
#######################################################
#                                                     #
#                        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   89 (   89),  selected   89 , name T0378TS393_5-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS393_5-D1.T0378_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    L       2      L       2           -
LGA    S       3      S       3           #
LGA    A       4      A       4          3.706
LGA    N       5      N       5          2.889
LGA    Q       6      Q       6          2.673
LGA    I       7      I       7          2.483
LGA    K       8      K       8          2.940
LGA    F       9      F       9          3.176
LGA    L      10      L      10          3.159
LGA    R      11      R      11          3.367
LGA    S      12      S      12          3.306
LGA    L      13      L      13          3.213
LGA    R      14      R      14          3.319
LGA    E      15      -       -           -
LGA    R      16      E      15          1.745
LGA    K      17      R      16           #
LGA    Y      18      K      17           #
LGA    R      19      Y      18          2.161
LGA    L      20      R      19           -
LGA    -       -      L      20           -
LGA    R      21      R      21          2.121
LGA    E      22      E      22          0.743
LGA    Q      23      Q      23          1.679
LGA    A      24      A      24          1.479
LGA    F      25      F      25          2.324
LGA    A      26      A      26          0.666
LGA    V      27      V      27          2.806
LGA    E      28      E      28          3.584
LGA    G      29      G      29          3.239
LGA    P      30      P      30          3.018
LGA    K      31      K      31          1.269
LGA    L      32      L      32          1.881
LGA    V      33      V      33          1.552
LGA    G      34      G      34          0.827
LGA    E      35      E      35          0.672
LGA    M      36      M      36          0.619
LGA    L      37      L      37          1.156
LGA    P      38      P      38          3.337
LGA    F      39      F      39          3.984
LGA    Y      40      Y      40          3.644
LGA    R      41      R      41          4.174
LGA    C      42      C      42          1.340
LGA    R      43      R      43          1.822
LGA    M      44      M      44          2.653
LGA    L      45      L      45          2.472
LGA    V      46      V      46          3.125
LGA    G      47      -       -           -
LGA    T      48      G      47           #
LGA    A      49      T      48          3.861
LGA    A      50      A      49          3.880
LGA    M      51      A      50          5.116
LGA    L      52      M      51          3.951
LGA    R      53      L      52          0.996
LGA    A      54      R      53          1.147
LGA    V      55      A      54          2.958
LGA    S      56      -       -           -
LGA    T      57      V      55          1.148
LGA    P      58      -       -           -
LGA    H      59      -       -           -
LGA    D      60      S      56          3.471
LGA    A      61      T      57          2.771
LGA    E      62      P      58          2.601
LGA    V      63      H      59           #
LGA    -       -      D      60           -
LGA    -       -      A      61           -
LGA    -       -      E      62           -
LGA    V      64      V      63          1.354
LGA    E      65      V      64          2.839
LGA    L      66      E      65          4.613
LGA    P      67      L      66          5.088
LGA    E      68      P      67          3.701
LGA    -       -      E      68           -
LGA    S      69      S      69          4.771
LGA    F      70      F      70          3.669
LGA    D      71      D      71          3.812
LGA    F      72      F      72          1.916
LGA    K      73      K      73          3.869
LGA    R      74      R      74          4.298
LGA    -       -      I      75           -
LGA    I      75      S      76          1.015
LGA    S      76      T      77          2.326
LGA    T      77      Q      78          2.016
LGA    Q      78      T      79          2.796
LGA    T      79      T      80          1.997
LGA    -       -      P      81           -
LGA    T      80      Q      82          2.531
LGA    P      81      P      83          3.010
LGA    Q      82      L      84          3.841
LGA    P      83      M      85          5.165
LGA    L      84      -       -           -
LGA    M      85      -       -           -
LGA    A      86      A      86          5.362
LGA    V      87      V      87           #
LGA    F      88      F      88          3.506
LGA    D      89      D      89          3.725

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   89   89    5.0     73    3.03    68.49     47.673     2.331

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.733294 * X  +  -0.431941 * Y  +   0.525077 * Z  +  18.781313
  Y_new =  -0.197853 * X  +  -0.603289 * Y  +  -0.772591 * Z  +  11.696031
  Z_new =   0.650487 * X  +  -0.670425 * Y  +   0.356927 * Z  +  47.461178 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.081574    2.060019  [ DEG:   -61.9696    118.0304 ]
  Theta =  -0.708226   -2.433367  [ DEG:   -40.5784   -139.4216 ]
  Phi   =  -2.878054    0.263539  [ DEG:  -164.9003     15.0997 ]
 
# 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: T0378TS393_5-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS393_5-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   89   89   5.0   73   3.03   68.49  47.673
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS393_5-D1
PFRMAT TS
TARGET T0378
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1       5.860  35.832  66.708  1.00 25.00           C
ATOM      2  CA  LEU     2       5.174  37.007  63.169  1.00 25.00           C
ATOM      3  CA  SER     3       3.465  37.296  59.813  1.00 25.00           C
ATOM      4  CA  ALA     4       5.530  38.706  56.873  1.00 25.00           C
ATOM      5  CA  ASN     5       9.143  38.143  55.716  1.00 25.00           C
ATOM      6  CA  GLN     6       7.800  34.816  54.376  1.00 25.00           C
ATOM      7  CA  ILE     7       8.570  35.920  50.791  1.00 25.00           C
ATOM      8  CA  LYS     8      12.125  36.898  51.830  1.00 25.00           C
ATOM      9  CA  PHE     9      12.599  33.488  53.509  1.00 25.00           C
ATOM     10  CA  LEU    10      11.359  31.729  50.340  1.00 25.00           C
ATOM     11  CA  ARG    11      13.794  33.784  48.217  1.00 25.00           C
ATOM     12  CA  SER    12      16.667  32.865  50.576  1.00 25.00           C
ATOM     13  CA  LEU    13      15.712  29.164  50.335  1.00 25.00           C
ATOM     14  CA  ARG    14      15.650  29.403  46.513  1.00 25.00           C
ATOM     15  CA  GLU    15      19.106  31.055  46.536  1.00 25.00           C
ATOM     16  CA  ARG    16      20.446  28.276  48.804  1.00 25.00           C
ATOM     17  CA  LYS    17      23.524  28.038  50.928  1.00 25.00           C
ATOM     18  CA  TYR    18      22.202  30.285  53.758  1.00 25.00           C
ATOM     19  CA  ARG    19      19.656  28.034  55.464  1.00 25.00           C
ATOM     20  CA  LEU    20      21.231  28.582  58.883  1.00 25.00           C
ATOM     21  CA  ARG    21      18.783  26.032  60.122  1.00 25.00           C
ATOM     22  CA  GLU    22      15.539  24.709  58.687  1.00 25.00           C
ATOM     23  CA  GLN    23      14.496  21.155  57.712  1.00 25.00           C
ATOM     24  CA  ALA    24      12.083  21.258  54.750  1.00 25.00           C
ATOM     25  CA  PHE    25      13.304  22.915  51.483  1.00 25.00           C
ATOM     26  CA  ALA    26      11.114  21.373  48.771  1.00 25.00           C
ATOM     27  CA  VAL    27       7.801  21.964  46.993  1.00 25.00           C
ATOM     28  CA  GLU    28       4.584  20.236  46.008  1.00 25.00           C
ATOM     29  CA  GLY    29       1.764  19.016  43.740  1.00 25.00           C
ATOM     30  CA  PRO    30       3.527  17.241  40.894  1.00 25.00           C
ATOM     31  CA  LYS    31       3.217  13.454  40.409  1.00 25.00           C
ATOM     32  CA  LEU    32       6.334  12.899  42.564  1.00 25.00           C
ATOM     33  CA  VAL    33       4.880  15.156  45.294  1.00 25.00           C
ATOM     34  CA  GLY    34       1.585  13.206  45.186  1.00 25.00           C
ATOM     35  CA  GLU    35       3.502   9.904  45.488  1.00 25.00           C
ATOM     36  CA  MET    36       5.448  11.279  48.486  1.00 25.00           C
ATOM     37  CA  LEU    37       2.174  12.382  50.137  1.00 25.00           C
ATOM     38  CA  PRO    38       0.682   8.901  49.560  1.00 25.00           C
ATOM     39  CA  PHE    39       2.957   7.115  52.058  1.00 25.00           C
ATOM     40  CA  TYR    40       4.729  10.235  53.457  1.00 25.00           C
ATOM     41  CA  ARG    41       2.969  13.090  55.327  1.00 25.00           C
ATOM     42  CA  CYS    42       4.833  16.369  54.768  1.00 25.00           C
ATOM     43  CA  ARG    43       5.186  20.145  55.386  1.00 25.00           C
ATOM     44  CA  MET    44       4.166  21.971  52.209  1.00 25.00           C
ATOM     45  CA  LEU    45       2.478  25.057  50.742  1.00 25.00           C
ATOM     46  CA  VAL    46       1.792  28.693  49.988  1.00 25.00           C
ATOM     47  CA  GLY    47      -1.548  30.381  50.374  1.00 25.00           C
ATOM     48  CA  THR    48      -4.951  29.521  48.942  1.00 25.00           C
ATOM     49  CA  ALA    49      -7.441  27.915  46.610  1.00 25.00           C
ATOM     50  CA  ALA    50      -8.913  25.533  49.222  1.00 25.00           C
ATOM     51  CA  MET    51     -11.048  23.852  46.524  1.00 25.00           C
ATOM     52  CA  LEU    52      -7.959  23.453  44.295  1.00 25.00           C
ATOM     53  CA  ARG    53      -6.021  21.907  47.215  1.00 25.00           C
ATOM     54  CA  ALA    54      -8.907  19.478  47.876  1.00 25.00           C
ATOM     55  CA  VAL    55      -8.966  18.501  44.173  1.00 25.00           C
ATOM     56  CA  SER    56      -5.185  17.905  44.244  1.00 25.00           C
ATOM     57  CA  THR    57      -5.563  15.724  47.369  1.00 25.00           C
ATOM     58  CA  PRO    58      -8.112  12.991  46.468  1.00 25.00           C
ATOM     59  CA  HIS    59      -9.061  14.329  49.939  1.00 25.00           C
ATOM     60  CA  ASP    60      -7.354  11.734  52.135  1.00 25.00           C
ATOM     61  CA  ALA    61      -5.963  14.858  53.862  1.00 25.00           C
ATOM     62  CA  GLU    62      -3.718  17.735  54.956  1.00 25.00           C
ATOM     63  CA  VAL    63      -0.586  19.797  54.507  1.00 25.00           C
ATOM     64  CA  VAL    64      -1.171  23.582  54.086  1.00 25.00           C
ATOM     65  CA  GLU    65      -2.649  25.385  51.089  1.00 25.00           C
ATOM     66  CA  LEU    66      -1.783  25.399  47.381  1.00 25.00           C
ATOM     67  CA  PRO    67      -0.468  27.593  44.497  1.00 25.00           C
ATOM     68  CA  GLU    68      -3.116  30.103  43.398  1.00 25.00           C
ATOM     69  CA  SER    69      -0.568  32.764  42.521  1.00 25.00           C
ATOM     70  CA  PHE    70       2.095  34.685  40.550  1.00 25.00           C
ATOM     71  CA  ASP    71       4.705  33.868  43.231  1.00 25.00           C
ATOM     72  CA  PHE    72       3.731  30.167  43.086  1.00 25.00           C
ATOM     73  CA  LYS    73       4.054  30.207  39.270  1.00 25.00           C
ATOM     74  CA  ARG    74       7.511  31.831  39.555  1.00 25.00           C
ATOM     75  CA  ILE    75       8.582  29.163  42.086  1.00 25.00           C
ATOM     76  CA  SER    76      10.429  26.135  40.752  1.00 25.00           C
ATOM     77  CA  THR    77      10.122  27.830  37.375  1.00 25.00           C
ATOM     78  CA  GLN    78       8.099  28.460  34.242  1.00 25.00           C
ATOM     79  CA  THR    79       6.231  25.153  33.908  1.00 25.00           C
ATOM     80  CA  THR    80       3.497  23.822  36.148  1.00 25.00           C
ATOM     81  CA  PRO    81       2.739  24.142  39.911  1.00 25.00           C
ATOM     82  CA  GLN    82       4.794  24.646  43.056  1.00 25.00           C
ATOM     83  CA  PRO    83       6.362  21.326  41.924  1.00 25.00           C
ATOM     84  CA  LEU    84       8.529  18.304  42.895  1.00 25.00           C
ATOM     85  CA  MET    85       9.630  17.011  46.262  1.00 25.00           C
ATOM     86  CA  ALA    86       8.280  17.009  49.848  1.00 25.00           C
ATOM     87  CA  VAL    87      11.862  16.852  51.014  1.00 25.00           C
ATOM     88  CA  PHE    88      10.404  15.195  54.090  1.00 25.00           C
ATOM     89  CA  ASP    89      12.411  14.017  57.119  1.00 25.00           C
TER
END
