
#######################################################
#                                                     #
#                        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   23 (  115),  selected   23 , name T0378TS239_3_2-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS239_3_2-D1.T0378_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      L       2           -
LGA    -       -      S       3           -
LGA    -       -      A       4           -
LGA    -       -      N       5           -
LGA    -       -      Q       6           -
LGA    -       -      I       7           -
LGA    -       -      K       8           -
LGA    -       -      F       9           -
LGA    -       -      L      10           -
LGA    -       -      R      11           -
LGA    M       1      S      12          3.478
LGA    L       2      L      13          4.135
LGA    S       3      R      14          2.080
LGA    A       4      E      15          2.010
LGA    N       5      R      16          3.023
LGA    -       -      K      17           -
LGA    -       -      Y      18           -
LGA    Q       6      R      19          1.511
LGA    I       7      L      20           -
LGA    K       8      R      21           -
LGA    -       -      E      22           -
LGA    -       -      Q      23           -
LGA    F       9      A      24          4.233
LGA    L      10      F      25          2.989
LGA    R      11      A      26          1.164
LGA    S      12      V      27          2.044
LGA    L      13      E      28           #
LGA    R      14      G      29          5.394
LGA    -       -      P      30           -
LGA    -       -      K      31           -
LGA    -       -      L      32           -
LGA    E      15      V      33          1.062
LGA    R      16      G      34          1.379
LGA    K      17      E      35          1.515
LGA    Y      18      M      36          1.612
LGA    R      19      L      37          1.448
LGA    L      20      P      38          1.225
LGA    R      21      F      39          0.914
LGA    E      22      Y      40          1.262
LGA    Q      23      R      41          3.955
LGA    -       -      C      42           -
LGA    -       -      R      43           -
LGA    -       -      M      44           -
LGA    -       -      L      45           -
LGA    -       -      V      46           -
LGA    -       -      G      47           -
LGA    -       -      T      48           -
LGA    -       -      A      49           -
LGA    -       -      A      50           -
LGA    -       -      M      51           -
LGA    -       -      L      52           -
LGA    -       -      R      53           -
LGA    -       -      A      54           -
LGA    -       -      V      55           -
LGA    -       -      S      56           -
LGA    -       -      T      57           -
LGA    -       -      P      58           -
LGA    -       -      H      59           -
LGA    -       -      D      60           -
LGA    -       -      A      61           -
LGA    -       -      E      62           -
LGA    -       -      V      63           -
LGA    -       -      V      64           -
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    -       -      P      67           -
LGA    -       -      E      68           -
LGA    -       -      S      69           -
LGA    -       -      F      70           -
LGA    -       -      D      71           -
LGA    -       -      F      72           -
LGA    -       -      K      73           -
LGA    -       -      R      74           -
LGA    -       -      I      75           -
LGA    -       -      S      76           -
LGA    -       -      T      77           -
LGA    -       -      Q      78           -
LGA    -       -      T      79           -
LGA    -       -      T      80           -
LGA    -       -      P      81           -
LGA    -       -      Q      82           -
LGA    -       -      P      83           -
LGA    -       -      L      84           -
LGA    -       -      M      85           -
LGA    -       -      A      86           -
LGA    -       -      V      87           -
LGA    -       -      F      88           -
LGA    -       -      D      89           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   23   89    5.0     20    2.65     5.00     15.588     0.728

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.520872 * X  +   0.824209 * Y  +   0.222200 * Z  + -24.803543
  Y_new =  -0.482064 * X  +   0.498827 * Y  +  -0.720268 * Z  +  28.382893
  Z_new =  -0.704490 * X  +   0.268052 * Y  +   0.657146 * Z  +  44.940205 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.387302   -2.754291  [ DEG:    22.1907   -157.8093 ]
  Theta =   0.781705    2.359888  [ DEG:    44.7884    135.2116 ]
  Phi   =  -0.746724    2.394869  [ DEG:   -42.7841    137.2159 ]
 
# 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: T0378TS239_3_2-D1                             
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS239_3_2-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   23   89   5.0   20   2.65    5.00  15.588
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS239_3_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0378
PARENT 1ipa_A
ATOM      1  N   MET     1      17.574  31.937  49.863  1.00  9.99
ATOM      2  CA  MET     1      17.876  31.188  48.653  1.00  9.99
ATOM      3  C   MET     1      16.999  29.957  48.496  1.00  9.99
ATOM      4  O   MET     1      16.872  29.149  49.416  1.00  9.99
ATOM      5  CB  MET     1      19.346  30.768  48.653  1.00  9.99
ATOM      6  N   LEU     2      16.403  29.818  47.318  1.00  9.99
ATOM      7  CA  LEU     2      15.541  28.682  47.032  1.00  9.99
ATOM      8  C   LEU     2      16.389  27.420  46.866  1.00  9.99
ATOM      9  O   LEU     2      15.870  26.304  46.871  1.00  9.99
ATOM     10  CB  LEU     2      14.706  28.928  45.750  1.00  9.99
ATOM     11  N   SER     3      17.701  27.613  46.733  1.00  9.99
ATOM     12  CA  SER     3      18.638  26.510  46.564  1.00  9.99
ATOM     13  C   SER     3      19.031  25.926  47.915  1.00  9.99
ATOM     14  O   SER     3      19.618  24.846  47.982  1.00  9.99
ATOM     15  CB  SER     3      19.881  26.991  45.823  1.00  9.99
ATOM     16  N   ALA     4      18.710  26.651  48.983  1.00  9.99
ATOM     17  CA  ALA     4      19.007  26.213  50.341  1.00  9.99
ATOM     18  C   ALA     4      18.455  24.793  50.507  1.00  9.99
ATOM     19  O   ALA     4      17.268  24.552  50.299  1.00  9.99
ATOM     20  CB  ALA     4      18.351  27.174  51.338  1.00  9.99
ATOM     21  N   ASN     5      19.316  23.835  50.887  1.00  9.99
ATOM     22  CA  ASN     5      18.920  22.431  51.073  1.00  9.99
ATOM     23  C   ASN     5      17.641  22.207  51.879  1.00  9.99
ATOM     24  O   ASN     5      16.880  21.280  51.597  1.00  9.99
ATOM     25  CB  ASN     5      20.157  21.804  51.727  1.00  9.99
ATOM     26  N   GLN     6      17.404  23.053  52.875  1.00  9.99
ATOM     27  CA  GLN     6      16.204  22.925  53.682  1.00  9.99
ATOM     28  C   GLN     6      14.981  23.245  52.837  1.00  9.99
ATOM     29  O   GLN     6      13.936  22.614  52.975  1.00  9.99
ATOM     30  CB  GLN     6      16.256  23.871  54.883  1.00  9.99
ATOM     31  N   ILE     7      15.124  24.230  51.960  1.00  9.99
ATOM     32  CA  ILE     7      14.039  24.642  51.093  1.00  9.99
ATOM     33  C   ILE     7      13.825  23.640  49.962  1.00  9.99
ATOM     34  O   ILE     7      12.711  23.477  49.466  1.00  9.99
ATOM     35  CB  ILE     7      14.305  26.042  50.498  1.00  9.99
ATOM     36  N   LYS     8      14.887  22.966  49.550  1.00  9.99
ATOM     37  CA  LYS     8      14.761  21.971  48.497  1.00  9.99
ATOM     38  C   LYS     8      13.998  20.763  49.039  1.00  9.99
ATOM     39  O   LYS     8      13.251  20.107  48.309  1.00  9.99
ATOM     40  CB  LYS     8      16.150  21.554  48.004  1.00  9.99
ATOM     41  N   PHE     9      14.175  20.480  50.327  1.00  9.99
ATOM     42  CA  PHE     9      13.493  19.356  50.953  1.00  9.99
ATOM     43  C   PHE     9      12.005  19.653  51.122  1.00  9.99
ATOM     44  O   PHE     9      11.167  18.790  50.904  1.00  9.99
ATOM     45  CB  PHE     9      14.113  19.041  52.315  1.00  9.99
ATOM     46  N   LEU    10      11.674  20.878  51.502  1.00  9.99
ATOM     47  CA  LEU    10      10.274  21.240  51.673  1.00  9.99
ATOM     48  C   LEU    10       9.527  21.328  50.332  1.00  9.99
ATOM     49  O   LEU    10       8.356  20.957  50.243  1.00  9.99
ATOM     50  CB  LEU    10      10.174  22.559  52.435  1.00  9.99
ATOM     51  N   ARG    11      10.210  21.796  49.289  1.00  9.99
ATOM     52  CA  ARG    11       9.590  21.924  47.964  1.00  9.99
ATOM     53  C   ARG    11       9.088  20.585  47.413  1.00  9.99
ATOM     54  O   ARG    11       8.108  20.540  46.667  1.00  9.99
ATOM     55  CB  ARG    11      10.574  22.568  46.970  1.00  9.99
ATOM     56  N   SER    12       9.760  19.499  47.775  1.00  9.99
ATOM     57  CA  SER    12       9.363  18.176  47.317  1.00  9.99
ATOM     58  C   SER    12       7.953  17.834  47.795  1.00  9.99
ATOM     59  O   SER    12       7.257  17.023  47.186  1.00  9.99
ATOM     60  CB  SER    12      10.349  17.126  47.839  1.00  9.99
ATOM     61  N   LEU    13       7.534  18.457  48.890  1.00  9.99
ATOM     62  CA  LEU    13       6.215  18.192  49.442  1.00  9.99
ATOM     63  C   LEU    13       5.092  18.706  48.541  1.00  9.99
ATOM     64  O   LEU    13       3.914  18.461  48.811  1.00  9.99
ATOM     65  CB  LEU    13       6.104  18.793  50.849  1.00  9.99
ATOM     66  N   ARG    14       5.446  19.411  47.465  1.00  9.99
ATOM     67  CA  ARG    14       4.417  19.898  46.547  1.00  9.99
ATOM     68  C   ARG    14       3.873  18.740  45.719  1.00  9.99
ATOM     69  O   ARG    14       2.788  18.830  45.149  1.00  9.99
ATOM     70  CB  ARG    14       4.954  21.003  45.635  1.00  9.99
ATOM     71  N   GLU    15       4.623  17.642  45.680  1.00  9.99
ATOM     72  CA  GLU    15       4.201  16.460  44.942  1.00  9.99
ATOM     73  C   GLU    15       3.646  15.404  45.906  1.00  9.99
ATOM     74  O   GLU    15       4.149  15.246  47.020  1.00  9.99
ATOM     75  CB  GLU    15       5.379  15.934  44.130  1.00  9.99
ATOM     76  N   ARG    16       2.607  14.686  45.482  1.00  9.99
ATOM     77  CA  ARG    16       1.975  13.701  46.355  1.00  9.99
ATOM     78  C   ARG    16       2.818  12.541  46.864  1.00  9.99
ATOM     79  O   ARG    16       2.784  12.244  48.051  1.00  9.99
ATOM     80  CB  ARG    16       0.709  13.123  45.714  1.00  9.99
ATOM     81  N   LYS    17       3.550  11.869  45.985  1.00  9.99
ATOM     82  CA  LYS    17       4.364  10.735  46.418  1.00  9.99
ATOM     83  C   LYS    17       5.295  11.095  47.581  1.00  9.99
ATOM     84  O   LYS    17       5.475  10.306  48.504  1.00  9.99
ATOM     85  CB  LYS    17       5.193  10.190  45.245  1.00  9.99
ATOM     86  N   TYR    18       5.881  12.286  47.526  1.00  9.99
ATOM     87  CA  TYR    18       6.790  12.749  48.561  1.00  9.99
ATOM     88  C   TYR    18       6.093  13.032  49.881  1.00  9.99
ATOM     89  O   TYR    18       6.667  12.815  50.943  1.00  9.99
ATOM     90  CB  TYR    18       7.528  13.989  48.070  1.00  9.99
ATOM     91  N   ARG    19       4.858  13.510  49.822  1.00  9.99
ATOM     92  CA  ARG    19       4.111  13.782  51.039  1.00  9.99
ATOM     93  C   ARG    19       3.750  12.465  51.703  1.00  9.99
ATOM     94  O   ARG    19       3.849  12.319  52.918  1.00  9.99
ATOM     95  CB  ARG    19       2.818  14.537  50.730  1.00  9.99
ATOM     96  N   LEU    20       3.332  11.501  50.892  1.00  9.99
ATOM     97  CA  LEU    20       2.923  10.207  51.413  1.00  9.99
ATOM     98  C   LEU    20       4.048   9.394  52.033  1.00  9.99
ATOM     99  O   LEU    20       3.878   8.810  53.100  1.00  9.99
ATOM    100  CB  LEU    20       2.248   9.377  50.315  1.00  9.99
ATOM    101  N   ARG    21       5.203   9.364  51.381  1.00  9.99
ATOM    102  CA  ARG    21       6.297   8.573  51.905  1.00  9.99
ATOM    103  C   ARG    21       6.881   9.188  53.164  1.00  9.99
ATOM    104  O   ARG    21       7.261   8.469  54.079  1.00  9.99
ATOM    105  CB  ARG    21       7.385   8.387  50.845  1.00  9.99
ATOM    106  N   GLU    22       6.933  10.513  53.226  1.00  9.99
ATOM    107  CA  GLU    22       7.488  11.187  54.400  1.00  9.99
ATOM    108  C   GLU    22       6.443  11.557  55.443  1.00  9.99
ATOM    109  O   GLU    22       6.785  12.039  56.517  1.00  9.99
ATOM    110  CB  GLU    22       8.226  12.451  53.990  1.00  9.99
ATOM    111  N   GLN    23       5.176  11.330  55.125  1.00  9.99
ATOM    112  CA  GLN    23       4.090  11.656  56.037  1.00  9.99
ATOM    113  C   GLN    23       4.130  13.106  56.502  1.00  9.99
ATOM    114  O   GLN    23       3.914  13.400  57.678  1.00  9.99
ATOM    115  CB  GLN    23       4.107  10.721  57.241  1.00  9.99
TER
END
