
#######################################################
#                                                     #
#                        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   40 (  160),  selected   40 , name T0349TS550_4-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS550_4-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           -
LGA    -       -      R       6           -
LGA    A      10      T       7           #
LGA    V      11      N       8           #
LGA    L      12      D       9          2.343
LGA    L      13      -       -           -
LGA    S      14      A      10          1.100
LGA    A      15      V      11          1.017
LGA    V      16      L      12          1.724
LGA    G      17      L      13          1.711
LGA    A      18      S      14          0.852
LGA    L      19      A      15          1.039
LGA    L      20      V      16          2.457
LGA    D      21      G      17          2.875
LGA    G      22      A      18          1.856
LGA    A      23      L      19          1.680
LGA    -       -      L      20           -
LGA    -       -      D      21           -
LGA    D      24      G      22          2.772
LGA    I      25      A      23          1.957
LGA    G      26      D      24          4.137
LGA    H      27      I      25          3.685
LGA    -       -      G      26           -
LGA    L      28      H      27          1.395
LGA    V      29      L      28          1.706
LGA    -       -      V      29           -
LGA    P      45      P      45          5.239
LGA    R      46      R      46          4.051
LGA    R      47      R      47          1.767
LGA    V      48      V      48          1.467
LGA    L      49      L      49          1.116
LGA    V      50      V      50          1.151
LGA    H      51      H      51          2.668
LGA    -       -      E      52           -
LGA    -       -      D      53           -
LGA    -       -      D      54           -
LGA    E      52      L      55          1.201
LGA    D      53      A      56          1.888
LGA    D      54      G      57          3.101
LGA    L      55      A      58          3.310
LGA    A      56      R      59          1.057
LGA    G      57      R      60          2.936
LGA    -       -      L      61           -
LGA    A      58      L      62          2.731
LGA    R      59      T      63          4.008
LGA    R      60      D      64          4.015
LGA    -       -      A      65           -
LGA    L      61      G      66          1.362
LGA    L      62      L      67          3.002
LGA    T      63      A      68          2.274
LGA    D      64      H      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      R      72           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   40   57    5.0     36    2.54    22.22     43.340     1.362

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.741415 * X  +   0.574668 * Y  +   0.346498 * Z  + -19.988312
  Y_new =   0.121521 * X  +   0.392837 * Y  +  -0.911544 * Z  + -32.967079
  Z_new =  -0.659952 * X  +   0.717939 * Y  +   0.221421 * Z  +  -2.006222 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.271640   -1.869953  [ DEG:    72.8596   -107.1404 ]
  Theta =   0.720755    2.420838  [ DEG:    41.2962    138.7038 ]
  Phi   =   0.162459   -2.979133  [ DEG:     9.3082   -170.6918 ]
 
# 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: T0349TS550_4-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS550_4-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   40   57   5.0   36   2.54   22.22  43.340
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS550_4-D1
PFRMAT TS
TARGET T0349
MODEL 4
PARENT 1in0_A
ATOM      1  N   ALA    10      -3.969 -10.883   2.280  1.00  0.00
ATOM      2  CA  ALA    10      -5.020  -9.924   2.464  1.00  0.00
ATOM      3  C   ALA    10      -5.258  -9.551   3.908  1.00  0.00
ATOM      4  O   ALA    10      -5.435  -8.361   4.140  1.00  0.00
ATOM      5  N   VAL    11      -5.211 -10.489   4.819  1.00  0.00
ATOM      6  CA  VAL    11      -5.535 -10.234   6.204  1.00  0.00
ATOM      7  C   VAL    11      -4.604  -9.195   6.808  1.00  0.00
ATOM      8  O   VAL    11      -5.082  -8.223   7.412  1.00  0.00
ATOM      9  N   LEU    12      -3.324  -9.404   6.560  1.00  0.00
ATOM     10  CA  LEU    12      -2.345  -8.447   7.083  1.00  0.00
ATOM     11  C   LEU    12      -2.472  -7.098   6.323  1.00  0.00
ATOM     12  O   LEU    12      -2.207  -6.088   6.912  1.00  0.00
ATOM     13  N   LEU    13      -2.745  -7.135   5.049  1.00  0.00
ATOM     14  CA  LEU    13      -2.874  -5.960   4.176  1.00  0.00
ATOM     15  C   LEU    13      -4.020  -5.062   4.657  1.00  0.00
ATOM     16  O   LEU    13      -3.879  -3.857   4.621  1.00  0.00
ATOM     17  N   SER    14      -5.097  -5.714   5.036  1.00  0.00
ATOM     18  CA  SER    14      -6.241  -5.038   5.616  1.00  0.00
ATOM     19  C   SER    14      -5.836  -4.459   6.952  1.00  0.00
ATOM     20  O   SER    14      -6.364  -3.377   7.245  1.00  0.00
ATOM     21  N   ALA    15      -4.905  -5.030   7.701  1.00  0.00
ATOM     22  CA  ALA    15      -4.555  -4.381   8.983  1.00  0.00
ATOM     23  C   ALA    15      -3.713  -3.133   8.729  1.00  0.00
ATOM     24  O   ALA    15      -3.748  -2.210   9.524  1.00  0.00
ATOM     25  N   VAL    16      -2.960  -3.195   7.641  1.00  0.00
ATOM     26  CA  VAL    16      -2.123  -2.073   7.214  1.00  0.00
ATOM     27  C   VAL    16      -3.067  -0.949   6.716  1.00  0.00
ATOM     28  O   VAL    16      -2.961   0.212   7.116  1.00  0.00
ATOM     29  N   GLY    17      -3.972  -1.317   5.818  1.00  0.00
ATOM     30  CA  GLY    17      -4.827  -0.330   5.217  1.00  0.00
ATOM     31  C   GLY    17      -5.678   0.333   6.306  1.00  0.00
ATOM     32  O   GLY    17      -5.866   1.560   6.340  1.00  0.00
ATOM     33  N   ALA    18      -6.091  -0.491   7.269  1.00  0.00
ATOM     34  CA  ALA    18      -6.855   0.070   8.364  1.00  0.00
ATOM     35  C   ALA    18      -6.061   1.069   9.198  1.00  0.00
ATOM     36  O   ALA    18      -6.572   2.056   9.742  1.00  0.00
ATOM     37  N   LEU    19      -4.789   0.769   9.457  1.00  0.00
ATOM     38  CA  LEU    19      -3.963   1.645  10.289  1.00  0.00
ATOM     39  C   LEU    19      -3.825   3.018   9.595  1.00  0.00
ATOM     40  O   LEU    19      -3.851   4.073  10.246  1.00  0.00
ATOM     41  N   LEU    20      -3.624   2.956   8.275  1.00  0.00
ATOM     42  CA  LEU    20      -3.494   4.180   7.475  1.00  0.00
ATOM     43  C   LEU    20      -4.762   5.043   7.614  1.00  0.00
ATOM     44  O   LEU    20      -4.679   6.206   8.022  1.00  0.00
ATOM     45  N   ASP    21      -5.924   4.483   7.390  1.00  0.00
ATOM     46  CA  ASP    21      -7.192   5.187   7.520  1.00  0.00
ATOM     47  C   ASP    21      -7.182   5.906   8.866  1.00  0.00
ATOM     48  O   ASP    21      -7.342   7.137   8.963  1.00  0.00
ATOM     49  N   GLY    22      -6.917   5.098   9.907  1.00  0.00
ATOM     50  CA  GLY    22      -6.853   5.702  11.239  1.00  0.00
ATOM     51  C   GLY    22      -5.783   6.764  11.461  1.00  0.00
ATOM     52  O   GLY    22      -5.893   7.537  12.419  1.00  0.00
ATOM     53  N   ALA    23      -4.663   6.771  10.745  1.00  0.00
ATOM     54  CA  ALA    23      -3.670   7.780  11.045  1.00  0.00
ATOM     55  C   ALA    23      -4.093   9.141  10.419  1.00  0.00
ATOM     56  O   ALA    23      -3.434  10.119  10.754  1.00  0.00
ATOM     57  N   ASP    24      -3.519   9.379  11.492  1.00  0.00
ATOM     58  CA  ASP    24      -3.931  10.522  12.303  1.00  0.00
ATOM     59  C   ASP    24      -3.398  11.833  11.685  1.00  0.00
ATOM     60  O   ASP    24      -3.813  12.946  12.049  1.00  0.00
ATOM     61  N   ILE    25      -2.508  11.689  10.704  1.00  0.00
ATOM     62  CA  ILE    25      -1.752  12.808  10.185  1.00  0.00
ATOM     63  C   ILE    25      -1.830  12.869   8.645  1.00  0.00
ATOM     64  O   ILE    25      -1.467  13.866   8.033  1.00  0.00
ATOM     65  N   GLY    26      -2.324  11.807   8.015  1.00  0.00
ATOM     66  CA  GLY    26      -2.349  11.736   6.555  1.00  0.00
ATOM     67  C   GLY    26      -3.528  10.894   6.078  1.00  0.00
ATOM     68  O   GLY    26      -3.972   9.991   6.775  1.00  0.00
ATOM     69  N   HIS    27      -4.024  11.195   4.886  1.00  0.00
ATOM     70  CA  HIS    27      -5.104  10.419   4.267  1.00  0.00
ATOM     71  C   HIS    27      -4.566   9.397   3.236  1.00  0.00
ATOM     72  O   HIS    27      -5.336   8.641   2.654  1.00  0.00
ATOM     73  N   LEU    28      -3.170   9.503   2.185  1.00  0.00
ATOM     74  CA  LEU    28      -2.547   8.662   1.133  1.00  0.00
ATOM     75  C   LEU    28      -3.540   7.578   0.763  1.00  0.00
ATOM     76  O   LEU    28      -4.444   7.312   1.560  1.00  0.00
ATOM     77  N   VAL    29      -3.413   7.024  -0.430  1.00  0.00
ATOM     78  CA  VAL    29      -4.267   5.944  -0.906  1.00  0.00
ATOM     79  C   VAL    29      -3.495   4.616  -0.766  1.00  0.00
ATOM     80  O   VAL    29      -2.272   4.567  -0.878  1.00  0.00
ATOM    141  N   PRO    45       1.508  -7.288  -1.827  1.00  0.00
ATOM    142  CA  PRO    45       2.060  -6.068  -1.199  1.00  0.00
ATOM    143  C   PRO    45       0.968  -5.042  -0.945  1.00  0.00
ATOM    144  O   PRO    45      -0.235  -5.272  -1.047  1.00  0.00
ATOM    145  N   ARG    46       1.371  -3.879  -0.494  1.00  0.00
ATOM    146  CA  ARG    46       0.440  -2.744  -0.320  1.00  0.00
ATOM    147  C   ARG    46       1.179  -1.557  -0.934  1.00  0.00
ATOM    148  O   ARG    46       2.323  -1.306  -0.513  1.00  0.00
ATOM    149  N   ARG    47       0.656  -0.982  -2.002  1.00  0.00
ATOM    150  CA  ARG    47       1.310   0.206  -2.608  1.00  0.00
ATOM    151  C   ARG    47       0.772   1.461  -1.924  1.00  0.00
ATOM    152  O   ARG    47      -0.450   1.548  -1.801  1.00  0.00
ATOM    153  N   VAL    48       1.571   2.402  -1.457  1.00  0.00
ATOM    154  CA  VAL    48       1.051   3.615  -0.791  1.00  0.00
ATOM    155  C   VAL    48       1.355   4.830  -1.688  1.00  0.00
ATOM    156  O   VAL    48       2.478   5.147  -2.095  1.00  0.00
ATOM    157  N   LEU    49       0.305   5.495  -2.128  1.00  0.00
ATOM    158  CA  LEU    49       0.425   6.578  -3.128  1.00  0.00
ATOM    159  C   LEU    49      -0.098   7.863  -2.478  1.00  0.00
ATOM    160  O   LEU    49      -1.176   7.791  -1.843  1.00  0.00
ATOM    161  N   VAL    50       0.607   8.983  -2.640  1.00  0.00
ATOM    162  CA  VAL    50       0.185  10.249  -2.045  1.00  0.00
ATOM    163  C   VAL    50       0.760  11.432  -2.814  1.00  0.00
ATOM    164  O   VAL    50       1.614  11.347  -3.703  1.00  0.00
ATOM    165  N   HIS    51       1.846  12.353  -1.388  1.00  0.00
ATOM    166  CA  HIS    51       2.798  13.430  -1.559  1.00  0.00
ATOM    167  C   HIS    51       3.995  12.841  -0.860  1.00  0.00
ATOM    168  O   HIS    51       3.973  11.654  -0.529  1.00  0.00
ATOM    169  N   GLU    52       5.572  13.716  -0.414  1.00  0.00
ATOM    170  CA  GLU    52       6.620  12.758   0.017  1.00  0.00
ATOM    171  C   GLU    52       6.805  12.721   1.533  1.00  0.00
ATOM    172  O   GLU    52       7.046  11.633   2.034  1.00  0.00
ATOM    173  N   ASP    53       6.683  13.850   2.224  1.00  0.00
ATOM    174  CA  ASP    53       6.703  13.975   3.651  1.00  0.00
ATOM    175  C   ASP    53       5.560  13.116   4.256  1.00  0.00
ATOM    176  O   ASP    53       5.750  12.511   5.316  1.00  0.00
ATOM    177  N   ASP    54       4.418  13.022   3.613  1.00  0.00
ATOM    178  CA  ASP    54       3.354  12.194   4.119  1.00  0.00
ATOM    179  C   ASP    54       3.798  10.724   3.882  1.00  0.00
ATOM    180  O   ASP    54       3.593   9.939   4.789  1.00  0.00
ATOM    181  N   LEU    55       4.195  10.414   2.674  1.00  0.00
ATOM    182  CA  LEU    55       4.678   9.063   2.429  1.00  0.00
ATOM    183  C   LEU    55       5.686   8.626   3.513  1.00  0.00
ATOM    184  O   LEU    55       5.644   7.456   3.983  1.00  0.00
ATOM    185  N   ALA    56       6.566   9.550   3.954  1.00  0.00
ATOM    186  CA  ALA    56       7.582   9.170   4.968  1.00  0.00
ATOM    187  C   ALA    56       6.921   8.919   6.332  1.00  0.00
ATOM    188  O   ALA    56       7.258   7.985   7.093  1.00  0.00
ATOM    189  N   GLY    57       5.930   9.816   6.597  1.00  0.00
ATOM    190  CA  GLY    57       5.189   9.540   7.822  1.00  0.00
ATOM    191  C   GLY    57       4.634   8.094   7.781  1.00  0.00
ATOM    192  O   GLY    57       4.685   7.421   8.810  1.00  0.00
ATOM    193  N   ALA    58       4.041   7.692   6.681  1.00  0.00
ATOM    194  CA  ALA    58       3.454   6.358   6.560  1.00  0.00
ATOM    195  C   ALA    58       4.479   5.270   6.924  1.00  0.00
ATOM    196  O   ALA    58       4.123   4.278   7.612  1.00  0.00
ATOM    197  N   ARG    59       5.705   5.528   6.439  1.00  0.00
ATOM    198  CA  ARG    59       6.769   4.525   6.667  1.00  0.00
ATOM    199  C   ARG    59       7.010   4.408   8.160  1.00  0.00
ATOM    200  O   ARG    59       6.952   3.343   8.771  1.00  0.00
ATOM    201  N   ARG    60       7.221   5.535   8.822  1.00  0.00
ATOM    202  CA  ARG    60       7.384   5.514  10.264  1.00  0.00
ATOM    203  C   ARG    60       6.215   4.909  11.021  1.00  0.00
ATOM    204  O   ARG    60       6.443   4.277  12.071  1.00  0.00
ATOM    205  N   LEU    61       5.003   5.159  10.541  1.00  0.00
ATOM    206  CA  LEU    61       3.803   4.628  11.185  1.00  0.00
ATOM    207  C   LEU    61       3.866   3.073  11.201  1.00  0.00
ATOM    208  O   LEU    61       3.697   2.436  12.237  1.00  0.00
ATOM    209  N   LEU    62       4.038   2.464  10.052  1.00  0.00
ATOM    210  CA  LEU    62       3.967   1.033   9.791  1.00  0.00
ATOM    211  C   LEU    62       5.175   0.412  10.500  1.00  0.00
ATOM    212  O   LEU    62       4.988  -0.502  11.309  1.00  0.00
ATOM    213  N   THR    63       6.329   1.073  10.476  1.00  0.00
ATOM    214  CA  THR    63       7.461   0.608  11.245  1.00  0.00
ATOM    215  C   THR    63       7.127   0.599  12.747  1.00  0.00
ATOM    216  O   THR    63       7.556  -0.287  13.489  1.00  0.00
ATOM    217  N   ASP    64       6.427   1.612  13.197  1.00  0.00
ATOM    218  CA  ASP    64       6.166   1.677  14.619  1.00  0.00
ATOM    219  C   ASP    64       5.189   0.638  15.129  1.00  0.00
ATOM    220  O   ASP    64       5.123   0.397  16.342  1.00  0.00
TER
END
