
#######################################################
#                                                     #
#                        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_5-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349AL333_5-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           -
LGA    R       2      R       2           -
LGA    E       3      E       3           -
LGA    L       4      L       4           -
LGA    -       -      L       5           -
LGA    -       -      R       6           -
LGA    D       9      T       7          1.746
LGA    A      10      N       8          3.602
LGA    V      11      D       9          2.926
LGA    -       -      A      10           -
LGA    -       -      V      11           -
LGA    L      12      L      12          1.787
LGA    L      13      L      13          1.430
LGA    S      14      S      14          1.295
LGA    A      15      A      15          1.583
LGA    V      16      V      16          1.302
LGA    G      17      G      17          1.714
LGA    A      18      A      18          2.865
LGA    L      19      L      19          3.313
LGA    L      20      L      20          3.330
LGA    D      21      D      21          1.403
LGA    G      22      G      22           #
LGA    -       -      A      23           -
LGA    -       -      D      24           -
LGA    A      23      I      25          3.220
LGA    D      24      G      26           #
LGA    I      25      H      27          4.852
LGA    G      26      L      28          2.658
LGA    H      27      V      29           #
LGA    -       -      P      45           -
LGA    -       -      R      46           -
LGA    L      28      R      47           #
LGA    V      29      V      48          1.625
LGA    P      45      -       -           -
LGA    R      46      -       -           -
LGA    R      47      -       -           -
LGA    V      48      L      49           #
LGA    L      49      V      50           -
LGA    V      50      H      51          4.364
LGA    H      51      E      52          3.471
LGA    E      52      -       -           -
LGA    D      53      D      53          4.800
LGA    D      54      D      54          1.375
LGA    L      55      L      55          0.651
LGA    A      56      A      56          0.582
LGA    G      57      G      57          0.906
LGA    A      58      A      58          0.854
LGA    R      59      R      59          0.690
LGA    R      60      R      60          0.229
LGA    L      61      L      61          0.724
LGA    L      62      L      62          0.835
LGA    T      63      T      63          0.938
LGA    D      64      D      64          1.627
LGA    A      65      A      65          3.018
LGA    -       -      G      66           -
LGA    G      66      L      67          1.155
LGA    L      67      A      68          3.768
LGA    A      68      -       -           -
LGA    H      69      H      69          5.203
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     35    2.56    71.43     43.694     1.315

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.552204 * X  +  -0.781309 * Y  +   0.290909 * Z  +  18.121029
  Y_new =   0.400549 * X  +  -0.554651 * Y  +  -0.729331 * Z  +  21.484926
  Z_new =   0.731185 * X  +  -0.286216 * Y  +   0.619233 * Z  + -24.100943 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.432962    2.708631  [ DEG:   -24.8069    155.1931 ]
  Theta =  -0.820057   -2.321535  [ DEG:   -46.9858   -133.0142 ]
  Phi   =   2.514045   -0.627547  [ DEG:   144.0442    -35.9558 ]
 
# 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_5-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349AL333_5-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   35   2.56   71.43  43.694
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL333_5-D1
REMARK Aligment from pdb entry: 1q1h_A
ATOM      1  N   MET     1       1.571 -14.759   3.843  1.00  0.00              
ATOM      2  CA  MET     1       1.080 -13.356   3.800  1.00  0.00              
ATOM      3  C   MET     1      -0.326 -13.296   3.212  1.00  0.00              
ATOM      4  O   MET     1      -1.292 -13.701   3.863  1.00  0.00              
ATOM      5  N   ARG     2      -0.436 -12.790   1.982  1.00  0.00              
ATOM      6  CA  ARG     2      -1.725 -12.682   1.286  1.00  0.00              
ATOM      7  C   ARG     2      -2.617 -11.571   1.873  1.00  0.00              
ATOM      8  O   ARG     2      -2.806 -10.508   1.260  1.00  0.00              
ATOM      9  N   GLU     3      -3.163 -11.819   3.059  1.00  0.00              
ATOM     10  CA  GLU     3      -4.016 -10.834   3.704  1.00  0.00              
ATOM     11  C   GLU     3      -3.182  -9.912   4.571  1.00  0.00              
ATOM     12  O   GLU     3      -3.667  -9.395   5.569  1.00  0.00              
ATOM     13  N   LEU     4      -1.922  -9.713   4.197  1.00  0.00              
ATOM     14  CA  LEU     4      -1.048  -8.835   4.963  1.00  0.00              
ATOM     15  C   LEU     4      -0.712  -7.551   4.197  1.00  0.00              
ATOM     16  O   LEU     4      -0.208  -6.596   4.780  1.00  0.00              
ATOM     17  N   ASP     9      -0.979  -7.526   2.892  1.00  0.00              
ATOM     18  CA  ASP     9      -0.721  -6.319   2.106  1.00  0.00              
ATOM     19  C   ASP     9      -2.009  -5.512   2.186  1.00  0.00              
ATOM     20  O   ASP     9      -2.236  -4.585   1.417  1.00  0.00              
ATOM     21  N   ALA    10      -2.852  -5.905   3.135  1.00  0.00              
ATOM     22  CA  ALA    10      -4.133  -5.257   3.390  1.00  0.00              
ATOM     23  C   ALA    10      -4.253  -5.054   4.898  1.00  0.00              
ATOM     24  O   ALA    10      -4.667  -4.000   5.364  1.00  0.00              
ATOM     25  N   VAL    11      -3.887  -6.074   5.660  1.00  0.00              
ATOM     26  CA  VAL    11      -3.916  -5.981   7.111  1.00  0.00              
ATOM     27  C   VAL    11      -2.883  -4.911   7.457  1.00  0.00              
ATOM     28  O   VAL    11      -2.741  -4.486   8.611  1.00  0.00              
ATOM     29  N   LEU    12      -2.166  -4.487   6.421  1.00  0.00              
ATOM     30  CA  LEU    12      -1.120  -3.479   6.532  1.00  0.00              
ATOM     31  C   LEU    12      -1.732  -2.129   6.164  1.00  0.00              
ATOM     32  O   LEU    12      -1.570  -1.146   6.892  1.00  0.00              
ATOM     33  N   LEU    13      -2.450  -2.096   5.043  1.00  0.00              
ATOM     34  CA  LEU    13      -3.096  -0.882   4.564  1.00  0.00              
ATOM     35  C   LEU    13      -4.321  -0.550   5.404  1.00  0.00              
ATOM     36  O   LEU    13      -4.932   0.501   5.243  1.00  0.00              
ATOM     37  N   SER    14      -4.668  -1.458   6.307  1.00  0.00              
ATOM     38  CA  SER    14      -5.812  -1.286   7.192  1.00  0.00              
ATOM     39  C   SER    14      -5.329  -0.711   8.526  1.00  0.00              
ATOM     40  O   SER    14      -5.909   0.241   9.051  1.00  0.00              
ATOM     41  N   ALA    15      -4.266  -1.287   9.074  1.00  0.00              
ATOM     42  CA  ALA    15      -3.703  -0.787  10.325  1.00  0.00              
ATOM     43  C   ALA    15      -3.241   0.646  10.090  1.00  0.00              
ATOM     44  O   ALA    15      -3.241   1.469  11.004  1.00  0.00              
ATOM     45  N   VAL    16      -2.839   0.931   8.854  1.00  0.00              
ATOM     46  CA  VAL    16      -2.390   2.267   8.493  1.00  0.00              
ATOM     47  C   VAL    16      -3.577   3.216   8.634  1.00  0.00              
ATOM     48  O   VAL    16      -3.596   4.081   9.516  1.00  0.00              
ATOM     49  N   GLY    17      -4.565   3.038   7.757  1.00  0.00              
ATOM     50  CA  GLY    17      -5.767   3.858   7.760  1.00  0.00              
ATOM     51  C   GLY    17      -6.216   4.145   9.178  1.00  0.00              
ATOM     52  O   GLY    17      -6.168   5.280   9.627  1.00  0.00              
ATOM     53  N   ALA    18      -6.634   3.112   9.897  1.00  0.00              
ATOM     54  CA  ALA    18      -7.117   3.301  11.257  1.00  0.00              
ATOM     55  C   ALA    18      -6.160   4.061  12.151  1.00  0.00              
ATOM     56  O   ALA    18      -6.468   4.306  13.310  1.00  0.00              
ATOM     57  N   LEU    19      -5.005   4.433  11.614  1.00  0.00              
ATOM     58  CA  LEU    19      -4.003   5.167  12.383  1.00  0.00              
ATOM     59  C   LEU    19      -3.685   6.533  11.809  1.00  0.00              
ATOM     60  O   LEU    19      -3.546   7.492  12.545  1.00  0.00              
ATOM     61  N   LEU    20      -3.560   6.625  10.494  1.00  0.00              
ATOM     62  CA  LEU    20      -3.249   7.905   9.876  1.00  0.00              
ATOM     63  C   LEU    20      -4.339   8.320   8.904  1.00  0.00              
ATOM     64  O   LEU    20      -5.462   7.825   8.951  1.00  0.00              
ATOM     65  N   ASP    21      -4.004   9.231   8.005  1.00  0.00              
ATOM     66  CA  ASP    21      -5.000   9.670   7.052  1.00  0.00              
ATOM     67  C   ASP    21      -5.371   8.597   6.048  1.00  0.00              
ATOM     68  O   ASP    21      -5.638   7.445   6.395  1.00  0.00              
ATOM     69  N   GLY    22      -5.408   9.027   4.795  1.00  0.00              
ATOM     70  CA  GLY    22      -5.699   8.205   3.640  1.00  0.00              
ATOM     71  C   GLY    22      -4.710   8.794   2.653  1.00  0.00              
ATOM     72  O   GLY    22      -4.268   8.134   1.710  1.00  0.00              
ATOM     73  N   ALA    23      -4.364  10.056   2.901  1.00  0.00              
ATOM     74  CA  ALA    23      -3.398  10.776   2.085  1.00  0.00              
ATOM     75  C   ALA    23      -2.143   9.928   2.180  1.00  0.00              
ATOM     76  O   ALA    23      -1.352   9.840   1.232  1.00  0.00              
ATOM     77  N   ASP    24      -1.984   9.301   3.343  1.00  0.00              
ATOM     78  CA  ASP    24      -0.843   8.445   3.635  1.00  0.00              
ATOM     79  C   ASP    24      -0.936   7.075   2.954  1.00  0.00              
ATOM     80  O   ASP    24      -0.002   6.653   2.264  1.00  0.00              
ATOM     81  N   ILE    25      -2.063   6.393   3.146  1.00  0.00              
ATOM     82  CA  ILE    25      -2.278   5.072   2.564  1.00  0.00              
ATOM     83  C   ILE    25      -1.904   5.015   1.090  1.00  0.00              
ATOM     84  O   ILE    25      -1.472   3.976   0.597  1.00  0.00              
ATOM     85  N   GLY    26      -2.069   6.128   0.386  1.00  0.00              
ATOM     86  CA  GLY    26      -1.725   6.184  -1.036  1.00  0.00              
ATOM     87  C   GLY    26      -0.234   5.972  -1.251  1.00  0.00              
ATOM     88  O   GLY    26       0.171   5.319  -2.213  1.00  0.00              
ATOM     89  N   HIS    27       0.575   6.527  -0.349  1.00  0.00              
ATOM     90  CA  HIS    27       2.024   6.393  -0.438  1.00  0.00              
ATOM     91  C   HIS    27       2.458   4.959  -0.183  1.00  0.00              
ATOM     92  O   HIS    27       3.169   4.363  -1.001  1.00  0.00              
ATOM     93  N   LEU    28       2.021   4.410   0.949  1.00  0.00              
ATOM     94  CA  LEU    28       2.364   3.040   1.326  1.00  0.00              
ATOM     95  C   LEU    28       2.120   2.103   0.153  1.00  0.00              
ATOM     96  O   LEU    28       2.832   1.118  -0.026  1.00  0.00              
ATOM     97  N   VAL    29       1.110   2.436  -0.645  1.00  0.00              
ATOM     98  CA  VAL    29       0.730   1.660  -1.815  1.00  0.00              
ATOM     99  C   VAL    29       1.849   1.486  -2.840  1.00  0.00              
ATOM    100  O   VAL    29       2.389   0.387  -2.974  1.00  0.00              
ATOM    141  N   PRO    45       7.008  10.251  -5.847  1.00  0.00              
ATOM    142  CA  PRO    45       6.383  11.513  -6.236  1.00  0.00              
ATOM    143  C   PRO    45       6.286  11.673  -7.755  1.00  0.00              
ATOM    144  O   PRO    45       5.302  12.215  -8.262  1.00  0.00              
ATOM    145  N   ARG    46       7.300  11.206  -8.483  1.00  0.00              
ATOM    146  CA  ARG    46       7.294  11.319  -9.943  1.00  0.00              
ATOM    147  C   ARG    46       6.268  10.390 -10.594  1.00  0.00              
ATOM    148  O   ARG    46       5.403  10.832 -11.349  1.00  0.00              
ATOM    149  N   ARG    47       6.377   9.100 -10.295  1.00  0.00              
ATOM    150  CA  ARG    47       5.478   8.086 -10.846  1.00  0.00              
ATOM    151  C   ARG    47       4.138   8.016 -10.104  1.00  0.00              
ATOM    152  O   ARG    47       3.527   6.949 -10.011  1.00  0.00              
ATOM    153  N   VAL    48       3.695   9.154  -9.576  1.00  0.00              
ATOM    154  CA  VAL    48       2.433   9.251  -8.848  1.00  0.00              
ATOM    155  C   VAL    48       1.800  10.588  -9.170  1.00  0.00              
ATOM    156  O   VAL    48       0.594  10.692  -9.384  1.00  0.00              
ATOM    157  N   LEU    49       2.651  11.609  -9.190  1.00  0.00              
ATOM    158  CA  LEU    49       2.264  12.985  -9.461  1.00  0.00              
ATOM    159  C   LEU    49       1.695  13.635  -8.201  1.00  0.00              
ATOM    160  O   LEU    49       0.524  13.457  -7.860  1.00  0.00              
ATOM    161  N   VAL    50       2.563  14.372  -7.513  1.00  0.00              
ATOM    162  CA  VAL    50       2.248  15.098  -6.285  1.00  0.00              
ATOM    163  C   VAL    50       3.524  15.792  -5.806  1.00  0.00              
ATOM    164  O   VAL    50       4.634  15.351  -6.112  1.00  0.00              
ATOM    165  N   HIS    51       3.372  16.876  -5.057  1.00  0.00              
ATOM    166  CA  HIS    51       4.539  17.582  -4.553  1.00  0.00              
ATOM    167  C   HIS    51       5.400  16.662  -3.687  1.00  0.00              
ATOM    168  O   HIS    51       4.912  16.071  -2.721  1.00  0.00              
ATOM    169  N   GLU    52       6.683  16.549  -4.043  1.00  0.00              
ATOM    170  CA  GLU    52       7.634  15.698  -3.317  1.00  0.00              
ATOM    171  C   GLU    52       7.661  16.064  -1.845  1.00  0.00              
ATOM    172  O   GLU    52       8.090  15.277  -1.002  1.00  0.00              
ATOM    173  N   ASP    53       7.210  17.274  -1.547  1.00  0.00              
ATOM    174  CA  ASP    53       7.184  17.755  -0.182  1.00  0.00              
ATOM    175  C   ASP    53       6.110  17.041   0.615  1.00  0.00              
ATOM    176  O   ASP    53       6.389  16.490   1.668  1.00  0.00              
ATOM    177  N   ASP    54       4.881  17.060   0.111  1.00  0.00              
ATOM    178  CA  ASP    54       3.762  16.402   0.782  1.00  0.00              
ATOM    179  C   ASP    54       3.969  14.885   0.737  1.00  0.00              
ATOM    180  O   ASP    54       3.347  14.132   1.488  1.00  0.00              
ATOM    181  N   LEU    55       4.850  14.452  -0.159  1.00  0.00              
ATOM    182  CA  LEU    55       5.182  13.049  -0.308  1.00  0.00              
ATOM    183  C   LEU    55       6.070  12.676   0.857  1.00  0.00              
ATOM    184  O   LEU    55       5.879  11.642   1.488  1.00  0.00              
ATOM    185  N   ALA    56       7.048  13.529   1.142  1.00  0.00              
ATOM    186  CA  ALA    56       7.969  13.282   2.245  1.00  0.00              
ATOM    187  C   ALA    56       7.221  13.468   3.554  1.00  0.00              
ATOM    188  O   ALA    56       7.583  12.901   4.573  1.00  0.00              
ATOM    189  N   GLY    57       6.176  14.279   3.523  1.00  0.00              
ATOM    190  CA  GLY    57       5.391  14.520   4.717  1.00  0.00              
ATOM    191  C   GLY    57       4.671  13.233   5.107  1.00  0.00              
ATOM    192  O   GLY    57       4.612  12.877   6.285  1.00  0.00              
ATOM    193  N   ALA    58       4.137  12.527   4.113  1.00  0.00              
ATOM    194  CA  ALA    58       3.452  11.275   4.374  1.00  0.00              
ATOM    195  C   ALA    58       4.467  10.281   4.904  1.00  0.00              
ATOM    196  O   ALA    58       4.314   9.755   6.007  1.00  0.00              
ATOM    197  N   ARG    59       5.520  10.042   4.137  1.00  0.00              
ATOM    198  CA  ARG    59       6.549   9.106   4.567  1.00  0.00              
ATOM    199  C   ARG    59       6.966   9.228   6.043  1.00  0.00              
ATOM    200  O   ARG    59       6.976   8.225   6.749  1.00  0.00              
ATOM    201  N   ARG    60       7.290  10.423   6.533  1.00  0.00              
ATOM    202  CA  ARG    60       7.718  10.532   7.931  1.00  0.00              
ATOM    203  C   ARG    60       6.625  10.222   8.942  1.00  0.00              
ATOM    204  O   ARG    60       6.929   9.833  10.062  1.00  0.00              
ATOM    205  N   LEU    61       5.363  10.416   8.548  1.00  0.00              
ATOM    206  CA  LEU    61       4.202  10.150   9.413  1.00  0.00              
ATOM    207  C   LEU    61       4.013   8.651   9.626  1.00  0.00              
ATOM    208  O   LEU    61       3.730   8.204  10.732  1.00  0.00              
ATOM    209  N   LEU    62       4.153   7.888   8.542  1.00  0.00              
ATOM    210  CA  LEU    62       4.038   6.430   8.566  1.00  0.00              
ATOM    211  C   LEU    62       5.268   5.932   9.303  1.00  0.00              
ATOM    212  O   LEU    62       5.174   5.140  10.243  1.00  0.00              
ATOM    213  N   THR    63       6.424   6.411   8.846  1.00  0.00              
ATOM    214  CA  THR    63       7.718   6.055   9.415  1.00  0.00              
ATOM    215  C   THR    63       7.622   6.106  10.922  1.00  0.00              
ATOM    216  O   THR    63       8.038   5.188  11.610  1.00  0.00              
ATOM    217  N   ASP    64       7.049   7.186  11.423  1.00  0.00              
ATOM    218  CA  ASP    64       6.869   7.385  12.854  1.00  0.00              
ATOM    219  C   ASP    64       6.077   6.242  13.475  1.00  0.00              
ATOM    220  O   ASP    64       6.344   5.840  14.603  1.00  0.00              
ATOM    221  N   ALA    65       5.104   5.717  12.739  1.00  0.00              
ATOM    222  CA  ALA    65       4.287   4.618  13.242  1.00  0.00              
ATOM    223  C   ALA    65       4.959   3.278  13.009  1.00  0.00              
ATOM    224  O   ALA    65       4.780   2.341  13.796  1.00  0.00              
ATOM    225  N   GLY    66       5.726   3.188  11.924  1.00  0.00              
ATOM    226  CA  GLY    66       6.436   1.959  11.627  1.00  0.00              
ATOM    227  C   GLY    66       5.915   1.179  10.442  1.00  0.00              
ATOM    228  O   GLY    66       6.010  -0.049  10.423  1.00  0.00              
ATOM    229  N   LEU    67       5.376   1.883   9.450  1.00  0.00              
ATOM    230  CA  LEU    67       4.849   1.228   8.259  1.00  0.00              
ATOM    231  C   LEU    67       5.855   1.371   7.148  1.00  0.00              
ATOM    232  O   LEU    67       5.630   0.921   6.028  1.00  0.00              
ATOM    233  N   ALA    68       6.975   2.001   7.476  1.00  0.00              
ATOM    234  CA  ALA    68       8.054   2.228   6.525  1.00  0.00              
ATOM    235  C   ALA    68       9.352   2.502   7.288  1.00  0.00              
ATOM    236  O   ALA    68       9.330   2.962   8.430  1.00  0.00              
ATOM    237  N   HIS    69      10.482   2.191   6.661  1.00  0.00              
ATOM    238  CA  HIS    69      11.804   2.444   7.244  1.00  0.00              
ATOM    239  C   HIS    69      12.651   3.051   6.146  1.00  0.00              
ATOM    240  O   HIS    69      12.462   2.734   4.976  1.00  0.00              
END
