
#######################################################
#                                                     #
#                        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   41 (  164),  selected   41 , name T0349TS383_2-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS383_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           -
LGA    -       -      R       2           -
LGA    -       -      E       3           -
LGA    -       -      L       4           -
LGA    -       -      L       5           -
LGA    -       -      R       6           -
LGA    -       -      T       7           -
LGA    -       -      N       8           -
LGA    -       -      D       9           -
LGA    -       -      A      10           -
LGA    -       -      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    A      10      L      20          4.039
LGA    V      11      D      21          2.167
LGA    L      12      G      22          3.001
LGA    L      13      -       -           -
LGA    S      14      -       -           -
LGA    A      15      A      23          4.526
LGA    V      16      D      24           -
LGA    G      17      I      25           -
LGA    A      18      G      26           -
LGA    L      19      H      27           -
LGA    L      20      L      28           -
LGA    D      21      V      29           -
LGA    G      22      P      45           -
LGA    A      23      -       -           -
LGA    D      24      -       -           -
LGA    I      25      -       -           -
LGA    G      26      -       -           -
LGA    H      27      -       -           -
LGA    L      28      -       -           -
LGA    V      29      -       -           -
LGA    P      45      R      46          0.322
LGA    R      46      R      47          0.357
LGA    R      47      V      48          0.289
LGA    V      48      L      49          0.894
LGA    L      49      V      50          2.792
LGA    V      50      H      51          4.465
LGA    -       -      E      52           -
LGA    -       -      D      53           -
LGA    -       -      D      54           -
LGA    A      56      L      55          2.124
LGA    G      57      A      56          1.034
LGA    A      58      G      57          2.133
LGA    -       -      A      58           -
LGA    R      59      R      59          1.110
LGA    R      60      R      60          1.121
LGA    L      61      L      61          1.214
LGA    L      62      L      62          1.324
LGA    T      63      T      63          1.114
LGA    D      64      D      64          0.650
LGA    A      65      A      65          2.240
LGA    -       -      G      66           -
LGA    G      66      L      67          1.962
LGA    L      67      A      68          2.725
LGA    E      70      H      69          2.534
LGA    -       -      E      70           -
LGA    L      71      L      71          0.524
LGA    R      72      R      72          0.235

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   41   57    5.0     25    2.19    44.00     36.741     1.092

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.894369 * X  +  -0.052792 * Y  +  -0.444205 * Z  +  51.474705
  Y_new =  -0.032628 * X  +  -0.982668 * Y  +   0.182480 * Z  +  24.879601
  Z_new =  -0.446139 * X  +   0.177698 * Y  +   0.877145 * Z  +  -4.940636 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.199881   -2.941711  [ DEG:    11.4524   -168.5476 ]
  Theta =   0.462447    2.679146  [ DEG:    26.4963    153.5037 ]
  Phi   =  -3.105127    0.036466  [ DEG:  -177.9107      2.0893 ]
 
# 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: T0349TS383_2-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS383_2-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   41   57   5.0   25   2.19   44.00  36.741
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS383_2-D1
PFRMAT TS
TARGET T0349
MODEL 2
PARENT 1rp0A
ATOM      1  N   ALA    10      -7.894   7.309   7.089  1.00  0.00
ATOM      2  CA  ALA    10      -6.501   7.711   7.241  1.00  0.00
ATOM      3  C   ALA    10      -6.343   9.109   7.840  1.00  0.00
ATOM      4  O   ALA    10      -5.424   9.359   8.622  1.00  0.00
ATOM      5  N   VAL    11      -7.200  10.044   7.461  1.00  0.00
ATOM      6  CA  VAL    11      -7.065  11.388   7.988  1.00  0.00
ATOM      7  C   VAL    11      -7.427  11.461   9.485  1.00  0.00
ATOM      8  O   VAL    11      -6.701  12.042  10.272  1.00  0.00
ATOM      9  N   LEU    12      -8.559  10.884   9.862  1.00  0.00
ATOM     10  CA  LEU    12      -8.956  10.880  11.255  1.00  0.00
ATOM     11  C   LEU    12      -8.022  10.131  12.168  1.00  0.00
ATOM     12  O   LEU    12      -7.767  10.571  13.266  1.00  0.00
ATOM     13  N   LEU    13      -7.519   8.976  11.730  1.00  0.00
ATOM     14  CA  LEU    13      -6.535   8.258  12.524  1.00  0.00
ATOM     15  C   LEU    13      -5.274   9.086  12.713  1.00  0.00
ATOM     16  O   LEU    13      -4.706   9.115  13.795  1.00  0.00
ATOM     17  N   SER    14      -4.821   9.721  11.644  1.00  0.00
ATOM     18  CA  SER    14      -3.628  10.559  11.694  1.00  0.00
ATOM     19  C   SER    14      -3.826  11.747  12.645  1.00  0.00
ATOM     20  O   SER    14      -2.923  12.128  13.377  1.00  0.00
ATOM     21  N   ALA    15      -5.006  12.358  12.630  1.00  0.00
ATOM     22  CA  ALA    15      -5.305  13.463  13.532  1.00  0.00
ATOM     23  C   ALA    15      -5.343  12.994  14.978  1.00  0.00
ATOM     24  O   ALA    15      -4.731  13.600  15.866  1.00  0.00
ATOM     25  N   VAL    16      -6.037  11.892  15.242  1.00  0.00
ATOM     26  CA  VAL    16      -6.078  11.363  16.603  1.00  0.00
ATOM     27  C   VAL    16      -4.706  10.965  17.147  1.00  0.00
ATOM     28  O   VAL    16      -4.406  11.198  18.325  1.00  0.00
ATOM     29  N   GLY    17      -3.889  10.347  16.293  1.00  0.00
ATOM     30  CA  GLY    17      -2.525   9.958  16.604  1.00  0.00
ATOM     31  C   GLY    17      -1.694  11.190  16.973  1.00  0.00
ATOM     32  O   GLY    17      -0.965  11.191  17.955  1.00  0.00
ATOM     33  N   ALA    18      -1.818  12.254  16.184  1.00  0.00
ATOM     34  CA  ALA    18      -1.067  13.475  16.451  1.00  0.00
ATOM     35  C   ALA    18      -1.491  14.150  17.757  1.00  0.00
ATOM     36  O   ALA    18      -0.630  14.523  18.549  1.00  0.00
ATOM     37  N   LEU    19      -2.798  14.280  17.988  1.00  0.00
ATOM     38  CA  LEU    19      -3.304  14.961  19.175  1.00  0.00
ATOM     39  C   LEU    19      -2.891  14.195  20.438  1.00  0.00
ATOM     40  O   LEU    19      -2.485  14.801  21.428  1.00  0.00
ATOM     41  N   LEU    20      -3.013  12.875  20.388  1.00  0.00
ATOM     42  CA  LEU    20      -2.923  12.079  21.609  1.00  0.00
ATOM     43  C   LEU    20      -1.474  11.858  22.011  1.00  0.00
ATOM     44  O   LEU    20      -1.212  11.268  23.052  1.00  0.00
ATOM     45  N   ASP    21      -0.537  12.340  21.203  1.00  0.00
ATOM     46  CA  ASP    21       0.844  12.446  21.652  1.00  0.00
ATOM     47  C   ASP    21       0.965  13.346  22.879  1.00  0.00
ATOM     48  O   ASP    21       1.908  13.233  23.640  1.00  0.00
ATOM     49  N   GLY    22       0.012  14.256  23.072  1.00  0.00
ATOM     50  CA  GLY    22      -0.147  14.978  24.327  1.00  0.00
ATOM     51  C   GLY    22      -1.006  14.132  25.264  1.00  0.00
ATOM     52  O   GLY    22      -2.191  13.925  24.993  1.00  0.00
ATOM     53  N   ALA    23      -0.425  13.585  26.322  1.00  0.00
ATOM     54  CA  ALA    23      -1.128  12.622  27.189  1.00  0.00
ATOM     55  C   ALA    23      -2.245  13.238  28.018  1.00  0.00
ATOM     56  O   ALA    23      -3.061  12.479  28.542  1.00  0.00
ATOM     57  N   ASP    24      -2.294  14.563  28.064  1.00  0.00
ATOM     58  CA  ASP    24      -3.222  15.330  28.880  1.00  0.00
ATOM     59  C   ASP    24      -4.514  15.621  28.119  1.00  0.00
ATOM     60  O   ASP    24      -5.461  16.191  28.667  1.00  0.00
ATOM     61  N   ILE    25      -4.536  15.267  26.842  1.00  0.00
ATOM     62  CA  ILE    25      -5.679  15.578  25.985  1.00  0.00
ATOM     63  C   ILE    25      -6.544  14.354  25.762  1.00  0.00
ATOM     64  O   ILE    25      -6.091  13.304  25.322  1.00  0.00
ATOM     65  N   GLY    26      -7.823  14.477  26.093  1.00  0.00
ATOM     66  CA  GLY    26      -8.774  13.402  25.864  1.00  0.00
ATOM     67  C   GLY    26      -9.313  13.391  24.448  1.00  0.00
ATOM     68  O   GLY    26      -9.769  14.438  23.955  1.00  0.00
ATOM     69  N   HIS    27      -9.202  12.232  23.813  1.00  0.00
ATOM     70  CA  HIS    27      -9.608  12.052  22.436  1.00  0.00
ATOM     71  C   HIS    27     -10.635  10.955  22.251  1.00  0.00
ATOM     72  O   HIS    27     -10.320   9.769  22.397  1.00  0.00
ATOM     73  N   LEU    28     -11.848  11.339  21.848  1.00  0.00
ATOM     74  CA  LEU    28     -12.851  10.360  21.454  1.00  0.00
ATOM     75  C   LEU    28     -12.855  10.239  19.931  1.00  0.00
ATOM     76  O   LEU    28     -12.811  11.261  19.268  1.00  0.00
ATOM     77  N   VAL    29     -12.904   9.029  19.417  1.00  0.00
ATOM     78  CA  VAL    29     -13.034   8.796  17.979  1.00  0.00
ATOM     79  C   VAL    29     -14.394   8.158  17.781  1.00  0.00
ATOM     80  O   VAL    29     -14.701   7.108  18.335  1.00  0.00
ATOM    137  N   PRO    45      -3.410  -3.472  -3.559  1.00  0.00
ATOM    138  CA  PRO    45      -2.976  -3.387  -2.151  1.00  0.00
ATOM    139  C   PRO    45      -2.060  -2.199  -1.848  1.00  0.00
ATOM    140  O   PRO    45      -2.080  -1.643  -0.745  1.00  0.00
ATOM    141  N   ARG    46      -1.224  -1.793  -2.801  1.00  0.00
ATOM    142  CA  ARG    46      -0.089  -0.926  -2.487  1.00  0.00
ATOM    143  C   ARG    46      -0.556   0.498  -2.247  1.00  0.00
ATOM    144  O   ARG    46      -1.470   1.004  -2.901  1.00  0.00
ATOM    145  N   ARG    47       0.084   1.101  -1.264  1.00  0.00
ATOM    146  CA  ARG    47      -0.227   2.423  -0.771  1.00  0.00
ATOM    147  C   ARG    47       0.912   3.345  -1.134  1.00  0.00
ATOM    148  O   ARG    47       2.057   3.259  -0.612  1.00  0.00
ATOM    149  N   VAL    48       0.627   4.272  -2.040  1.00  0.00
ATOM    150  CA  VAL    48       1.622   5.252  -2.465  1.00  0.00
ATOM    151  C   VAL    48       1.507   6.495  -1.588  1.00  0.00
ATOM    152  O   VAL    48       0.423   7.057  -1.419  1.00  0.00
ATOM    153  N   LEU    49       2.634   6.889  -1.015  1.00  0.00
ATOM    154  CA  LEU    49       2.750   8.078  -0.183  1.00  0.00
ATOM    155  C   LEU    49       3.859   8.973  -0.741  1.00  0.00
ATOM    156  O   LEU    49       5.046   8.584  -0.825  1.00  0.00
ATOM    157  N   VAL    50       3.499  10.182  -1.174  1.00  0.00
ATOM    158  CA  VAL    50       4.485  11.093  -1.717  1.00  0.00
ATOM    159  C   VAL    50       5.376  11.693  -0.629  1.00  0.00
ATOM    160  O   VAL    50       4.927  12.005   0.485  1.00  0.00
ATOM    161  N   ALA    56       6.647  11.867  -0.959  1.00  0.00
ATOM    162  CA  ALA    56       7.537  12.597  -0.083  1.00  0.00
ATOM    163  C   ALA    56       7.091  14.049   0.068  1.00  0.00
ATOM    164  O   ALA    56       6.569  14.633  -0.885  1.00  0.00
ATOM    165  N   GLY    57       7.322  14.675   1.212  1.00  0.00
ATOM    166  CA  GLY    57       8.014  14.098   2.367  1.00  0.00
ATOM    167  C   GLY    57       7.183  13.417   3.457  1.00  0.00
ATOM    168  O   GLY    57       7.637  13.320   4.593  1.00  0.00
ATOM    169  N   ALA    58       5.999  12.914   3.129  1.00  0.00
ATOM    170  CA  ALA    58       5.155  12.292   4.142  1.00  0.00
ATOM    171  C   ALA    58       5.693  10.946   4.588  1.00  0.00
ATOM    172  O   ALA    58       5.199  10.362   5.537  1.00  0.00
ATOM    173  N   ARG    59       6.724  10.455   3.912  1.00  0.00
ATOM    174  CA  ARG    59       7.324   9.203   4.333  1.00  0.00
ATOM    175  C   ARG    59       7.985   9.396   5.713  1.00  0.00
ATOM    176  O   ARG    59       8.144   8.417   6.449  1.00  0.00
ATOM    177  N   ARG    60       8.305  10.636   6.067  1.00  0.00
ATOM    178  CA  ARG    60       8.821  10.909   7.423  1.00  0.00
ATOM    179  C   ARG    60       7.769  10.572   8.474  1.00  0.00
ATOM    180  O   ARG    60       8.110  10.200   9.594  1.00  0.00
ATOM    181  N   LEU    61       6.488  10.703   8.135  1.00  0.00
ATOM    182  CA  LEU    61       5.415  10.390   9.063  1.00  0.00
ATOM    183  C   LEU    61       5.370   8.887   9.242  1.00  0.00
ATOM    184  O   LEU    61       5.221   8.386  10.370  1.00  0.00
ATOM    185  N   LEU    62       5.503   8.160   8.133  1.00  0.00
ATOM    186  CA  LEU    62       5.596   6.697   8.215  1.00  0.00
ATOM    187  C   LEU    62       6.753   6.220   9.093  1.00  0.00
ATOM    188  O   LEU    62       6.608   5.232   9.845  1.00  0.00
ATOM    189  N   THR    63       7.891   6.898   8.973  1.00  0.00
ATOM    190  CA  THR    63       9.063   6.606   9.788  1.00  0.00
ATOM    191  C   THR    63       8.698   6.704  11.270  1.00  0.00
ATOM    192  O   THR    63       9.045   5.823  12.071  1.00  0.00
ATOM    193  N   ASP    64       8.027   7.796  11.626  1.00  0.00
ATOM    194  CA  ASP    64       7.676   7.994  13.025  1.00  0.00
ATOM    195  C   ASP    64       6.761   6.911  13.599  1.00  0.00
ATOM    196  O   ASP    64       6.929   6.513  14.760  1.00  0.00
ATOM    197  N   ALA    65       5.771   6.477  12.814  1.00  0.00
ATOM    198  CA  ALA    65       4.819   5.478  13.241  1.00  0.00
ATOM    199  C   ALA    65       5.387   4.068  13.166  1.00  0.00
ATOM    200  O   ALA    65       4.875   3.147  13.790  1.00  0.00
ATOM    201  N   GLY    66       6.454   3.898  12.396  1.00  0.00
ATOM    202  CA  GLY    66       7.128   2.615  12.251  1.00  0.00
ATOM    203  C   GLY    66       6.556   1.715  11.164  1.00  0.00
ATOM    204  O   GLY    66       6.396   0.503  11.340  1.00  0.00
ATOM    205  N   LEU    67       6.272   2.319  10.022  1.00  0.00
ATOM    206  CA  LEU    67       5.739   1.593   8.890  1.00  0.00
ATOM    207  C   LEU    67       6.809   1.569   7.811  1.00  0.00
ATOM    208  O   LEU    67       7.207   2.638   7.348  1.00  0.00
ATOM    209  N   GLU    70       7.228   0.378   7.393  1.00  0.00
ATOM    210  CA  GLU    70       8.246   0.191   6.361  1.00  0.00
ATOM    211  C   GLU    70       7.649   0.522   4.990  1.00  0.00
ATOM    212  O   GLU    70       6.423   0.416   4.791  1.00  0.00
ATOM    213  N   LEU    71       8.525   0.848   4.062  1.00  0.00
ATOM    214  CA  LEU    71       8.130   1.138   2.680  1.00  0.00
ATOM    215  C   LEU    71       9.286   0.865   1.722  1.00  0.00
ATOM    216  O   LEU    71      10.464   0.818   2.100  1.00  0.00
ATOM    217  N   ARG    72       8.949   0.729   0.439  1.00  0.00
ATOM    218  CA  ARG    72       9.904   0.713  -0.642  1.00  0.00
ATOM    219  C   ARG    72      10.102   2.149  -1.117  1.00  0.00
ATOM    220  O   ARG    72       9.163   2.800  -1.606  1.00  0.00
TER
END
