
#######################################################
#                                                     #
#                        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   50 (  200),  selected   50 , name T0349AL333_1-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349AL333_1-D1.T0349_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    E       3      M       1           -
LGA    L       4      R       2           -
LGA    L       5      E       3           -
LGA    -       -      L       4           -
LGA    -       -      L       5           -
LGA    -       -      R       6           -
LGA    -       -      T       7           -
LGA    -       -      N       8           -
LGA    -       -      D       9           -
LGA    R       6      A      10           #
LGA    T       7      V      11          4.307
LGA    N       8      -       -           -
LGA    D       9      -       -           -
LGA    A      10      L      12          4.900
LGA    V      11      L      13          4.191
LGA    -       -      S      14           -
LGA    -       -      A      15           -
LGA    L      12      V      16          1.859
LGA    L      13      G      17          3.278
LGA    S      14      A      18           #
LGA    A      15      L      19           -
LGA    V      16      L      20           -
LGA    G      17      D      21           -
LGA    A      18      G      22           -
LGA    L      19      A      23           -
LGA    L      20      D      24           -
LGA    D      21      I      25           -
LGA    G      22      G      26           -
LGA    A      23      H      27           -
LGA    D      24      -       -           -
LGA    I      25      L      28           #
LGA    G      26      V      29           -
LGA    H      27      P      45          5.072
LGA    L      28      R      46          1.125
LGA    V      29      R      47           #
LGA    P      45      V      48           -
LGA    R      46      L      49           -
LGA    R      47      -       -           -
LGA    V      48      -       -           -
LGA    L      49      -       -           -
LGA    V      50      -       -           -
LGA    H      51      -       -           -
LGA    E      52      -       -           -
LGA    D      53      -       -           -
LGA    D      54      V      50          2.534
LGA    -       -      H      51           -
LGA    -       -      E      52           -
LGA    -       -      D      53           -
LGA    -       -      D      54           -
LGA    L      55      L      55          1.049
LGA    A      56      A      56          1.102
LGA    G      57      G      57          0.775
LGA    A      58      A      58          0.766
LGA    R      59      R      59          0.943
LGA    R      60      R      60          0.868
LGA    L      61      L      61          0.595
LGA    L      62      L      62          0.936
LGA    T      63      T      63          1.458
LGA    D      64      D      64          1.460
LGA    L      67      A      65          2.286
LGA    A      68      G      66          3.154
LGA    -       -      L      67           -
LGA    H      69      A      68          4.423
LGA    -       -      H      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      R      72           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   50   57    5.0     21    2.70    47.62     27.250     0.750

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.389283 * X  +  -0.117409 * Y  +  -0.913605 * Z  +   1.506385
  Y_new =  -0.906749 * X  +  -0.223352 * Y  +  -0.357658 * Z  +  13.935389
  Z_new =  -0.162063 * X  +   0.967641 * Y  +  -0.193408 * Z  + -14.743461 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.768073   -1.373520  [ DEG:   101.3031    -78.6969 ]
  Theta =   0.162781    2.978811  [ DEG:     9.3267    170.6733 ]
  Phi   =  -1.165275    1.976318  [ DEG:   -66.7654    113.2346 ]
 
# 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: T0349AL333_1-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349AL333_1-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   50   57   5.0   21   2.70   47.62  27.250
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL333_1-D1
REMARK Aligment from pdb entry: 1jfu_A
ATOM      1  N   GLU     3     -12.850 -14.061  -0.425  1.00  0.00              
ATOM      2  CA  GLU     3     -12.607 -14.745   0.839  1.00  0.00              
ATOM      3  C   GLU     3     -12.751 -13.756   1.992  1.00  0.00              
ATOM      4  O   GLU     3     -12.252 -12.635   1.905  1.00  0.00              
ATOM      5  N   LEU     4     -13.465 -14.139   3.043  1.00  0.00              
ATOM      6  CA  LEU     4     -13.641 -13.253   4.201  1.00  0.00              
ATOM      7  C   LEU     4     -12.333 -12.901   4.901  1.00  0.00              
ATOM      8  O   LEU     4     -11.452 -13.745   5.136  1.00  0.00              
ATOM      9  N   LEU     5     -12.224 -11.616   5.213  1.00  0.00              
ATOM     10  CA  LEU     5     -11.115 -11.041   5.946  1.00  0.00              
ATOM     11  C   LEU     5     -11.669 -10.218   7.100  1.00  0.00              
ATOM     12  O   LEU     5     -12.821  -9.773   7.091  1.00  0.00              
ATOM     13  N   ARG     6     -10.841 -10.019   8.112  1.00  0.00              
ATOM     14  CA  ARG     6     -11.214  -9.160   9.215  1.00  0.00              
ATOM     15  C   ARG     6      -9.973  -8.316   9.517  1.00  0.00              
ATOM     16  O   ARG     6      -8.830  -8.716   9.224  1.00  0.00              
ATOM     17  N   THR     7     -10.199  -7.141  10.087  1.00  0.00              
ATOM     18  CA  THR     7      -9.088  -6.284  10.497  1.00  0.00              
ATOM     19  C   THR     7      -8.091  -7.028  11.375  1.00  0.00              
ATOM     20  O   THR     7      -6.890  -6.863  11.230  1.00  0.00              
ATOM     21  N   ASN     8      -8.593  -7.868  12.270  1.00  0.00              
ATOM     22  CA  ASN     8      -7.724  -8.611  13.175  1.00  0.00              
ATOM     23  C   ASN     8      -6.859  -9.639  12.453  1.00  0.00              
ATOM     24  O   ASN     8      -5.898 -10.115  13.008  1.00  0.00              
ATOM     25  N   ASP     9      -7.182  -9.964  11.200  1.00  0.00              
ATOM     26  CA  ASP     9      -6.268 -10.818  10.437  1.00  0.00              
ATOM     27  C   ASP     9      -4.911 -10.146  10.192  1.00  0.00              
ATOM     28  O   ASP     9      -3.887 -10.816   9.951  1.00  0.00              
ATOM     29  N   ALA    10       1.413  -2.428  11.445  1.00  0.00              
ATOM     30  CA  ALA    10       0.826  -1.092  11.433  1.00  0.00              
ATOM     31  C   ALA    10       0.147  -1.050  10.082  1.00  0.00              
ATOM     32  O   ALA    10       0.663  -1.571   9.100  1.00  0.00              
ATOM     33  N   VAL    11      -1.003  -0.393  10.026  1.00  0.00              
ATOM     34  CA  VAL    11      -1.783  -0.364   8.787  1.00  0.00              
ATOM     35  C   VAL    11      -2.300   1.030   8.506  1.00  0.00              
ATOM     36  O   VAL    11      -2.581   1.808   9.413  1.00  0.00              
ATOM     37  N   LEU    12      -2.496   1.318   7.221  1.00  0.00              
ATOM     38  CA  LEU    12      -3.320   2.480   6.880  1.00  0.00              
ATOM     39  C   LEU    12      -4.561   1.832   6.283  1.00  0.00              
ATOM     40  O   LEU    12      -4.485   1.180   5.218  1.00  0.00              
ATOM     41  N   LEU    13      -5.683   1.942   6.998  1.00  0.00              
ATOM     42  CA  LEU    13      -6.950   1.403   6.532  1.00  0.00              
ATOM     43  C   LEU    13      -7.708   2.510   5.836  1.00  0.00              
ATOM     44  O   LEU    13      -7.993   3.513   6.460  1.00  0.00              
ATOM     45  N   SER    14      -8.044   2.348   4.558  1.00  0.00              
ATOM     46  CA  SER    14      -8.723   3.405   3.813  1.00  0.00              
ATOM     47  C   SER    14     -10.074   2.890   3.357  1.00  0.00              
ATOM     48  O   SER    14     -10.195   1.707   3.101  1.00  0.00              
ATOM     49  N   ALA    15     -11.105   3.749   3.365  1.00  0.00              
ATOM     50  CA  ALA    15     -12.386   3.367   2.760  1.00  0.00              
ATOM     51  C   ALA    15     -12.535   4.239   1.523  1.00  0.00              
ATOM     52  O   ALA    15     -12.388   5.474   1.599  1.00  0.00              
ATOM     53  N   VAL    16     -15.366  -1.090  -9.518  1.00  0.00              
ATOM     54  CA  VAL    16     -14.095  -0.766  -8.843  1.00  0.00              
ATOM     55  C   VAL    16     -12.927  -1.574  -9.429  1.00  0.00              
ATOM     56  O   VAL    16     -11.802  -1.079  -9.485  1.00  0.00              
ATOM     57  N   GLY    17     -13.205  -2.807  -9.846  1.00  0.00              
ATOM     58  CA  GLY    17     -12.176  -3.679 -10.423  1.00  0.00              
ATOM     59  C   GLY    17     -11.695  -3.036 -11.714  1.00  0.00              
ATOM     60  O   GLY    17     -10.490  -2.968 -11.971  1.00  0.00              
ATOM     61  N   ALA    18     -12.639  -2.586 -12.534  1.00  0.00              
ATOM     62  CA  ALA    18     -12.280  -1.934 -13.781  1.00  0.00              
ATOM     63  C   ALA    18     -11.524  -0.656 -13.470  1.00  0.00              
ATOM     64  O   ALA    18     -10.554  -0.344 -14.137  1.00  0.00              
ATOM     65  N   LEU    19     -11.962   0.095 -12.459  1.00  0.00              
ATOM     66  CA  LEU    19     -11.268   1.328 -12.123  1.00  0.00              
ATOM     67  C   LEU    19      -9.783   1.082 -11.799  1.00  0.00              
ATOM     68  O   LEU    19      -8.883   1.740 -12.342  1.00  0.00              
ATOM     69  N   LEU    20      -9.530   0.117 -10.927  1.00  0.00              
ATOM     70  CA  LEU    20      -8.155  -0.168 -10.529  1.00  0.00              
ATOM     71  C   LEU    20      -7.311  -0.644 -11.712  1.00  0.00              
ATOM     72  O   LEU    20      -6.151  -0.236 -11.879  1.00  0.00              
ATOM     73  N   ASP    21      -7.910  -1.481 -12.549  1.00  0.00              
ATOM     74  CA  ASP    21      -7.198  -2.012 -13.704  1.00  0.00              
ATOM     75  C   ASP    21      -6.841  -0.912 -14.696  1.00  0.00              
ATOM     76  O   ASP    21      -5.703  -0.844 -15.159  1.00  0.00              
ATOM     77  N   GLY    22      -7.800  -0.055 -15.033  1.00  0.00              
ATOM     78  CA  GLY    22      -7.528   1.020 -15.991  1.00  0.00              
ATOM     79  C   GLY    22      -6.517   2.016 -15.439  1.00  0.00              
ATOM     80  O   GLY    22      -5.809   2.690 -16.196  1.00  0.00              
ATOM     81  N   ALA    23      -6.455   2.112 -14.117  1.00  0.00              
ATOM     82  CA  ALA    23      -5.520   3.012 -13.457  1.00  0.00              
ATOM     83  C   ALA    23      -4.171   2.330 -13.202  1.00  0.00              
ATOM     84  O   ALA    23      -3.225   2.968 -12.731  1.00  0.00              
ATOM     85  N   ASP    24      -4.090   1.043 -13.529  1.00  0.00              
ATOM     86  CA  ASP    24      -2.888   0.237 -13.324  1.00  0.00              
ATOM     87  C   ASP    24      -2.443   0.289 -11.870  1.00  0.00              
ATOM     88  O   ASP    24      -1.268   0.496 -11.566  1.00  0.00              
ATOM     89  N   ILE    25      -3.406   0.121 -10.981  1.00  0.00              
ATOM     90  CA  ILE    25      -3.129   0.061  -9.546  1.00  0.00              
ATOM     91  C   ILE    25      -3.347  -1.373  -9.139  1.00  0.00              
ATOM     92  O   ILE    25      -4.502  -1.833  -9.026  1.00  0.00              
ATOM     93  N   GLY    26      -2.236  -2.081  -8.933  1.00  0.00              
ATOM     94  CA  GLY    26      -2.263  -3.491  -8.599  1.00  0.00              
ATOM     95  C   GLY    26      -1.659  -3.847  -7.241  1.00  0.00              
ATOM     96  O   GLY    26      -1.872  -4.968  -6.745  1.00  0.00              
ATOM     97  N   HIS    27      -0.934  -2.927  -6.624  1.00  0.00              
ATOM     98  CA  HIS    27      -0.286  -3.257  -5.361  1.00  0.00              
ATOM     99  C   HIS    27      -1.253  -3.329  -4.190  1.00  0.00              
ATOM    100  O   HIS    27      -0.951  -3.912  -3.155  1.00  0.00              
ATOM    101  N   LEU    28      -2.394  -2.674  -4.334  1.00  0.00              
ATOM    102  CA  LEU    28      -3.417  -2.651  -3.275  1.00  0.00              
ATOM    103  C   LEU    28      -4.286  -3.899  -3.182  1.00  0.00              
ATOM    104  O   LEU    28      -5.018  -4.068  -2.213  1.00  0.00              
ATOM    105  N   VAL    29      -4.204  -4.791  -4.175  1.00  0.00              
ATOM    106  CA  VAL    29      -5.101  -5.929  -4.227  1.00  0.00              
ATOM    107  C   VAL    29      -6.517  -5.438  -4.493  1.00  0.00              
ATOM    108  O   VAL    29      -6.723  -4.464  -5.214  1.00  0.00              
ATOM    169  N   PRO    45     -13.117  10.224   1.269  1.00  0.00              
ATOM    170  CA  PRO    45     -12.638   9.000   1.928  1.00  0.00              
ATOM    171  C   PRO    45     -12.452   9.200   3.421  1.00  0.00              
ATOM    172  O   PRO    45     -12.415  10.341   3.885  1.00  0.00              
ATOM    173  N   ARG    46     -12.350   8.086   4.147  1.00  0.00              
ATOM    174  CA  ARG    46     -11.858   8.090   5.510  1.00  0.00              
ATOM    175  C   ARG    46     -10.640   7.151   5.558  1.00  0.00              
ATOM    176  O   ARG    46     -10.679   6.067   4.989  1.00  0.00              
ATOM    177  N   ARG    47      -9.578   7.549   6.253  1.00  0.00              
ATOM    178  CA  ARG    47      -8.427   6.635   6.407  1.00  0.00              
ATOM    179  C   ARG    47      -8.003   6.677   7.864  1.00  0.00              
ATOM    180  O   ARG    47      -7.998   7.748   8.505  1.00  0.00              
ATOM    181  N   VAL    48      -7.670   5.503   8.389  1.00  0.00              
ATOM    182  CA  VAL    48      -7.237   5.412   9.778  1.00  0.00              
ATOM    183  C   VAL    48      -5.893   4.737   9.829  1.00  0.00              
ATOM    184  O   VAL    48      -5.717   3.673   9.221  1.00  0.00              
ATOM    185  N   LEU    49      -4.948   5.354  10.552  1.00  0.00              
ATOM    186  CA  LEU    49      -3.646   4.729  10.774  1.00  0.00              
ATOM    187  C   LEU    49      -3.834   3.873  12.028  1.00  0.00              
ATOM    188  O   LEU    49      -4.214   4.400  13.064  1.00  0.00              
ATOM    189  N   VAL    50      -3.541   2.561  11.923  1.00  0.00              
ATOM    190  CA  VAL    50      -3.886   1.555  12.951  1.00  0.00              
ATOM    191  C   VAL    50      -2.622   0.874  13.442  1.00  0.00              
ATOM    192  O   VAL    50      -1.730   0.597  12.635  1.00  0.00              
ATOM    193  N   HIS    51      -2.489   0.669  14.752  1.00  0.00              
ATOM    194  CA  HIS    51      -1.285  -0.010  15.255  1.00  0.00              
ATOM    195  C   HIS    51      -1.423  -1.530  15.190  1.00  0.00              
ATOM    196  O   HIS    51      -2.450  -2.021  14.795  1.00  0.00              
ATOM    197  N   GLU    52      -0.351  -2.268  15.507  1.00  0.00              
ATOM    198  CA  GLU    52      -0.391  -3.738  15.539  1.00  0.00              
ATOM    199  C   GLU    52      -1.412  -4.401  16.482  1.00  0.00              
ATOM    200  O   GLU    52      -1.608  -5.625  16.347  1.00  0.00              
ATOM    201  N   ASP    53      -2.045  -3.654  17.379  1.00  0.00              
ATOM    202  CA  ASP    53      -3.116  -4.208  18.227  1.00  0.00              
ATOM    203  C   ASP    53      -4.519  -3.806  17.698  1.00  0.00              
ATOM    204  O   ASP    53      -5.562  -4.074  18.326  1.00  0.00              
ATOM    205  N   ASP    54       1.800   9.632  -0.866  1.00  0.00              
ATOM    206  CA  ASP    54       3.131   9.225  -1.324  1.00  0.00              
ATOM    207  C   ASP    54       4.148  10.365  -1.175  1.00  0.00              
ATOM    208  O   ASP    54       5.336  10.226  -1.554  1.00  0.00              
ATOM    209  N   LEU    55       3.673  11.464  -0.597  1.00  0.00              
ATOM    210  CA  LEU    55       4.520  12.631  -0.330  1.00  0.00              
ATOM    211  C   LEU    55       5.563  12.389   0.764  1.00  0.00              
ATOM    212  O   LEU    55       5.462  11.481   1.561  1.00  0.00              
ATOM    213  N   ALA    56       6.567  13.240   0.808  1.00  0.00              
ATOM    214  CA  ALA    56       7.597  13.142   1.836  1.00  0.00              
ATOM    215  C   ALA    56       7.022  13.245   3.244  1.00  0.00              
ATOM    216  O   ALA    56       7.420  12.477   4.141  1.00  0.00              
ATOM    217  N   GLY    57       6.093  14.185   3.444  1.00  0.00              
ATOM    218  CA  GLY    57       5.482  14.382   4.765  1.00  0.00              
ATOM    219  C   GLY    57       4.783  13.099   5.181  1.00  0.00              
ATOM    220  O   GLY    57       4.910  12.646   6.316  1.00  0.00              
ATOM    221  N   ALA    58       4.022  12.519   4.269  1.00  0.00              
ATOM    222  CA  ALA    58       3.276  11.310   4.594  1.00  0.00              
ATOM    223  C   ALA    58       4.170  10.103   4.878  1.00  0.00              
ATOM    224  O   ALA    58       3.950   9.405   5.851  1.00  0.00              
ATOM    225  N   ARG    59       5.188   9.869   4.048  1.00  0.00              
ATOM    226  CA  ARG    59       6.103   8.769   4.303  1.00  0.00              
ATOM    227  C   ARG    59       6.809   8.918   5.627  1.00  0.00              
ATOM    228  O   ARG    59       6.992   7.933   6.346  1.00  0.00              
ATOM    229  N   ARG    60       7.205  10.142   5.953  1.00  0.00              
ATOM    230  CA  ARG    60       7.955  10.344   7.186  1.00  0.00              
ATOM    231  C   ARG    60       7.068  10.009   8.375  1.00  0.00              
ATOM    232  O   ARG    60       7.515   9.388   9.328  1.00  0.00              
ATOM    233  N   LEU    61       5.818  10.461   8.328  1.00  0.00              
ATOM    234  CA  LEU    61       4.895  10.172   9.415  1.00  0.00              
ATOM    235  C   LEU    61       4.618   8.679   9.537  1.00  0.00              
ATOM    236  O   LEU    61       4.648   8.141  10.636  1.00  0.00              
ATOM    237  N   LEU    62       4.361   8.012   8.421  1.00  0.00              
ATOM    238  CA  LEU    62       4.050   6.586   8.487  1.00  0.00              
ATOM    239  C   LEU    62       5.227   5.766   8.964  1.00  0.00              
ATOM    240  O   LEU    62       5.031   4.854   9.759  1.00  0.00              
ATOM    241  N   THR    63       6.429   6.065   8.468  1.00  0.00              
ATOM    242  CA  THR    63       7.613   5.361   8.938  1.00  0.00              
ATOM    243  C   THR    63       7.783   5.552  10.438  1.00  0.00              
ATOM    244  O   THR    63       8.087   4.585  11.171  1.00  0.00              
ATOM    245  N   ASP    64       7.634   6.784  10.905  1.00  0.00              
ATOM    246  CA  ASP    64       7.767   7.051  12.326  1.00  0.00              
ATOM    247  C   ASP    64       6.758   6.255  13.151  1.00  0.00              
ATOM    248  O   ASP    64       7.066   5.808  14.251  1.00  0.00              
ATOM    249  N   LEU    67       5.551   6.086  12.638  1.00  0.00              
ATOM    250  CA  LEU    67       4.537   5.354  13.376  1.00  0.00              
ATOM    251  C   LEU    67       4.829   3.874  13.425  1.00  0.00              
ATOM    252  O   LEU    67       4.552   3.223  14.425  1.00  0.00              
ATOM    253  N   ALA    68       5.421   3.361  12.357  1.00  0.00              
ATOM    254  CA  ALA    68       5.710   1.950  12.211  1.00  0.00              
ATOM    255  C   ALA    68       6.808   1.413  13.125  1.00  0.00              
ATOM    256  O   ALA    68       6.607   0.395  13.822  1.00  0.00              
ATOM    257  N   HIS    69       7.962   2.082  13.082  1.00  0.00              
ATOM    258  CA  HIS    69       9.163   1.663  13.792  1.00  0.00              
ATOM    259  C   HIS    69       9.158   2.029  15.263  1.00  0.00              
ATOM    260  O   HIS    69       8.133   1.826  15.929  1.00  0.00              
END
