
#######################################################
#                                                     #
#                        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   52 (  208),  selected   52 , name T0349AL242_2-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349AL242_2-D1.T0349_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1          2.054
LGA    R       2      R       2          1.107
LGA    E       3      E       3          1.920
LGA    L       4      L       4          1.336
LGA    L       5      L       5          2.023
LGA    R       6      -       -           -
LGA    T       7      -       -           -
LGA    N       8      -       -           -
LGA    L      13      -       -           -
LGA    S      14      -       -           -
LGA    A      15      -       -           -
LGA    V      16      -       -           -
LGA    G      17      -       -           -
LGA    A      18      -       -           -
LGA    L      19      -       -           -
LGA    L      20      -       -           -
LGA    D      21      -       -           -
LGA    G      22      -       -           -
LGA    A      23      -       -           -
LGA    D      24      R       6          5.690
LGA    I      25      T       7           -
LGA    G      26      N       8           -
LGA    H      27      D       9           -
LGA    L      28      A      10           -
LGA    V      29      V      11           -
LGA    -       -      L      12           -
LGA    -       -      L      13           -
LGA    -       -      S      14           -
LGA    -       -      A      15           -
LGA    -       -      V      16           -
LGA    -       -      G      17           -
LGA    -       -      A      18           -
LGA    -       -      L      19           -
LGA    -       -      L      20           -
LGA    -       -      D      21           -
LGA    -       -      G      22           -
LGA    -       -      A      23           -
LGA    -       -      D      24           -
LGA    -       -      I      25           -
LGA    -       -      G      26           -
LGA    -       -      H      27           -
LGA    -       -      L      28           -
LGA    -       -      V      29           -
LGA    R      46      P      45          2.755
LGA    R      47      R      46          1.554
LGA    V      48      R      47          1.593
LGA    L      49      V      48          2.696
LGA    V      50      -       -           -
LGA    H      51      L      49          2.246
LGA    E      52      V      50          1.138
LGA    D      53      H      51          2.277
LGA    D      54      E      52          1.836
LGA    L      55      -       -           -
LGA    A      56      D      53          3.721
LGA    G      57      D      54          0.907
LGA    A      58      L      55          1.020
LGA    R      59      A      56          0.702
LGA    R      60      G      57          0.537
LGA    L      61      A      58          0.547
LGA    L      62      R      59          0.460
LGA    T      63      R      60          0.936
LGA    D      64      L      61          1.044
LGA    A      65      L      62          0.738
LGA    G      66      T      63           -
LGA    L      67      D      64           -
LGA    A      68      A      65           -
LGA    H      69      G      66           -
LGA    E      70      L      67           -
LGA    L      71      A      68           -
LGA    R      72      H      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      R      72           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   52   57    5.0     24    2.06    25.00     33.710     1.112

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.080889 * X  +   0.581289 * Y  +   0.809667 * Z  +   3.810707
  Y_new =   0.555140 * X  +  -0.648393 * Y  +   0.520966 * Z  +   3.610835
  Z_new =   0.827814 * X  +   0.491619 * Y  +  -0.270249 * Z  +   5.927841 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.073419   -1.068173  [ DEG:   118.7982    -61.2018 ]
  Theta =  -0.975200   -2.166393  [ DEG:   -55.8748   -124.1252 ]
  Phi   =   1.715487   -1.426106  [ DEG:    98.2902    -81.7098 ]
 
# 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: T0349AL242_2-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349AL242_2-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   52   57   5.0   24   2.06   25.00  33.710
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL242_2-D1
REMARK Aligment from pdb entry: 1gh9_A
ATOM      1  N   MET     1       2.038   8.674  -9.878  1.00  0.00              
ATOM      2  CA  MET     1       2.072   9.279  -8.521  1.00  0.00              
ATOM      3  C   MET     1       3.095   8.582  -7.631  1.00  0.00              
ATOM      4  O   MET     1       3.838   7.712  -8.088  1.00  0.00              
ATOM      5  N   ARG     2       3.129   8.969  -6.359  1.00  0.00              
ATOM      6  CA  ARG     2       4.062   8.381  -5.405  1.00  0.00              
ATOM      7  C   ARG     2       3.346   7.419  -4.462  1.00  0.00              
ATOM      8  O   ARG     2       2.145   7.547  -4.218  1.00  0.00              
ATOM      9  N   GLU     3       4.092   6.446  -3.949  1.00  0.00              
ATOM     10  CA  GLU     3       3.546   5.451  -3.037  1.00  0.00              
ATOM     11  C   GLU     3       4.402   5.338  -1.782  1.00  0.00              
ATOM     12  O   GLU     3       5.560   5.753  -1.773  1.00  0.00              
ATOM     13  N   LEU     4       3.844   4.741  -0.735  1.00  0.00              
ATOM     14  CA  LEU     4       4.575   4.544   0.508  1.00  0.00              
ATOM     15  C   LEU     4       4.519   3.073   0.927  1.00  0.00              
ATOM     16  O   LEU     4       3.563   2.367   0.618  1.00  0.00              
ATOM     17  N   LEU     5       5.566   2.610   1.598  1.00  0.00              
ATOM     18  CA  LEU     5       5.644   1.217   2.024  1.00  0.00              
ATOM     19  C   LEU     5       6.320   1.110   3.385  1.00  0.00              
ATOM     20  O   LEU     5       6.527   2.118   4.062  1.00  0.00              
ATOM     21  N   ARG     6       6.673  -0.111   3.784  1.00  0.00              
ATOM     22  CA  ARG     6       7.308  -0.326   5.079  1.00  0.00              
ATOM     23  C   ARG     6       8.421  -1.363   4.994  1.00  0.00              
ATOM     24  O   ARG     6       8.221  -2.467   4.490  1.00  0.00              
ATOM     25  N   THR     7       9.595  -1.005   5.512  1.00  0.00              
ATOM     26  CA  THR     7      10.731  -1.912   5.522  1.00  0.00              
ATOM     27  C   THR     7      10.562  -2.952   6.622  1.00  0.00              
ATOM     28  O   THR     7       9.759  -2.766   7.536  1.00  0.00              
ATOM     29  N   ASN     8      11.357  -4.018   6.556  1.00  0.00              
ATOM     30  CA  ASN     8      11.264  -5.101   7.533  1.00  0.00              
ATOM     31  C   ASN     8      11.593  -4.600   8.933  1.00  0.00              
ATOM     32  O   ASN     8      11.067  -5.108   9.924  1.00  0.00              
ATOM     33  N   LEU    13      12.446  -3.586   9.007  1.00  0.00              
ATOM     34  CA  LEU    13      12.805  -2.982  10.283  1.00  0.00              
ATOM     35  C   LEU    13      11.649  -2.146  10.820  1.00  0.00              
ATOM     36  O   LEU    13      11.778  -1.466  11.838  1.00  0.00              
ATOM     37  N   SER    14      10.523  -2.191  10.113  1.00  0.00              
ATOM     38  CA  SER    14       9.371  -1.398  10.492  1.00  0.00              
ATOM     39  C   SER    14       9.486   0.020   9.974  1.00  0.00              
ATOM     40  O   SER    14       8.817   0.930  10.464  1.00  0.00              
ATOM     41  N   ALA    15      10.396   0.209   9.023  1.00  0.00              
ATOM     42  CA  ALA    15      10.637   1.525   8.437  1.00  0.00              
ATOM     43  C   ALA    15       9.587   1.866   7.386  1.00  0.00              
ATOM     44  O   ALA    15       8.579   1.174   7.255  1.00  0.00              
ATOM     45  N   VAL    16       9.831   2.946   6.646  1.00  0.00              
ATOM     46  CA  VAL    16       8.920   3.382   5.594  1.00  0.00              
ATOM     47  C   VAL    16       9.646   4.254   4.573  1.00  0.00              
ATOM     48  O   VAL    16      10.560   5.001   4.923  1.00  0.00              
ATOM     49  N   GLY    17       9.241   4.153   3.308  1.00  0.00              
ATOM     50  CA  GLY    17       9.854   4.948   2.246  1.00  0.00              
ATOM     51  C   GLY    17       8.825   5.360   1.192  1.00  0.00              
ATOM     52  O   GLY    17       7.627   5.141   1.362  1.00  0.00              
ATOM     53  N   ALA    18       9.308   5.964   0.105  1.00  0.00              
ATOM     54  CA  ALA    18       8.438   6.422  -0.978  1.00  0.00              
ATOM     55  C   ALA    18       9.041   6.094  -2.345  1.00  0.00              
ATOM     56  O   ALA    18      10.257   6.163  -2.528  1.00  0.00              
ATOM     57  N   LEU    19       8.183   5.741  -3.301  1.00  0.00              
ATOM     58  CA  LEU    19       8.632   5.415  -4.655  1.00  0.00              
ATOM     59  C   LEU    19       7.508   5.636  -5.664  1.00  0.00              
ATOM     60  O   LEU    19       6.457   6.174  -5.324  1.00  0.00              
ATOM     61  N   LEU    20       7.739   5.232  -6.910  1.00  0.00              
ATOM     62  CA  LEU    20       6.735   5.385  -7.958  1.00  0.00              
ATOM     63  C   LEU    20       5.632   4.342  -7.818  1.00  0.00              
ATOM     64  O   LEU    20       5.877   3.216  -7.384  1.00  0.00              
ATOM     65  N   ASP    21       4.414   4.730  -8.185  1.00  0.00              
ATOM     66  CA  ASP    21       3.263   3.837  -8.108  1.00  0.00              
ATOM     67  C   ASP    21       3.505   2.551  -8.894  1.00  0.00              
ATOM     68  O   ASP    21       3.488   2.554 -10.124  1.00  0.00              
ATOM     69  N   GLY    22       3.718   1.450  -8.177  1.00  0.00              
ATOM     70  CA  GLY    22       3.941   0.173  -8.830  1.00  0.00              
ATOM     71  C   GLY    22       4.980  -0.678  -8.125  1.00  0.00              
ATOM     72  O   GLY    22       5.194  -1.834  -8.494  1.00  0.00              
ATOM     73  N   ALA    23       5.643  -0.102  -7.128  1.00  0.00              
ATOM     74  CA  ALA    23       6.662  -0.822  -6.375  1.00  0.00              
ATOM     75  C   ALA    23       6.028  -1.820  -5.414  1.00  0.00              
ATOM     76  O   ALA    23       5.390  -1.434  -4.435  1.00  0.00              
ATOM     77  N   ASP    24       6.195  -3.108  -5.706  1.00  0.00              
ATOM     78  CA  ASP    24       5.649  -4.160  -4.858  1.00  0.00              
ATOM     79  C   ASP    24       6.651  -4.561  -3.782  1.00  0.00              
ATOM     80  O   ASP    24       6.275  -4.868  -2.650  1.00  0.00              
ATOM     81  N   ILE    25       7.929  -4.557  -4.144  1.00  0.00              
ATOM     82  CA  ILE    25       8.986  -4.917  -3.209  1.00  0.00              
ATOM     83  C   ILE    25      10.246  -4.099  -3.465  1.00  0.00              
ATOM     84  O   ILE    25      10.931  -4.290  -4.470  1.00  0.00              
ATOM     85  N   GLY    26      10.547  -3.192  -2.544  1.00  0.00              
ATOM     86  CA  GLY    26      11.730  -2.349  -2.657  1.00  0.00              
ATOM     87  C   GLY    26      12.930  -3.016  -1.995  1.00  0.00              
ATOM     88  O   GLY    26      12.865  -4.184  -1.608  1.00  0.00              
ATOM     89  N   HIS    27      14.025  -2.274  -1.869  1.00  0.00              
ATOM     90  CA  HIS    27      15.233  -2.802  -1.253  1.00  0.00              
ATOM     91  C   HIS    27      16.030  -1.691  -0.583  1.00  0.00              
ATOM     92  O   HIS    27      16.110  -0.573  -1.095  1.00  0.00              
ATOM     93  N   LEU    28      16.621  -2.007   0.562  1.00  0.00              
ATOM     94  CA  LEU    28      17.422  -1.042   1.298  1.00  0.00              
ATOM     95  C   LEU    28      18.900  -1.240   0.994  1.00  0.00              
ATOM     96  O   LEU    28      19.430  -2.345   1.120  1.00  0.00              
ATOM     97  N   VAL    29      19.556  -0.167   0.575  1.00  0.00              
ATOM     98  CA  VAL    29      20.970  -0.219   0.226  1.00  0.00              
ATOM     99  C   VAL    29      21.827  -0.460   1.462  1.00  0.00              
ATOM    100  O   VAL    29      22.984  -0.868   1.359  1.00  0.00              
ATOM    137  N   ARG    46      -2.135  -5.356   0.138  1.00  0.00              
ATOM    138  CA  ARG    46      -3.010  -5.169  -1.010  1.00  0.00              
ATOM    139  C   ARG    46      -2.311  -4.313  -2.066  1.00  0.00              
ATOM    140  O   ARG    46      -1.360  -4.763  -2.705  1.00  0.00              
ATOM    141  N   ARG    47      -2.776  -3.080  -2.241  1.00  0.00              
ATOM    142  CA  ARG    47      -2.166  -2.167  -3.200  1.00  0.00              
ATOM    143  C   ARG    47      -0.862  -1.591  -2.648  1.00  0.00              
ATOM    144  O   ARG    47       0.216  -2.139  -2.876  1.00  0.00              
ATOM    145  N   VAL    48      -0.974  -0.477  -1.930  1.00  0.00              
ATOM    146  CA  VAL    48       0.187   0.194  -1.358  1.00  0.00              
ATOM    147  C   VAL    48      -0.216   1.038  -0.150  1.00  0.00              
ATOM    148  O   VAL    48      -1.370   1.446  -0.024  1.00  0.00              
ATOM    149  N   LEU    49       0.748   1.312   0.723  1.00  0.00              
ATOM    150  CA  LEU    49       0.499   2.139   1.895  1.00  0.00              
ATOM    151  C   LEU    49       0.776   3.603   1.569  1.00  0.00              
ATOM    152  O   LEU    49       1.670   3.909   0.788  1.00  0.00              
ATOM    153  N   VAL    50      -0.019   4.496   2.145  1.00  0.00              
ATOM    154  CA  VAL    50       0.154   5.919   1.907  1.00  0.00              
ATOM    155  C   VAL    50       0.301   6.262   0.436  1.00  0.00              
ATOM    156  O   VAL    50       1.403   6.220  -0.110  1.00  0.00              
ATOM    157  N   HIS    51      -0.807   6.607  -0.207  1.00  0.00              
ATOM    158  CA  HIS    51      -0.780   6.984  -1.613  1.00  0.00              
ATOM    159  C   HIS    51      -0.607   8.489  -1.748  1.00  0.00              
ATOM    160  O   HIS    51      -1.580   9.244  -1.726  1.00  0.00              
ATOM    161  N   GLU    52       0.642   8.919  -1.851  1.00  0.00              
ATOM    162  CA  GLU    52       0.958  10.337  -1.945  1.00  0.00              
ATOM    163  C   GLU    52       1.106  10.786  -3.391  1.00  0.00              
ATOM    164  O   GLU    52       1.925  10.253  -4.137  1.00  0.00              
ATOM    165  N   ASP    53       0.316  11.781  -3.778  1.00  0.00              
ATOM    166  CA  ASP    53       0.382  12.330  -5.125  1.00  0.00              
ATOM    167  C   ASP    53       1.490  13.372  -5.220  1.00  0.00              
ATOM    168  O   ASP    53       2.203  13.449  -6.221  1.00  0.00              
ATOM    169  N   ASP    54       1.603  14.195  -4.181  1.00  0.00              
ATOM    170  CA  ASP    54       2.625  15.235  -4.131  1.00  0.00              
ATOM    171  C   ASP    54       3.913  14.705  -3.510  1.00  0.00              
ATOM    172  O   ASP    54       3.880  14.009  -2.496  1.00  0.00              
ATOM    173  N   LEU    55       5.045  15.044  -4.119  1.00  0.00              
ATOM    174  CA  LEU    55       6.342  14.622  -3.604  1.00  0.00              
ATOM    175  C   LEU    55       6.530  15.095  -2.166  1.00  0.00              
ATOM    176  O   LEU    55       7.103  14.389  -1.337  1.00  0.00              
ATOM    177  N   ALA    56       6.036  16.297  -1.879  1.00  0.00              
ATOM    178  CA  ALA    56       6.136  16.866  -0.539  1.00  0.00              
ATOM    179  C   ALA    56       5.301  16.062   0.449  1.00  0.00              
ATOM    180  O   ALA    56       5.735  15.793   1.570  1.00  0.00              
ATOM    181  N   GLY    57       4.103  15.672   0.022  1.00  0.00              
ATOM    182  CA  GLY    57       3.212  14.883   0.863  1.00  0.00              
ATOM    183  C   GLY    57       3.777  13.482   1.074  1.00  0.00              
ATOM    184  O   GLY    57       3.491  12.831   2.078  1.00  0.00              
ATOM    185  N   ALA    58       4.578  13.028   0.114  1.00  0.00              
ATOM    186  CA  ALA    58       5.198  11.710   0.191  1.00  0.00              
ATOM    187  C   ALA    58       6.071  11.588   1.435  1.00  0.00              
ATOM    188  O   ALA    58       5.889  10.681   2.246  1.00  0.00              
ATOM    189  N   ARG    59       7.023  12.505   1.574  1.00  0.00              
ATOM    190  CA  ARG    59       7.932  12.502   2.715  1.00  0.00              
ATOM    191  C   ARG    59       7.166  12.629   4.029  1.00  0.00              
ATOM    192  O   ARG    59       7.570  12.069   5.048  1.00  0.00              
ATOM    193  N   ARG    60       6.065  13.373   4.000  1.00  0.00              
ATOM    194  CA  ARG    60       5.247  13.576   5.190  1.00  0.00              
ATOM    195  C   ARG    60       4.521  12.291   5.578  1.00  0.00              
ATOM    196  O   ARG    60       4.387  11.973   6.760  1.00  0.00              
ATOM    197  N   LEU    61       4.049  11.559   4.573  1.00  0.00              
ATOM    198  CA  LEU    61       3.337  10.308   4.802  1.00  0.00              
ATOM    199  C   LEU    61       4.277   9.241   5.351  1.00  0.00              
ATOM    200  O   LEU    61       3.909   8.466   6.233  1.00  0.00              
ATOM    201  N   LEU    62       5.501   9.226   4.835  1.00  0.00              
ATOM    202  CA  LEU    62       6.508   8.266   5.273  1.00  0.00              
ATOM    203  C   LEU    62       6.880   8.489   6.734  1.00  0.00              
ATOM    204  O   LEU    62       7.087   7.534   7.482  1.00  0.00              
ATOM    205  N   THR    63       6.963   9.754   7.134  1.00  0.00              
ATOM    206  CA  THR    63       7.310  10.094   8.508  1.00  0.00              
ATOM    207  C   THR    63       6.274   9.529   9.466  1.00  0.00              
ATOM    208  O   THR    63       6.616   8.964  10.505  1.00  0.00              
ATOM    209  N   ASP    64       5.006   9.663   9.099  1.00  0.00              
ATOM    210  CA  ASP    64       3.924   9.111   9.899  1.00  0.00              
ATOM    211  C   ASP    64       3.976   7.590   9.853  1.00  0.00              
ATOM    212  O   ASP    64       3.699   6.915  10.844  1.00  0.00              
ATOM    213  N   ALA    65       4.327   7.061   8.683  1.00  0.00              
ATOM    214  CA  ALA    65       4.443   5.621   8.494  1.00  0.00              
ATOM    215  C   ALA    65       5.625   5.060   9.277  1.00  0.00              
ATOM    216  O   ALA    65       5.710   3.856   9.515  1.00  0.00              
ATOM    217  N   GLY    66       0.292   8.667  19.417  1.00  0.00              
ATOM    218  CA  GLY    66      -1.000   8.011  19.483  1.00  0.00              
ATOM    219  C   GLY    66      -1.620   8.093  20.863  1.00  0.00              
ATOM    220  O   GLY    66      -2.760   8.534  21.013  1.00  0.00              
ATOM    221  N   LEU    67      -0.868   7.674  21.875  1.00  0.00              
ATOM    222  CA  LEU    67      -1.350   7.704  23.250  1.00  0.00              
ATOM    223  C   LEU    67      -1.036   9.045  23.905  1.00  0.00              
ATOM    224  O   LEU    67      -0.017   9.197  24.578  1.00  0.00              
ATOM    225  N   ALA    68      -1.921  10.017  23.701  1.00  0.00              
ATOM    226  CA  ALA    68      -1.740  11.349  24.268  1.00  0.00              
ATOM    227  C   ALA    68      -2.264  11.410  25.698  1.00  0.00              
ATOM    228  O   ALA    68      -3.367  11.902  25.945  1.00  0.00              
ATOM    229  N   HIS    69      -1.468  10.913  26.638  1.00  0.00              
ATOM    230  CA  HIS    69      -1.853  10.912  28.045  1.00  0.00              
ATOM    231  C   HIS    69      -0.744  11.491  28.917  1.00  0.00              
ATOM    232  O   HIS    69      -1.008  12.255  29.846  1.00  0.00              
ATOM    233  N   GLU    70       0.498  11.125  28.611  1.00  0.00              
ATOM    234  CA  GLU    70       1.646  11.613  29.367  1.00  0.00              
ATOM    235  C   GLU    70       1.912  13.083  29.059  1.00  0.00              
ATOM    236  O   GLU    70       1.548  13.967  29.837  1.00  0.00              
ATOM    237  N   LEU    71       2.546  13.338  27.919  1.00  0.00              
ATOM    238  CA  LEU    71       2.856  14.702  27.502  1.00  0.00              
ATOM    239  C   LEU    71       1.814  15.220  26.519  1.00  0.00              
ATOM    240  O   LEU    71       1.303  14.467  25.689  1.00  0.00              
ATOM    241  N   ARG    72       1.504  16.508  26.615  1.00  0.00              
ATOM    242  CA  ARG    72       0.525  17.126  25.730  1.00  0.00              
ATOM    243  C   ARG    72       1.135  17.408  24.357  1.00  0.00              
ATOM    244  O   ARG    72       2.326  17.699  24.249  1.00  0.00              
END
