
#######################################################
#                                                     #
#                        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   45 (  188),  selected   45 , name T0349AL333_2-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349AL333_2-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    M       1      M       1           -
LGA    -       -      R       2           -
LGA    -       -      E       3           -
LGA    -       -      L       4           -
LGA    -       -      L       5           -
LGA    -       -      R       6           -
LGA    S      14      T       7           #
LGA    A      15      N       8          1.756
LGA    V      16      D       9          2.989
LGA    -       -      A      10           -
LGA    -       -      V      11           -
LGA    -       -      L      12           -
LGA    -       -      L      13           -
LGA    G      17      S      14          2.840
LGA    A      18      A      15          3.770
LGA    -       -      V      16           -
LGA    -       -      G      17           -
LGA    L      19      A      18          1.991
LGA    L      20      L      19          3.835
LGA    D      21      L      20          3.087
LGA    -       -      D      21           -
LGA    -       -      G      22           -
LGA    -       -      A      23           -
LGA    G      22      D      24          1.873
LGA    -       -      I      25           -
LGA    A      23      G      26           #
LGA    D      24      H      27           #
LGA    I      25      L      28           #
LGA    G      26      V      29          3.110
LGA    H      27      P      45           -
LGA    L      28      -       -           -
LGA    V      29      R      46          3.992
LGA    P      45      R      47           -
LGA    -       -      V      48           -
LGA    R      46      L      49          4.306
LGA    R      47      V      50          2.705
LGA    V      48      H      51          2.522
LGA    -       -      E      52           -
LGA    -       -      D      53           -
LGA    -       -      D      54           -
LGA    L      49      L      55          3.468
LGA    V      50      A      56          2.615
LGA    -       -      G      57           -
LGA    -       -      A      58           -
LGA    H      51      R      59          1.040
LGA    E      52      R      60          2.047
LGA    D      53      L      61          4.278
LGA    -       -      L      62           -
LGA    -       -      T      63           -
LGA    -       -      D      64           -
LGA    -       -      A      65           -
LGA    D      54      G      66           #
LGA    L      55      L      67          4.166
LGA    A      56      A      68          3.977
LGA    G      57      H      69          3.167
LGA    A      58      -       -           -
LGA    R      59      E      70          4.849
LGA    R      60      L      71           -
LGA    L      61      R      72           -
LGA    L      62      -       -           -
LGA    T      63      -       -           -
LGA    D      64      -       -           -
LGA    A      65      -       -           -
LGA    G      66      -       -           -
LGA    L      67      -       -           -
LGA    A      68      -       -           -
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)   45   57    5.0     22    3.25    22.73     23.094     0.656

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.981998 * X  +  -0.058898 * Y  +   0.179475 * Z  + -10.387083
  Y_new =  -0.066484 * X  +  -0.781577 * Y  +  -0.620256 * Z  +  40.151894
  Z_new =   0.176805 * X  +  -0.621023 * Y  +   0.763591 * Z  + -19.323820 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.682794    2.458799  [ DEG:   -39.1212    140.8788 ]
  Theta =  -0.177740   -2.963853  [ DEG:   -10.1837   -169.8163 ]
  Phi   =  -3.073992    0.067600  [ DEG:  -176.1268      3.8732 ]
 
# 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_2-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349AL333_2-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   45   57   5.0   22   3.25   22.73  23.094
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL333_2-D1
REMARK Aligment from pdb entry: 1c1y_B
ATOM      1  N   MET     1      -5.337 -14.124   2.266  1.00  0.00              
ATOM      2  CA  MET     1      -5.099 -12.789   1.635  1.00  0.00              
ATOM      3  C   MET     1      -3.996 -12.048   2.374  1.00  0.00              
ATOM      4  O   MET     1      -4.112 -11.767   3.569  1.00  0.00              
ATOM      5  N   SER    14      -2.931 -11.723   1.653  1.00  0.00              
ATOM      6  CA  SER    14      -1.793 -11.029   2.239  1.00  0.00              
ATOM      7  C   SER    14      -1.962  -9.513   2.143  1.00  0.00              
ATOM      8  O   SER    14      -1.226  -8.848   1.422  1.00  0.00              
ATOM      9  N   ALA    15      -2.944  -8.970   2.857  1.00  0.00              
ATOM     10  CA  ALA    15      -3.180  -7.528   2.820  1.00  0.00              
ATOM     11  C   ALA    15      -3.139  -6.877   4.189  1.00  0.00              
ATOM     12  O   ALA    15      -3.181  -7.551   5.216  1.00  0.00              
ATOM     13  N   VAL    16      -3.051  -5.551   4.178  1.00  0.00              
ATOM     14  CA  VAL    16      -3.050  -4.746   5.389  1.00  0.00              
ATOM     15  C   VAL    16      -3.869  -3.501   5.074  1.00  0.00              
ATOM     16  O   VAL    16      -3.680  -2.896   4.022  1.00  0.00              
ATOM     17  N   GLY    17      -4.813  -3.161   5.947  1.00  0.00              
ATOM     18  CA  GLY    17      -5.607  -1.952   5.760  1.00  0.00              
ATOM     19  C   GLY    17      -4.926  -0.864   6.579  1.00  0.00              
ATOM     20  O   GLY    17      -4.605  -1.067   7.750  1.00  0.00              
ATOM     21  N   ALA    18      -4.743   0.299   5.975  1.00  0.00              
ATOM     22  CA  ALA    18      -4.066   1.395   6.650  1.00  0.00              
ATOM     23  C   ALA    18      -4.854   2.688   6.579  1.00  0.00              
ATOM     24  O   ALA    18      -5.176   3.168   5.493  1.00  0.00              
ATOM     25  N   LEU    19      -5.125   3.257   7.748  1.00  0.00              
ATOM     26  CA  LEU    19      -5.841   4.514   7.855  1.00  0.00              
ATOM     27  C   LEU    19      -4.805   5.625   7.776  1.00  0.00              
ATOM     28  O   LEU    19      -3.782   5.591   8.461  1.00  0.00              
ATOM     29  N   LEU    20      -5.064   6.580   6.897  1.00  0.00              
ATOM     30  CA  LEU    20      -4.148   7.684   6.636  1.00  0.00              
ATOM     31  C   LEU    20      -4.697   9.032   7.073  1.00  0.00              
ATOM     32  O   LEU    20      -5.882   9.159   7.387  1.00  0.00              
ATOM     33  N   ASP    21      -3.830  10.058   7.116  1.00  0.00              
ATOM     34  CA  ASP    21      -4.247  11.404   7.511  1.00  0.00              
ATOM     35  C   ASP    21      -5.319  11.929   6.555  1.00  0.00              
ATOM     36  O   ASP    21      -5.435  11.464   5.414  1.00  0.00              
ATOM     37  N   GLY    22      -6.069  12.921   7.023  1.00  0.00              
ATOM     38  CA  GLY    22      -7.146  13.544   6.253  1.00  0.00              
ATOM     39  C   GLY    22      -8.235  12.535   5.896  1.00  0.00              
ATOM     40  O   GLY    22      -8.761  12.540   4.780  1.00  0.00              
ATOM     41  N   ALA    23      -8.526  11.646   6.844  1.00  0.00              
ATOM     42  CA  ALA    23      -9.572  10.631   6.715  1.00  0.00              
ATOM     43  C   ALA    23      -9.529   9.784   5.438  1.00  0.00              
ATOM     44  O   ALA    23     -10.566   9.486   4.838  1.00  0.00              
ATOM     45  N   ASP    24      -8.326   9.385   5.044  1.00  0.00              
ATOM     46  CA  ASP    24      -8.122   8.566   3.854  1.00  0.00              
ATOM     47  C   ASP    24      -7.723   7.164   4.306  1.00  0.00              
ATOM     48  O   ASP    24      -7.440   6.939   5.490  1.00  0.00              
ATOM     49  N  AILE    25      -7.703   6.227   3.365  1.00  0.00              
ATOM     50  N  BILE    25      -7.713   6.220   3.372  1.00  0.00              
ATOM     51  CA AILE    25      -7.343   4.846   3.680  1.00  0.00              
ATOM     52  CA BILE    25      -7.327   4.846   3.691  1.00  0.00              
ATOM     53  C  AILE    25      -6.826   4.132   2.438  1.00  0.00              
ATOM     54  C  BILE    25      -6.862   4.109   2.445  1.00  0.00              
ATOM     55  O  AILE    25      -7.055   4.571   1.308  1.00  0.00              
ATOM     56  O  BILE    25      -7.164   4.507   1.319  1.00  0.00              
ATOM     57  N   GLY    26      -6.127   3.024   2.658  1.00  0.00              
ATOM     58  CA  GLY    26      -5.614   2.233   1.562  1.00  0.00              
ATOM     59  C   GLY    26      -5.460   0.804   2.066  1.00  0.00              
ATOM     60  O   GLY    26      -5.403   0.563   3.271  1.00  0.00              
ATOM     61  N   HIS    27      -5.559  -0.144   1.149  1.00  0.00              
ATOM     62  CA  HIS    27      -5.343  -1.544   1.489  1.00  0.00              
ATOM     63  C   HIS    27      -4.218  -1.922   0.542  1.00  0.00              
ATOM     64  O   HIS    27      -4.329  -1.718  -0.666  1.00  0.00              
ATOM     65  N   LEU    28      -3.109  -2.391   1.104  1.00  0.00              
ATOM     66  CA  LEU    28      -1.953  -2.753   0.294  1.00  0.00              
ATOM     67  C   LEU    28      -1.633  -4.242   0.325  1.00  0.00              
ATOM     68  O   LEU    28      -1.943  -4.932   1.292  1.00  0.00              
ATOM     69  N   VAL    29      -1.051  -4.722  -0.771  1.00  0.00              
ATOM     70  CA  VAL    29      -0.641  -6.119  -0.895  1.00  0.00              
ATOM     71  C   VAL    29       0.725  -6.250  -0.250  1.00  0.00              
ATOM     72  O   VAL    29       1.570  -5.360  -0.379  1.00  0.00              
ATOM    145  N   PRO    45       3.088   8.317  -1.381  1.00  0.00              
ATOM    146  CA  PRO    45       3.548   9.200  -2.452  1.00  0.00              
ATOM    147  C   PRO    45       2.417   9.852  -3.256  1.00  0.00              
ATOM    148  O   PRO    45       2.460  11.049  -3.527  1.00  0.00              
ATOM    149  N   ARG    46       1.412   9.069  -3.644  1.00  0.00              
ATOM    150  CA  ARG    46       0.298   9.612  -4.420  1.00  0.00              
ATOM    151  C   ARG    46      -0.604  10.541  -3.610  1.00  0.00              
ATOM    152  O   ARG    46      -1.519  11.149  -4.167  1.00  0.00              
ATOM    153  N   ARG    47      -0.368  10.616  -2.298  1.00  0.00              
ATOM    154  CA  ARG    47      -1.144  11.493  -1.416  1.00  0.00              
ATOM    155  C   ARG    47      -0.259  12.618  -0.874  1.00  0.00              
ATOM    156  O   ARG    47      -0.680  13.393  -0.009  1.00  0.00              
ATOM    157  N   VAL    48       0.975  12.677  -1.374  1.00  0.00              
ATOM    158  CA  VAL    48       1.921  13.698  -0.956  1.00  0.00              
ATOM    159  C   VAL    48       2.397  13.577   0.476  1.00  0.00              
ATOM    160  O   VAL    48       2.770  14.573   1.089  1.00  0.00              
ATOM    161  N   LEU    49       2.388  12.359   1.011  1.00  0.00              
ATOM    162  CA  LEU    49       2.817  12.112   2.383  1.00  0.00              
ATOM    163  C   LEU    49       4.225  11.541   2.415  1.00  0.00              
ATOM    164  O   LEU    49       4.608  10.761   1.542  1.00  0.00              
ATOM    165  N   VAL    50       4.991  11.928   3.429  1.00  0.00              
ATOM    166  CA  VAL    50       6.361  11.451   3.588  1.00  0.00              
ATOM    167  C   VAL    50       6.497  10.670   4.888  1.00  0.00              
ATOM    168  O   VAL    50       6.215  11.192   5.967  1.00  0.00              
ATOM    169  N   HIS    51       6.945   9.407   4.800  1.00  0.00              
ATOM    170  CA  HIS    51       7.124   8.535   5.964  1.00  0.00              
ATOM    171  C   HIS    51       8.007   9.104   7.073  1.00  0.00              
ATOM    172  O   HIS    51       7.731   8.891   8.250  1.00  0.00              
ATOM    173  N   GLU    52       9.042   9.858   6.706  1.00  0.00              
ATOM    174  CA  GLU    52       9.935  10.436   7.711  1.00  0.00              
ATOM    175  C   GLU    52       9.241  11.486   8.572  1.00  0.00              
ATOM    176  O   GLU    52       9.723  11.822   9.652  1.00  0.00              
ATOM    177  N   ASP    53       8.115  12.004   8.083  1.00  0.00              
ATOM    178  CA  ASP    53       7.344  13.011   8.810  1.00  0.00              
ATOM    179  C   ASP    53       6.122  12.399   9.485  1.00  0.00              
ATOM    180  O   ASP    53       5.303  13.112  10.068  1.00  0.00              
ATOM    181  N   ASP    54       8.013   0.436  13.981  1.00  0.00              
ATOM    182  CA  ASP    54       9.167   0.939  13.260  1.00  0.00              
ATOM    183  C   ASP    54       8.813   0.857  11.775  1.00  0.00              
ATOM    184  O   ASP    54       8.168  -0.101  11.352  1.00  0.00              
ATOM    185  N   LEU    55       9.205   1.866  10.998  1.00  0.00              
ATOM    186  CA  LEU    55       8.933   1.873   9.563  1.00  0.00              
ATOM    187  C   LEU    55       9.639   0.729   8.839  1.00  0.00              
ATOM    188  O   LEU    55       9.242   0.342   7.736  1.00  0.00              
ATOM    189  N   ALA    56      10.668   0.172   9.471  1.00  0.00              
ATOM    190  CA  ALA    56      11.432  -0.917   8.871  1.00  0.00              
ATOM    191  C   ALA    56      10.941  -2.300   9.281  1.00  0.00              
ATOM    192  O   ALA    56      11.587  -3.309   8.987  1.00  0.00              
ATOM    193  N   GLY    57       9.787  -2.347   9.942  1.00  0.00              
ATOM    194  CA  GLY    57       9.195  -3.608  10.383  1.00  0.00              
ATOM    195  C   GLY    57       8.942  -4.524   9.183  1.00  0.00              
ATOM    196  O   GLY    57       8.587  -4.053   8.101  1.00  0.00              
ATOM    197  N   ALA    58       9.135  -5.827   9.374  1.00  0.00              
ATOM    198  CA  ALA    58       8.888  -6.799   8.312  1.00  0.00              
ATOM    199  C   ALA    58       7.371  -6.825   8.068  1.00  0.00              
ATOM    200  O   ALA    58       6.597  -7.136   8.971  1.00  0.00              
ATOM    201  N   ARG    59       6.961  -6.487   6.848  1.00  0.00              
ATOM    202  CA  ARG    59       5.544  -6.424   6.488  1.00  0.00              
ATOM    203  C   ARG    59       4.759  -7.724   6.620  1.00  0.00              
ATOM    204  O   ARG    59       3.610  -7.706   7.063  1.00  0.00              
ATOM    205  N   ARG    60       5.368  -8.843   6.232  1.00  0.00              
ATOM    206  CA  ARG    60       4.700 -10.145   6.310  1.00  0.00              
ATOM    207  C   ARG    60       4.212 -10.456   7.722  1.00  0.00              
ATOM    208  O   ARG    60       3.224 -11.176   7.905  1.00  0.00              
ATOM    209  N   LEU    61       4.900  -9.902   8.716  1.00  0.00              
ATOM    210  CA  LEU    61       4.541 -10.109  10.112  1.00  0.00              
ATOM    211  C   LEU    61       3.311  -9.294  10.527  1.00  0.00              
ATOM    212  O   LEU    61       2.768  -9.490  11.617  1.00  0.00              
ATOM    213  N   LEU    62       2.883  -8.380   9.659  1.00  0.00              
ATOM    214  CA  LEU    62       1.738  -7.516   9.940  1.00  0.00              
ATOM    215  C   LEU    62       0.485  -7.842   9.125  1.00  0.00              
ATOM    216  O   LEU    62      -0.504  -7.108   9.188  1.00  0.00              
ATOM    217  N   THR    63       0.525  -8.932   8.363  1.00  0.00              
ATOM    218  CA  THR    63      -0.621  -9.324   7.545  1.00  0.00              
ATOM    219  C   THR    63      -1.859  -9.490   8.422  1.00  0.00              
ATOM    220  O   THR    63      -1.802 -10.099   9.487  1.00  0.00              
ATOM    221  N   ASP    64      -2.955  -8.867   8.005  1.00  0.00              
ATOM    222  CA  ASP    64      -4.183  -8.948   8.775  1.00  0.00              
ATOM    223  C   ASP    64      -4.310  -7.856   9.819  1.00  0.00              
ATOM    224  O   ASP    64      -5.379  -7.679  10.391  1.00  0.00              
ATOM    225  N   ALA    65      -3.224  -7.141  10.102  1.00  0.00              
ATOM    226  CA  ALA    65      -3.270  -6.057  11.082  1.00  0.00              
ATOM    227  C   ALA    65      -3.836  -4.791  10.434  1.00  0.00              
ATOM    228  O   ALA    65      -3.803  -4.638   9.211  1.00  0.00              
ATOM    229  N   GLY    66      -4.417  -3.917  11.249  1.00  0.00              
ATOM    230  CA  GLY    66      -4.956  -2.654  10.752  1.00  0.00              
ATOM    231  C   GLY    66      -4.067  -1.585  11.350  1.00  0.00              
ATOM    232  O   GLY    66      -3.866  -1.538  12.564  1.00  0.00              
ATOM    233  N   LEU    67      -3.506  -0.751  10.485  1.00  0.00              
ATOM    234  CA  LEU    67      -2.584   0.280  10.920  1.00  0.00              
ATOM    235  C   LEU    67      -3.121   1.675  10.721  1.00  0.00              
ATOM    236  O   LEU    67      -4.113   1.883  10.019  1.00  0.00              
ATOM    237  N  AALA    68      -2.449   2.639  11.343  1.00  0.00              
ATOM    238  N  BALA    68      -2.435   2.636  11.326  1.00  0.00              
ATOM    239  CA AALA    68      -2.821   4.043  11.232  1.00  0.00              
ATOM    240  CA BALA    68      -2.806   4.033  11.208  1.00  0.00              
ATOM    241  C  AALA    68      -1.553   4.883  11.136  1.00  0.00              
ATOM    242  C  BALA    68      -1.542   4.871  11.122  1.00  0.00              
ATOM    243  O  AALA    68      -0.625   4.710  11.927  1.00  0.00              
ATOM    244  O  BALA    68      -0.610   4.688  11.907  1.00  0.00              
ATOM    245  N   HIS    69      -1.507   5.761  10.139  1.00  0.00              
ATOM    246  CA  HIS    69      -0.364   6.639   9.941  1.00  0.00              
ATOM    247  C   HIS    69      -0.785   8.049  10.359  1.00  0.00              
ATOM    248  O   HIS    69      -1.805   8.556   9.895  1.00  0.00              
ATOM    249  N   GLU    70      -0.027   8.635  11.282  1.00  0.00              
ATOM    250  CA  GLU    70      -0.277   9.989  11.783  1.00  0.00              
ATOM    251  C   GLU    70       0.979  10.824  11.557  1.00  0.00              
ATOM    252  O   GLU    70       2.078  10.279  11.460  1.00  0.00              
ATOM    253  N   LEU    71       0.817  12.142  11.482  1.00  0.00              
ATOM    254  CA  LEU    71       1.957  13.040  11.311  1.00  0.00              
ATOM    255  C   LEU    71       2.683  13.183  12.640  1.00  0.00              
ATOM    256  O   LEU    71       2.074  13.087  13.703  1.00  0.00              
ATOM    257  N   ARG    72       3.985  13.420  12.577  1.00  0.00              
ATOM    258  CA  ARG    72       4.774  13.627  13.784  1.00  0.00              
ATOM    259  C   ARG    72       4.528  15.057  14.278  1.00  0.00              
ATOM    260  O   ARG    72       4.307  15.939  13.418  1.00  0.00              
END
