA  ILE    22      65.575   3.178  22.410  1.00  0.00              
ATOM     67  C   ILE    22      66.716   3.641  23.286  1.00  0.00              
ATOM     68  O   ILE    22      66.664   3.565  24.517  1.00  0.00              
ATOM     69  N   ARG    23      67.795   4.127  22.665  1.00  0.00              
ATOM     70  CA  ARG    23      68.973   4.556  23.459  1.00  0.00              
ATOM     71  C   ARG    23      68.580   5.645  24.443  1.00  0.00              
ATOM     72  O   ARG    23      69.023   5.651  25.604  1.00  0.00              
ATOM     73  N   ARG    24      67.763   6.580  23.997  1.00  0.00              
ATOM     74  CA  ARG    24      67.378   7.700  24.866  1.00  0.00              
ATOM     75  C   ARG    24      66.451   7.228  25.983  1.00  0.00              
ATOM     76  O   ARG    24      66.616   7.656  27.152  1.00  0.00              
ATOM     77  N   PHE    25      65.488   6.342  25.697  1.00  0.00              
ATOM     78  CA  PHE    25      64.643   5.844  26.769  1.00  0.00              
ATOM     79  C   PHE    25      65.417   5.001  27.754  1.00  0.00              
ATOM     80  O   PHE    25      65.143   5.116  28.955  1.00  0.00              
ATOM     81  N   LYS    26      66.349   4.210  27.255  1.00  0.00              
ATOM     82  CA  LYS    26      67.161   3.386  28.178  1.00  0.00              
ATOM     83  C   LYS    26      67.972   4.273  29.097  1.00  0.00              
ATOM     84  O   LYS    26      68.067   4.038  30.300  1.00  0.00              
ATOM     85  N   ILE    28      67.300   7.323  30.061  1.00  0.00              
ATOM     86  CA  ILE    28      66.394   7.952  31.026  1.00  0.00              
ATOM     87  C   ILE    28      66.072   6.996  32.151  1.00  0.00              
ATOM     88  O   ILE    28      66.146   7.289  33.330  1.00  0.00              
ATOM     89  N   GLY    29      65.644   5.794  31.771  1.00  0.00              
ATOM     90  CA  GLY    29      65.252   4.769  32.728  1.00  0.00              
ATOM     91  C   GLY    29      66.389   4.511  33.700  1.00  0.00              
ATOM     92  O   GLY    29      66.208   4.490  34.942  1.00  0.00              
ATOM     93  N   ALA    31      66.894   6.948  36.505  1.00  0.00              
ATOM     94  CA  ALA    31      65.939   6.795  37.632  1.00  0.00              
ATOM     95  C   ALA    31      65.940   5.391  38.242  1.00  0.00              
ATOM     96  O   ALA    31      64.994   5.031  38.956  1.00  0.00              
ATOM     97  N   ILE    33      65.810   2.357  36.893  1.00  0.00              
ATOM     98  CA  ILE    33      64.985   1.320  36.236  1.00  0.00              
ATOM     99  C   ILE    33      65.857   0.691  35.143  1.00  0.00              
ATOM    100  O   ILE    33      66.172   1.406  34.206  1.00  0.00              
ATOM    101  N   GLU    35      64.862  -1.610  30.599  1.00  0.00              
ATOM    102  CA  GLU    35      64.677  -1.240  29.191  1.00  0.00              
ATOM    103  C   GLU    35      65.811  -1.823  28.358  1.00  0.00              
ATOM    104  O   GLU    35      66.820  -1.181  28.053  1.00  0.00              
ATOM    105  N   MET    36      65.646  -3.093  28.024  1.00  0.00              
ATOM    106  CA  MET    36      66.555  -3.731  27.070  1.00  0.00              
ATOM    107  C   MET    36      65.820  -3.873  25.739  1.00  0.00              
ATOM    108  O   MET    36      64.676  -3.419  25.537  1.00  0.00              
ATOM    109  N   ASP    38      62.346  -5.528  25.901  1.00  0.00              
ATOM    110  CA  ASP    38      61.305  -4.671  26.483  1.00  0.00              
ATOM    111  C   ASP    38      60.935  -3.553  25.534  1.00  0.00              
ATOM    112  O   ASP    38      59.764  -3.171  25.404  1.00  0.00              
ATOM    113  N   PRO    39      61.934  -3.054  24.802  1.00  0.00              
ATOM    114  CA  PRO    39      61.728  -1.910  23.919  1.00  0.00              
ATOM    115  C   PRO    39      60.745  -2.246  22.817  1.00  0.00              
ATOM    116  O   PRO    39      60.158  -1.310  22.257  1.00  0.00              
ATOM    117  N   TYR    40      60.507  -3.533  22.492  1.00  0.00              
ATOM    118  CA  TYR    40      59.468  -3.805  21.463  1.00  0.00              
ATOM    119  C   TYR    40      58.111  -3.335  21.944  1.00  0.00              
ATOM    120  O   TYR    40      57.250  -3.017  21.098  1.00  0.00              
ATOM    121  N   GLN    42      57.684  -0.519  23.537  1.00  0.00              
ATOM    122  CA  GLN    42      57.771   0.931  23.445  1.00  0.00              
ATOM    123  C   GLN    42      57.726   1.443  22.001  1.00  0.00              
ATOM    124  O   GLN    42      57.363   2.613  21.819  1.00  0.00              
ATOM    125  N   LYS    43      58.094   0.601  21.022  1.00  0.00              
ATOM    126  CA  LYS    43      58.117   1.109  19.653  1.00  0.00              
ATOM    127  C   LYS    43      56.708   1.558  19.249  1.00  0.00              
ATOM    128  O   LYS    43      55.717   0.857  19.477  1.00  0.00              
ATOM    129  N   LEU    45      54.825   3.892  20.470  1.00  0.00              
ATOM    130  CA  LEU    45      54.056   4.406  21.588  1.00  0.00              
ATOM    131  C   LEU    45      54.429   5.845  21.872  1.00  0.00              
ATOM    132  O   LEU    45      55.620   6.217  21.739  1.00  0.00              
ATOM    133  N   PHE    46      53.467   6.686  22.271  1.00  0.00              
ATOM    134  CA  PHE    46      53.730   8.108  22.443  1.00  0.00              
ATOM    135  C   PHE    46      54.786   8.362  23.518  1.00  0.00              
ATOM    136  O   PHE    46      55.135   7.467  24.280  1.00  0.00              
ATOM    137  N   LEU    47      55.256   9.607  23.576  1.00  0.00              
ATOM    138  CA  LEU    47      56.243   9.977  24.584  1.00  0.00              
ATOM    139  C   LEU    47      55.763   9.657  25.998  1.00  0.00              
ATOM    140  O   LEU    47      56.459   9.002  26.802  1.00  0.00              
ATOM    141  N   ASP    48      54.567  10.152  26.346  1.00  0.00              
ATOM    142  CA  ASP    48      54.044   9.992  27.724  1.00  0.00              
ATOM    143  C   ASP    48      53.705   8.538  27.965  1.00  0.00              
ATOM    144  O   ASP    48      53.865   8.012  29.061  1.00  0.00              
ATOM    145  N   SER    51      55.157   5.946  26.621  1.00  0.00              
ATOM    146  CA  SER    51      56.442   5.289  26.780  1.00  0.00              
ATOM    147  C   SER    51      56.969   5.456  28.202  1.00  0.00              
ATOM    148  O   SER    51      57.355   4.457  28.825  1.00  0.00              
ATOM    149  N   GLY    52      56.971   6.732  28.649  1.00  0.00              
ATOM    150  CA  GLY    52      57.460   6.953  30.022  1.00  0.00              
ATOM    151  C   GLY    52      56.650   6.147  31.024  1.00  0.00              
ATOM    152  O   GLY    52      57.188   5.524  31.940  1.00  0.00              
ATOM    153  N   ARG    53      55.303   6.110  30.846  1.00  0.00              
ATOM    154  CA  ARG    53      54.532   5.404  31.867  1.00  0.00              
ATOM    155  C   ARG    53      54.780   3.908  31.785  1.00  0.00              
ATOM    156  O   ARG    53      54.772   3.256  32.840  1.00  0.00              
ATOM    157  N   LYS    54      54.994   3.319  30.601  1.00  0.00              
ATOM    158  CA  LYS    54      55.306   1.897  30.506  1.00  0.00              
ATOM    159  C   LYS    54      56.605   1.614  31.267  1.00  0.00              
ATOM    160  O   LYS    54      56.728   0.580  31.912  1.00  0.00              
ATOM    161  N   SER    55      57.577   2.516  31.206  1.00  0.00              
ATOM    162  CA  SER    55      58.854   2.348  31.950  1.00  0.00              
ATOM    163  C   SER    55      58.582   2.518  33.434  1.00  0.00              
ATOM    164  O   SER    55      59.040   1.694  34.222  1.00  0.00              
ATOM    165  N   GLU    56      57.795   3.527  33.815  1.00  0.00              
ATOM    166  CA  GLU    56      57.511   3.723  35.261  1.00  0.00              
ATOM    167  C   GLU    56      56.691   2.580  35.826  1.00  0.00              
ATOM    168  O   GLU    56      56.760   2.285  37.030  1.00  0.00              
ATOM    169  N   PHE    59      56.380   8.397  40.685  1.00  0.00              
ATOM    170  CA  PHE    59      57.025   9.702  40.630  1.00  0.00              
ATOM    171  C   PHE    59      55.926  10.785  40.731  1.00  0.00              
ATOM    172  O   PHE    59      54.730  10.501  40.421  1.00  0.00              
ATOM    173  N   GLU    62      57.837  15.496  38.434  1.00  0.00              
ATOM    174  CA  GLU    62      58.956  14.693  37.916  1.00  0.00              
ATOM    175  C   GLU    62      58.554  14.028  36.620  1.00  0.00              
ATOM    176  O   GLU    62      59.416  13.945  35.704  1.00  0.00              
ATOM    177  N   LEU    63      57.317  13.516  36.483  1.00  0.00              
ATOM    178  CA  LEU    63      56.894  12.894  35.253  1.00  0.00              
ATOM    179  C   LEU    63      57.136  13.837  34.085  1.00  0.00              
ATOM    180  O   LEU    63      57.703  13.475  33.041  1.00  0.00              
ATOM    181  N   TYR    66      60.851  14.311  33.302  1.00  0.00              
ATOM    182  CA  TYR    66      61.477  13.153  32.716  1.00  0.00              
ATOM    183  C   TYR    66      61.179  13.070  31.222  1.00  0.00              
ATOM    184  O   TYR    66      62.060  12.742  30.420  1.00  0.00              
ATOM    185  N   GLY    68      63.255  15.642  29.517  1.00  0.00              
ATOM    186  CA  GLY    68      64.655  15.282  29.592  1.00  0.00              
ATOM    187  C   GLY    68      65.012  14.332  28.484  1.00  0.00              
ATOM    188  O   GLY    68      65.986  14.480  27.740  1.00  0.00              
ATOM    189  N   LYS    69      64.194  13.277  28.367  1.00  0.00              
ATOM    190  CA  LYS    69      64.372  12.331  27.269  1.00  0.00              
ATOM    191  C   LYS    69      64.273  13.020  25.911  1.00  0.00              
ATOM    192  O   LYS    69      65.083  12.750  25.002  1.00  0.00              
ATOM    193  N   GLU    70      63.261  13.867  25.735  1.00  0.00              
ATOM    194  CA  GLU    70      63.096  14.492  24.424  1.00  0.00              
ATOM    195  C   GLU    70      64.280  15.403  24.103  1.00  0.00              
ATOM    196  O   GLU    70      64.764  15.418  22.955  1.00  0.00              
ATOM    197  N   THR    72      67.339  15.077  24.987  1.00  0.00              
ATOM    198  CA  THR    72      68.479  14.199  24.630  1.00  0.00              
ATOM    199  C   THR    72      68.279  13.658  23.229  1.00  0.00              
ATOM    200  O   THR    72      69.175  13.718  22.373  1.00  0.00              
ATOM    201  N   TYR    73      67.095  13.116  22.957  1.00  0.00              
ATOM    202  CA  TYR    73      66.769  12.595  21.643  1.00  0.00              
ATOM    203  C   TYR    73      66.932  13.632  20.555  1.00  0.00              
ATOM    204  O   TYR    73      67.493  13.387  19.465  1.00  0.00              
ATOM    205  N   GLN    74      66.449  14.861  20.772  1.00  0.00              
ATOM    206  CA  GLN    74      66.557  15.943  19.801  1.00  0.00              
ATOM    207  C   GLN    74      68.025  16.262  19.527  1.00  0.00              
ATOM    208  O   GLN    74      68.426  16.493  18.379  1.00  0.00              
ATOM    209  N   VAL    76      70.430  13.977  19.687  1.00  0.00              
ATOM    210  CA  VAL    76      70.927  12.809  18.969  1.00  0.00              
ATOM    211  C   VAL    76      70.613  12.915  17.467  1.00  0.00              
ATOM    212  O   VAL    76      71.376  12.392  16.670  1.00  0.00              
ATOM    213  N   TYR    77      69.484  13.536  17.120  1.00  0.00              
ATOM    214  CA  TYR    77      69.075  13.506  15.708  1.00  0.00              
ATOM    215  C   TYR    77      69.550  14.735  14.941  1.00  0.00              
ATOM    216  O   TYR    77      69.198  14.888  13.765  1.00  0.00              
ATOM    217  N   ALA    79      71.222  13.850  11.505  1.00  0.00              
ATOM    218  CA  ALA    79      70.553  13.006  10.514  1.00  0.00              
ATOM    219  C   ALA    79      70.593  13.716   9.156  1.00  0.00              
ATOM    220  O   ALA    79      70.412  14.946   9.081  1.00  0.00              
ATOM    221  N   LEU    80      70.820  12.957   8.096  1.00  0.00              
ATOM    222  CA  LEU    80      70.953  13.548   6.756  1.00  0.00              
ATOM    223  C   LEU    80      70.296  12.692   5.708  1.00  0.00              
ATOM    224  O   LEU    80      69.832  11.557   6.012  1.00  0.00              
ATOM    225  N   GLY    82      71.058   9.003   5.577  1.00  0.00              
ATOM    226  CA  GLY    82      70.474   8.094   6.595  1.00  0.00              
ATOM    227  C   GLY    82      69.133   7.564   6.203  1.00  0.00              
ATOM    228  O   GLY    82      68.588   6.753   6.969  1.00  0.00              
ATOM    229  N   PHE    83      68.554   7.968   5.056  1.00  0.00              
ATOM    230  CA  PHE    83      67.252   7.368   4.665  1.00  0.00              
ATOM    231  C   PHE    83      67.507   5.893   4.501  1.00  0.00              
ATOM    232  O   PHE    83      68.504   5.449   3.864  1.00  0.00              
END
