
#######################################################
#                                                     #
#                        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   46 (  184),  selected   46 , name T0349AL381_1-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349AL381_1-D1.T0349_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      R       2           -
LGA    -       -      E       3           -
LGA    -       -      L       4           -
LGA    L       5      L       5          1.946
LGA    R       6      R       6          1.335
LGA    T       7      T       7          3.653
LGA    N       8      N       8           #
LGA    D       9      D       9          4.442
LGA    A      10      A      10          4.397
LGA    V      11      V      11          3.712
LGA    L      12      L      12          1.895
LGA    L      13      L      13          1.689
LGA    S      14      S      14          1.902
LGA    A      15      A      15          0.629
LGA    V      16      V      16          2.233
LGA    G      17      G      17          3.155
LGA    A      18      A      18          1.826
LGA    L      19      L      19          3.870
LGA    L      20      L      20           #
LGA    D      21      D      21          4.881
LGA    G      22      G      22          4.995
LGA    A      23      A      23           -
LGA    D      24      D      24          3.213
LGA    I      25      I      25           #
LGA    G      26      G      26          4.288
LGA    -       -      H      27           -
LGA    -       -      L      28           -
LGA    -       -      V      29           -
LGA    -       -      P      45           -
LGA    P      45      R      46          2.864
LGA    R      46      R      47          2.385
LGA    R      47      V      48          3.479
LGA    V      48      L      49          2.782
LGA    L      49      V      50          3.355
LGA    V      50      H      51          1.255
LGA    H      51      E      52          3.501
LGA    E      52      D      53          3.477
LGA    D      53      -       -           -
LGA    D      54      D      54          2.403
LGA    L      55      L      55          2.317
LGA    A      56      A      56          2.293
LGA    G      57      G      57          2.811
LGA    A      58      A      58          1.776
LGA    R      59      R      59          1.417
LGA    R      60      R      60          2.525
LGA    L      61      L      61          2.557
LGA    L      62      L      62          2.435
LGA    T      63      T      63          2.961
LGA    D      64      D      64          3.986
LGA    -       -      A      65           -
LGA    -       -      G      66           -
LGA    A      65      L      67          0.858
LGA    G      66      A      68          2.330
LGA    L      67      H      69          3.736
LGA    A      68      E      70          1.542
LGA    -       -      L      71           -
LGA    -       -      R      72           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   46   57    5.0     41    2.96    73.17     48.988     1.340

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.554482 * X  +   0.827253 * Y  +  -0.090564 * Z  + -28.377661
  Y_new =  -0.774220 * X  +   0.552698 * Y  +   0.308395 * Z  +  12.962625
  Z_new =   0.305175 * X  +  -0.100883 * Y  +   0.946937 * Z  + -39.557316 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.106136    3.035456  [ DEG:    -6.0812    173.9189 ]
  Theta =  -0.310123   -2.831470  [ DEG:   -17.7687   -162.2313 ]
  Phi   =  -0.949292    2.192300  [ DEG:   -54.3905    125.6095 ]
 
# 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: T0349AL381_1-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349AL381_1-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46   57   5.0   41   2.96   73.17  48.988
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL381_1-D1
REMARK Aligment from pdb entry: 1vjqA
ATOM      1  N   LEU     5       2.632   1.658  -1.170  1.00  0.00              
ATOM      2  CA  LEU     5       2.782   1.134   0.189  1.00  0.00              
ATOM      3  C   LEU     5       2.265  -0.289   0.203  1.00  0.00              
ATOM      4  O   LEU     5       1.207  -0.569  -0.369  1.00  0.00              
ATOM      5  N   ARG     6       2.997  -1.191   0.854  1.00  0.00              
ATOM      6  CA  ARG     6       2.563  -2.598   0.935  1.00  0.00              
ATOM      7  C   ARG     6       2.575  -3.120   2.372  1.00  0.00              
ATOM      8  O   ARG     6       3.626  -3.448   2.926  1.00  0.00              
ATOM      9  N   THR     7       1.388  -3.145   2.986  1.00  0.00              
ATOM     10  CA  THR     7       1.246  -3.663   4.343  1.00  0.00              
ATOM     11  C   THR     7       1.479  -5.174   4.337  1.00  0.00              
ATOM     12  O   THR     7       1.079  -5.843   3.393  1.00  0.00              
ATOM     13  N   ASN     8       2.150  -5.679   5.373  1.00  0.00              
ATOM     14  CA  ASN     8       2.593  -7.074   5.419  1.00  0.00              
ATOM     15  C   ASN     8       1.857  -7.886   6.469  1.00  0.00              
ATOM     16  O   ASN     8       2.076  -9.080   6.568  1.00  0.00              
ATOM     17  N   ASP     9       1.012  -7.223   7.264  1.00  0.00              
ATOM     18  CA  ASP     9       0.091  -7.907   8.174  1.00  0.00              
ATOM     19  C   ASP     9      -1.204  -7.095   8.335  1.00  0.00              
ATOM     20  O   ASP     9      -1.323  -6.015   7.753  1.00  0.00              
ATOM     21  N   ALA    10      -2.170  -7.614   9.090  1.00  0.00              
ATOM     22  CA  ALA    10      -3.512  -7.002   9.132  1.00  0.00              
ATOM     23  C   ALA    10      -3.493  -5.746   9.975  1.00  0.00              
ATOM     24  O   ALA    10      -4.290  -4.847   9.779  1.00  0.00              
ATOM     25  N   VAL    11      -2.554  -5.694  10.901  1.00  0.00              
ATOM     26  CA  VAL    11      -2.361  -4.539  11.753  1.00  0.00              
ATOM     27  C   VAL    11      -1.938  -3.301  10.925  1.00  0.00              
ATOM     28  O   VAL    11      -2.434  -2.201  11.136  1.00  0.00              
ATOM     29  N   LEU    12      -1.061  -3.499   9.948  1.00  0.00              
ATOM     30  CA  LEU    12      -0.626  -2.423   9.053  1.00  0.00              
ATOM     31  C   LEU    12      -1.730  -2.061   8.039  1.00  0.00              
ATOM     32  O   LEU    12      -1.892  -0.899   7.666  1.00  0.00              
ATOM     33  N   LEU    13      -2.487  -3.055   7.571  1.00  0.00              
ATOM     34  CA  LEU    13      -3.665  -2.756   6.746  1.00  0.00              
ATOM     35  C   LEU    13      -4.669  -1.883   7.512  1.00  0.00              
ATOM     36  O   LEU    13      -5.176  -0.892   6.981  1.00  0.00              
ATOM     37  N   SER    14      -4.951  -2.275   8.753  1.00  0.00              
ATOM     38  CA  SER    14      -5.865  -1.539   9.615  1.00  0.00              
ATOM     39  C   SER    14      -5.370  -0.122   9.874  1.00  0.00              
ATOM     40  O   SER    14      -6.141   0.799   9.829  1.00  0.00              
ATOM     41  N   ALA    15      -4.074   0.052  10.127  1.00  0.00              
ATOM     42  CA  ALA    15      -3.474   1.393  10.294  1.00  0.00              
ATOM     43  C   ALA    15      -3.712   2.279   9.056  1.00  0.00              
ATOM     44  O   ALA    15      -4.168   3.413   9.171  1.00  0.00              
ATOM     45  N   VAL    16      -3.413   1.751   7.872  1.00  0.00              
ATOM     46  CA  VAL    16      -3.618   2.494   6.619  1.00  0.00              
ATOM     47  C   VAL    16      -5.095   2.780   6.348  1.00  0.00              
ATOM     48  O   VAL    16      -5.442   3.855   5.856  1.00  0.00              
ATOM     49  N   GLY    17      -5.967   1.836   6.702  1.00  0.00              
ATOM     50  CA  GLY    17      -7.420   2.074   6.620  1.00  0.00              
ATOM     51  C   GLY    17      -7.851   3.277   7.470  1.00  0.00              
ATOM     52  O   GLY    17      -8.664   4.083   7.005  1.00  0.00              
ATOM     53  N   ALA    18      -7.277   3.414   8.676  1.00  0.00              
ATOM     54  CA  ALA    18      -7.580   4.546   9.579  1.00  0.00              
ATOM     55  C   ALA    18      -7.200   5.915   9.012  1.00  0.00              
ATOM     56  O   ALA    18      -7.957   6.875   9.156  1.00  0.00              
ATOM     57  N   LEU    19      -6.019   6.003   8.398  1.00  0.00              
ATOM     58  CA  LEU    19      -5.581   7.202   7.664  1.00  0.00              
ATOM     59  C   LEU    19      -6.503   7.479   6.495  1.00  0.00              
ATOM     60  O   LEU    19      -7.000   8.587   6.329  1.00  0.00              
ATOM     61  N   LEU    20      -6.728   6.470   5.660  1.00  0.00              
ATOM     62  CA  LEU    20      -7.541   6.682   4.437  1.00  0.00              
ATOM     63  C   LEU    20      -8.940   7.195   4.751  1.00  0.00              
ATOM     64  O   LEU    20      -9.586   7.837   3.917  1.00  0.00              
ATOM     65  N   ASP    21      -9.391   6.916   5.966  1.00  0.00              
ATOM     66  CA  ASP    21     -10.702   7.345   6.452  1.00  0.00              
ATOM     67  C   ASP    21     -10.799   8.861   6.658  1.00  0.00              
ATOM     68  O   ASP    21     -11.887   9.420   6.726  1.00  0.00              
ATOM     69  N   GLY    22      -9.653   9.512   6.795  1.00  0.00              
ATOM     70  CA  GLY    22      -9.586  10.938   7.019  1.00  0.00              
ATOM     71  C   GLY    22      -9.540  11.548   5.644  1.00  0.00              
ATOM     72  O   GLY    22      -8.625  11.267   4.860  1.00  0.00              
ATOM     73  N   ALA    23     -10.538  12.351   5.331  1.00  0.00              
ATOM     74  CA  ALA    23     -10.604  13.010   4.045  1.00  0.00              
ATOM     75  C   ALA    23      -9.739  14.253   4.172  1.00  0.00              
ATOM     76  O   ALA    23     -10.223  15.312   4.592  1.00  0.00              
ATOM     77  N   ASP    24      -8.453  14.089   3.854  1.00  0.00              
ATOM     78  CA  ASP    24      -7.473  15.168   3.917  1.00  0.00              
ATOM     79  C   ASP    24      -7.135  15.617   2.504  1.00  0.00              
ATOM     80  O   ASP    24      -6.720  14.815   1.661  1.00  0.00              
ATOM     81  N   ILE    25      -7.301  16.914   2.279  1.00  0.00              
ATOM     82  CA  ILE    25      -7.050  17.550   0.989  1.00  0.00              
ATOM     83  C   ILE    25      -5.664  17.210   0.436  1.00  0.00              
ATOM     84  O   ILE    25      -4.663  17.306   1.145  1.00  0.00              
ATOM     85  N   GLY    26      -5.621  16.793  -0.823  1.00  0.00              
ATOM     86  CA  GLY    26      -4.367  16.474  -1.507  1.00  0.00              
ATOM     87  C   GLY    26      -3.595  15.240  -0.985  1.00  0.00              
ATOM     88  O   GLY    26      -2.551  14.916  -1.549  1.00  0.00              
ATOM    133  N   PRO    45      -0.651  -3.852  -2.676  1.00  0.00              
ATOM    134  CA  PRO    45      -0.233  -2.458  -2.742  1.00  0.00              
ATOM    135  C   PRO    45      -1.361  -1.482  -2.489  1.00  0.00              
ATOM    136  O   PRO    45      -2.515  -1.721  -2.866  1.00  0.00              
ATOM    137  N   ARG    46      -1.011  -0.395  -1.819  1.00  0.00              
ATOM    138  CA  ARG    46      -1.910   0.733  -1.640  1.00  0.00              
ATOM    139  C   ARG    46      -1.185   1.923  -2.209  1.00  0.00              
ATOM    140  O   ARG    46      -0.021   2.174  -1.869  1.00  0.00              
ATOM    141  N   ARG    47      -1.859   2.655  -3.080  1.00  0.00              
ATOM    142  CA  ARG    47      -1.222   3.781  -3.752  1.00  0.00              
ATOM    143  C   ARG    47      -1.840   5.091  -3.339  1.00  0.00              
ATOM    144  O   ARG    47      -3.062   5.268  -3.342  1.00  0.00              
ATOM    145  N   VAL    48      -0.973   6.014  -2.978  1.00  0.00              
ATOM    146  CA  VAL    48      -1.384   7.359  -2.605  1.00  0.00              
ATOM    147  C   VAL    48      -0.535   8.419  -3.303  1.00  0.00              
ATOM    148  O   VAL    48       0.657   8.249  -3.524  1.00  0.00              
ATOM    149  N   LEU    49      -1.195   9.503  -3.684  1.00  0.00              
ATOM    150  CA  LEU    49      -0.545  10.690  -4.243  1.00  0.00              
ATOM    151  C   LEU    49      -0.623  11.764  -3.152  1.00  0.00              
ATOM    152  O   LEU    49      -1.692  11.981  -2.603  1.00  0.00              
ATOM    153  N   VAL    50       0.503  12.392  -2.830  1.00  0.00              
ATOM    154  CA  VAL    50       0.579  13.459  -1.812  1.00  0.00              
ATOM    155  C   VAL    50       1.395  14.657  -2.332  1.00  0.00              
ATOM    156  O   VAL    50       2.087  14.518  -3.313  1.00  0.00              
ATOM    157  N   HIS    51       1.248  15.838  -1.735  1.00  0.00              
ATOM    158  CA  HIS    51       2.125  16.968  -2.056  1.00  0.00              
ATOM    159  C   HIS    51       3.568  16.628  -1.760  1.00  0.00              
ATOM    160  O   HIS    51       3.863  16.044  -0.724  1.00  0.00              
ATOM    161  N   GLU    52       4.467  16.997  -2.652  1.00  0.00              
ATOM    162  CA  GLU    52       5.865  16.600  -2.531  1.00  0.00              
ATOM    163  C   GLU    52       6.536  17.173  -1.305  1.00  0.00              
ATOM    164  O   GLU    52       7.490  16.591  -0.798  1.00  0.00              
ATOM    165  N   ASP    53       6.044  18.294  -0.801  1.00  0.00              
ATOM    166  CA  ASP    53       6.641  18.875   0.403  1.00  0.00              
ATOM    167  C   ASP    53       6.293  18.109   1.695  1.00  0.00              
ATOM    168  O   ASP    53       6.754  18.475   2.773  1.00  0.00              
ATOM    169  N   ASP    54       5.517  17.031   1.585  1.00  0.00              
ATOM    170  CA  ASP    54       5.141  16.219   2.753  1.00  0.00              
ATOM    171  C   ASP    54       5.716  14.820   2.719  1.00  0.00              
ATOM    172  O   ASP    54       5.341  13.965   3.548  1.00  0.00              
ATOM    173  N   LEU    55       6.621  14.607   1.764  1.00  0.00              
ATOM    174  CA  LEU    55       7.221  13.316   1.520  1.00  0.00              
ATOM    175  C   LEU    55       8.129  12.919   2.701  1.00  0.00              
ATOM    176  O   LEU    55       8.078  11.784   3.187  1.00  0.00              
ATOM    177  N   ALA    56       8.938  13.859   3.166  1.00  0.00              
ATOM    178  CA  ALA    56       9.963  13.532   4.155  1.00  0.00              
ATOM    179  C   ALA    56       9.317  13.014   5.430  1.00  0.00              
ATOM    180  O   ALA    56       9.749  11.990   5.958  1.00  0.00              
ATOM    181  N   GLY    57       8.287  13.703   5.923  1.00  0.00              
ATOM    182  CA  GLY    57       7.637  13.246   7.156  1.00  0.00              
ATOM    183  C   GLY    57       6.760  12.026   6.944  1.00  0.00              
ATOM    184  O   GLY    57       6.628  11.216   7.860  1.00  0.00              
ATOM    185  N   ALA    58       6.170  11.896   5.747  1.00  0.00              
ATOM    186  CA  ALA    58       5.277  10.785   5.449  1.00  0.00              
ATOM    187  C   ALA    58       6.039   9.479   5.392  1.00  0.00              
ATOM    188  O   ALA    58       5.566   8.479   5.884  1.00  0.00              
ATOM    189  N   ARG    59       7.218   9.491   4.791  1.00  0.00              
ATOM    190  CA  ARG    59       8.040   8.294   4.736  1.00  0.00              
ATOM    191  C   ARG    59       8.637   7.942   6.097  1.00  0.00              
ATOM    192  O   ARG    59       8.699   6.766   6.440  1.00  0.00              
ATOM    193  N   ARG    60       9.049   8.935   6.884  1.00  0.00              
ATOM    194  CA  ARG    60       9.509   8.662   8.264  1.00  0.00              
ATOM    195  C   ARG    60       8.453   7.959   9.109  1.00  0.00              
ATOM    196  O   ARG    60       8.789   7.101   9.929  1.00  0.00              
ATOM    197  N   LEU    61       7.189   8.335   8.915  1.00  0.00              
ATOM    198  CA  LEU    61       6.096   7.713   9.616  1.00  0.00              
ATOM    199  C   LEU    61       5.969   6.250   9.192  1.00  0.00              
ATOM    200  O   LEU    61       5.896   5.371  10.024  1.00  0.00              
ATOM    201  N   LEU    62       5.906   5.997   7.892  1.00  0.00              
ATOM    202  CA  LEU    62       5.801   4.628   7.411  1.00  0.00              
ATOM    203  C   LEU    62       6.970   3.780   7.920  1.00  0.00              
ATOM    204  O   LEU    62       6.776   2.632   8.309  1.00  0.00              
ATOM    205  N   THR    63       8.165   4.368   7.923  1.00  0.00              
ATOM    206  CA  THR    63       9.373   3.687   8.415  1.00  0.00              
ATOM    207  C   THR    63       9.304   3.412   9.891  1.00  0.00              
ATOM    208  O   THR    63       9.591   2.300  10.339  1.00  0.00              
ATOM    209  N   ASP    64       8.930   4.434  10.653  1.00  0.00              
ATOM    210  CA  ASP    64       8.701   4.285  12.087  1.00  0.00              
ATOM    211  C   ASP    64       7.802   3.085  12.331  1.00  0.00              
ATOM    212  O   ASP    64       8.030   2.315  13.261  1.00  0.00              
ATOM    213  N   ALA    65       6.794   2.925  11.481  1.00  0.00              
ATOM    214  CA  ALA    65       5.867   1.803  11.582  1.00  0.00              
ATOM    215  C   ALA    65       6.351   0.491  10.913  1.00  0.00              
ATOM    216  O   ALA    65       5.684  -0.535  11.007  1.00  0.00              
ATOM    217  N   GLY    66       7.507   0.503  10.260  1.00  0.00              
ATOM    218  CA  GLY    66       7.991  -0.685   9.563  1.00  0.00              
ATOM    219  C   GLY    66       7.091  -1.151   8.420  1.00  0.00              
ATOM    220  O   GLY    66       7.004  -2.349   8.142  1.00  0.00              
ATOM    221  N   LEU    67       6.419  -0.212   7.752  1.00  0.00              
ATOM    222  CA  LEU    67       5.543  -0.539   6.609  1.00  0.00              
ATOM    223  C   LEU    67       6.330  -0.361   5.328  1.00  0.00              
ATOM    224  O   LEU    67       6.783   0.744   5.052  1.00  0.00              
ATOM    225  N   ALA    68       6.539  -1.436   4.563  1.00  0.00              
ATOM    226  CA  ALA    68       7.257  -1.343   3.296  1.00  0.00              
ATOM    227  C   ALA    68       6.611  -0.407   2.278  1.00  0.00              
ATOM    228  O   ALA    68       5.397  -0.413   2.094  1.00  0.00              
END
