
#######################################################
#                                                     #
#                        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   22 (  174),  selected   22 , name T0382TS009_3_1-D1
# Molecule2: number of CA atoms  119 (  920),  selected  119 , name T0382_D1.pdb
# PARAMETERS: T0382TS009_3_1-D1.T0382_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      L       4           -
LGA    -       -      D       5           -
LGA    -       -      L       6           -
LGA    -       -      H       7           -
LGA    -       -      Q       8           -
LGA    -       -      M       9           -
LGA    -       -      T      10           -
LGA    -       -      T      11           -
LGA    -       -      Q      12           -
LGA    -       -      D      13           -
LGA    -       -      L      14           -
LGA    -       -      V      15           -
LGA    -       -      A      16           -
LGA    -       -      L      17           -
LGA    -       -      F      18           -
LGA    -       -      A      19           -
LGA    -       -      K      20           -
LGA    -       -      V      21           -
LGA    -       -      T      22           -
LGA    -       -      V      23           -
LGA    -       -      E      24           -
LGA    -       -      Q      25           -
LGA    -       -      D      26           -
LGA    -       -      D      27           -
LGA    -       -      A      28           -
LGA    -       -      L      29           -
LGA    -       -      L      30           -
LGA    L       4      G      31          1.867
LGA    D       5      N      32          2.749
LGA    L       6      Q      33          1.887
LGA    H       7      I      34          1.989
LGA    Q       8      S      35          2.619
LGA    M       9      R      36          1.591
LGA    -       -      F      37           -
LGA    T      10      N      38          0.743
LGA    T      11      R      39          0.763
LGA    Q      12      L      40          0.828
LGA    D      13      F      41          3.853
LGA    -       -      G      42           -
LGA    -       -      V      43           -
LGA    L      14      M      44          1.387
LGA    V      15      A      45          2.649
LGA    -       -      E      46           -
LGA    A      16      I      47          4.454
LGA    L      17      A      48          4.381
LGA    F      18      D      49          0.439
LGA    -       -      E      50           -
LGA    A      19      L      51          2.822
LGA    K      20      K      52          4.386
LGA    -       -      A      53           -
LGA    -       -      R      54           -
LGA    -       -      D      55           -
LGA    -       -      G      56           -
LGA    -       -      D      57           -
LGA    -       -      Q      58           -
LGA    V      21      R      59          3.683
LGA    T      22      T      60          1.080
LGA    -       -      A      61           -
LGA    -       -      L      62           -
LGA    -       -      L      63           -
LGA    -       -      S      64           -
LGA    -       -      L      65           -
LGA    -       -      F      66           -
LGA    -       -      E      67           -
LGA    -       -      Y      68           -
LGA    -       -      P      69           -
LGA    -       -      N      70           -
LGA    -       -      M      71           -
LGA    -       -      Q      72           -
LGA    -       -      V      73           -
LGA    -       -      R      74           -
LGA    -       -      L      75           -
LGA    -       -      Q      76           -
LGA    -       -      A      77           -
LGA    -       -      A      78           -
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      T      81           -
LGA    V      23      L      82           #
LGA    E      24      A      83          3.092
LGA    Q      25      V      84          4.660
LGA    -       -      A      85           -
LGA    -       -      P      86           -
LGA    -       -      V      87           -
LGA    -       -      K      88           -
LGA    -       -      A      89           -
LGA    -       -      R      90           -
LGA    -       -      E      91           -
LGA    -       -      Q      92           -
LGA    -       -      L      93           -
LGA    -       -      E      94           -
LGA    -       -      A      95           -
LGA    -       -      I      96           -
LGA    -       -      V      97           -
LGA    -       -      S      98           -
LGA    -       -      S      99           -
LGA    -       -      K     100           -
LGA    -       -      W     101           -
LGA    -       -      F     102           -
LGA    -       -      P     103           -
LGA    -       -      Q     104           -
LGA    -       -      A     105           -
LGA    -       -      G     106           -
LGA    -       -      D     107           -
LGA    -       -      A     108           -
LGA    -       -      G     109           -
LGA    -       -      M     110           -
LGA    -       -      C     111           -
LGA    -       -      L     112           -
LGA    -       -      D     113           -
LGA    -       -      L     114           -
LGA    -       -      L     115           -
LGA    -       -      D     116           -
LGA    -       -      D     117           -
LGA    -       -      G     118           -
LGA    -       -      T     119           -
LGA    -       -      F     120           -
LGA    -       -      K     121           -
LGA    -       -      P     122           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   22  119    5.0     21    2.81     9.52     11.978     0.721

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.558889 * X  +  -0.636652 * Y  +  -0.531335 * Z  + -17.522093
  Y_new =   0.810204 * X  +  -0.555748 * Y  +  -0.186316 * Z  +  33.219456
  Z_new =  -0.176670 * X  +  -0.534620 * Y  +   0.826420 * Z  +  20.618366 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.574200    2.567392  [ DEG:   -32.8993    147.1007 ]
  Theta =   0.177602    2.963990  [ DEG:    10.1759    169.8241 ]
  Phi   =   2.174653   -0.966940  [ DEG:   124.5984    -55.4016 ]
 
# 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: T0382TS009_3_1-D1                             
REMARK     2: T0382_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0382TS009_3_1-D1.T0382_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   22  119   5.0   21   2.81    9.52  11.978
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS009_3_1-D1
REMARK PARENT number 1
PFRMAT TS                                                                       
TARGET T0382                                                                    
PARENT N/A                                                                      
ATOM     24  N   LEU     4     -10.157  33.062  16.805  1.00  0.00             
ATOM     25  CA  LEU     4      -9.027  33.191  17.718  1.00  0.00             
ATOM     26  C   LEU     4      -7.702  33.147  16.967  1.00  0.00             
ATOM     27  O   LEU     4      -7.142  34.185  16.615  1.00  0.00             
ATOM     28  CB  LEU     4      -9.134  34.490  18.521  1.00  0.00             
ATOM     29  CG  LEU     4      -9.318  34.339  20.032  1.00  0.00             
ATOM     30  CD1 LEU     4      -8.731  35.534  20.767  1.00  0.00             
ATOM     31  CD2 LEU     4      -8.693  33.043  20.523  1.00  0.00             
ATOM     32  N   ASP     5      -7.205  31.939  16.725  1.00  0.00             
ATOM     33  CA  ASP     5      -5.944  31.756  16.015  1.00  0.00             
ATOM     34  C   ASP     5      -5.886  32.625  14.763  1.00  0.00             
ATOM     35  O   ASP     5      -5.244  33.675  14.754  1.00  0.00             
ATOM     36  CB  ASP     5      -4.762  32.075  16.932  1.00  0.00             
ATOM     37  CG  ASP     5      -4.058  30.828  17.430  1.00  0.00             
ATOM     38  OD1 ASP     5      -2.887  30.616  17.052  1.00  0.00             
ATOM     39  OD2 ASP     5      -4.678  30.063  18.198  1.00  0.00             
ATOM     40  N   LEU     6      -6.560  32.181  13.708  1.00  0.00             
ATOM     41  CA  LEU     6      -6.587  32.916  12.449  1.00  0.00             
ATOM     42  C   LEU     6      -6.073  34.340  12.633  1.00  0.00             
ATOM     43  O   LEU     6      -5.917  35.083  11.664  1.00  0.00             
ATOM     44  CB  LEU     6      -5.759  32.191  11.387  1.00  0.00             
ATOM     45  CG  LEU     6      -6.448  31.943  10.043  1.00  0.00             
ATOM     46  CD1 LEU     6      -5.438  31.981   8.907  1.00  0.00             
ATOM     47  CD2 LEU     6      -7.559  32.956   9.813  1.00  0.00             
ATOM     48  N   HIS     7      -5.811  34.714  13.881  1.00  0.00             
ATOM     49  CA  HIS     7      -5.315  36.049  14.192  1.00  0.00             
ATOM     50  C   HIS     7      -4.542  36.638  13.017  1.00  0.00             
ATOM     51  O   HIS     7      -4.946  37.648  12.440  1.00  0.00             
ATOM     52  CB  HIS     7      -6.469  36.973  14.579  1.00  0.00             
ATOM     53  CG  HIS     7      -6.237  37.732  15.850  1.00  0.00             
ATOM     54  ND1 HIS     7      -5.375  37.294  16.831  1.00  0.00             
ATOM     55  CD2 HIS     7      -6.755  38.900  16.298  1.00  0.00             
ATOM     56  CE1 HIS     7      -5.372  38.160  17.828  1.00  0.00             
ATOM     57  NE2 HIS     7      -6.200  39.142  17.532  1.00  0.00             
ATOM     58  N   GLN     8      -3.428  36.002  12.668  1.00  0.00             
ATOM     59  CA  GLN     8      -2.597  36.462  11.561  1.00  0.00             
ATOM     60  C   GLN     8      -3.298  36.254  10.223  1.00  0.00             
ATOM     61  O   GLN     8      -3.184  37.080   9.317  1.00  0.00             
ATOM     62  CB  GLN     8      -2.235  37.938  11.741  1.00  0.00             
ATOM     63  CG  GLN     8      -0.769  38.251  11.490  1.00  0.00             
ATOM     64  CD  GLN     8      -0.491  39.740  11.443  1.00  0.00             
ATOM     65  OE1 GLN     8       0.609  40.166  11.092  1.00  0.00             
ATOM     66  NE2 GLN     8      -1.491  40.539  11.798  1.00  0.00             
ATOM     67  N   MET     9      -4.020  35.144  10.105  1.00  0.00             
ATOM     68  CA  MET     9      -4.740  34.826   8.878  1.00  0.00             
ATOM     69  C   MET     9      -4.430  35.837   7.778  1.00  0.00             
ATOM     70  O   MET     9      -4.657  35.573   6.598  1.00  0.00             
ATOM     71  CB  MET     9      -4.393  33.413   8.404  1.00  0.00             
ATOM     72  CG  MET     9      -5.338  32.337   8.917  1.00  0.00             
ATOM     73  SD  MET     9      -4.613  30.688   8.856  1.00  0.00             
ATOM     74  CE  MET     9      -5.934  29.711   9.570  1.00  0.00             
ATOM     75  N   THR    10      -3.910  36.994   8.175  1.00  0.00             
ATOM     76  CA  THR    10      -3.562  38.070   7.204  1.00  0.00             
ATOM     77  C   THR    10      -3.519  37.532   5.777  1.00  0.00             
ATOM     78  O   THR    10      -3.750  38.270   4.819  1.00  0.00             
ATOM     79  CB  THR    10      -4.562  39.239   7.272  1.00  0.00             
ATOM     80  OG1 THR    10      -5.682  38.866   8.086  1.00  0.00             
ATOM     81  CG2 THR    10      -3.900  40.474   7.864  1.00  0.00             
ATOM     82  N   THR    11      -3.222  36.244   5.645  1.00  0.00             
ATOM     83  CA  THR    11      -3.146  35.591   4.306  1.00  0.00             
ATOM     84  C   THR    11      -4.297  36.038   3.409  1.00  0.00             
ATOM     85  O   THR    11      -4.117  36.243   2.209  1.00  0.00             
ATOM     86  CB  THR    11      -1.811  35.899   3.603  1.00  0.00             
ATOM     87  OG1 THR    11      -1.130  36.949   4.301  1.00  0.00             
ATOM     88  CG2 THR    11      -0.928  34.661   3.572  1.00  0.00             
ATOM     89  N   GLN    12      -5.477  36.185   4.000  1.00  0.00             
ATOM     90  CA  GLN    12      -6.659  36.607   3.257  1.00  0.00             
ATOM     91  C   GLN    12      -6.308  37.671   2.222  1.00  0.00             
ATOM     92  O   GLN    12      -7.164  38.107   1.452  1.00  0.00             
ATOM     93  CB  GLN    12      -7.319  35.407   2.574  1.00  0.00             
ATOM     94  CG  GLN    12      -8.838  35.418   2.634  1.00  0.00             
ATOM     95  CD  GLN    12      -9.451  34.147   2.081  1.00  0.00             
ATOM     96  OE1 GLN    12     -10.622  33.853   2.324  1.00  0.00             
ATOM     97  NE2 GLN    12      -8.661  33.387   1.330  1.00  0.00             
ATOM     98  N   ASP    13      -5.045  38.084   2.210  1.00  0.00             
ATOM     99  CA  ASP    13      -4.580  39.097   1.270  1.00  0.00             
ATOM    100  C   ASP    13      -5.734  39.958   0.770  1.00  0.00             
ATOM    101  O   ASP    13      -5.581  40.730  -0.176  1.00  0.00             
ATOM    102  CB  ASP    13      -3.509  39.977   1.918  1.00  0.00             
ATOM    103  CG  ASP    13      -2.163  39.859   1.230  1.00  0.00             
ATOM    104  OD1 ASP    13      -1.517  40.904   1.005  1.00  0.00             
ATOM    105  OD2 ASP    13      -1.754  38.722   0.917  1.00  0.00             
ATOM    106  N   LEU    14      -6.889  39.821   1.412  1.00  0.00             
ATOM    107  CA  LEU    14      -8.072  40.585   1.035  1.00  0.00             
ATOM    108  C   LEU    14      -7.783  41.495  -0.154  1.00  0.00             
ATOM    109  O   LEU    14      -7.728  42.717  -0.013  1.00  0.00             
ATOM    110  CB  LEU    14      -9.235  39.646   0.708  1.00  0.00             
ATOM    111  CG  LEU    14     -10.249  39.406   1.829  1.00  0.00             
ATOM    112  CD1 LEU    14     -11.664  39.673   1.341  1.00  0.00             
ATOM    113  CD2 LEU    14      -9.923  40.267   3.041  1.00  0.00             
ATOM    114  N   VAL    15      -7.601  40.893  -1.324  1.00  0.00             
ATOM    115  CA  VAL    15      -7.312  41.665  -2.566  1.00  0.00             
ATOM    116  C   VAL    15      -7.902  43.069  -2.494  1.00  0.00             
ATOM    117  O   VAL    15      -7.320  44.025  -3.007  1.00  0.00             
ATOM    118  CB  VAL    15      -5.797  41.768  -2.827  1.00  0.00             
ATOM    119  CG1 VAL    15      -5.370  40.767  -3.889  1.00  0.00             
ATOM    120  CG2 VAL    15      -5.019  41.552  -1.538  1.00  0.00             
ATOM    121  N   ALA    16      -9.061  43.186  -1.854  1.00  0.00             
ATOM    122  CA  ALA    16      -9.732  44.472  -1.712  1.00  0.00             
ATOM    123  C   ALA    16      -8.891  45.600  -2.300  1.00  0.00             
ATOM    124  O   ALA    16      -9.358  46.356  -3.152  1.00  0.00             
ATOM    125  CB  ALA    16     -11.098  44.433  -2.380  1.00  0.00             
ATOM    126  N   LEU    17      -7.649  45.708  -1.839  1.00  0.00             
ATOM    127  CA  LEU    17      -6.741  46.743  -2.318  1.00  0.00             
ATOM    128  C   LEU    17      -7.004  47.072  -3.784  1.00  0.00             
ATOM    129  O   LEU    17      -7.172  48.236  -4.148  1.00  0.00             
ATOM    130  CB  LEU    17      -6.871  48.006  -1.464  1.00  0.00             
ATOM    131  CG  LEU    17      -5.582  48.529  -0.827  1.00  0.00             
ATOM    132  CD1 LEU    17      -5.646  50.037  -0.645  1.00  0.00             
ATOM    133  CD2 LEU    17      -4.373  48.135  -1.659  1.00  0.00             
ATOM    134  N   PHE    18      -7.037  46.039  -4.620  1.00  0.00             
ATOM    135  CA  PHE    18      -7.279  46.216  -6.046  1.00  0.00             
ATOM    136  C   PHE    18      -8.585  46.962  -6.297  1.00  0.00             
ATOM    137  O   PHE    18      -9.022  47.762  -5.469  1.00  0.00             
ATOM    138  CB  PHE    18      -6.113  46.962  -6.699  1.00  0.00             
ATOM    139  CG  PHE    18      -5.372  46.151  -7.723  1.00  0.00             
ATOM    140  CD1 PHE    18      -5.929  44.999  -8.250  1.00  0.00             
ATOM    141  CD2 PHE    18      -4.118  46.541  -8.160  1.00  0.00             
ATOM    142  CE1 PHE    18      -5.248  44.253  -9.194  1.00  0.00             
ATOM    143  CE2 PHE    18      -3.436  45.795  -9.103  1.00  0.00             
ATOM    144  CZ  PHE    18      -3.996  44.655  -9.620  1.00  0.00             
ATOM    145  N   ALA    19      -9.203  46.696  -7.442  1.00  0.00             
ATOM    146  CA  ALA    19     -10.460  47.342  -7.803  1.00  0.00             
ATOM    147  C   ALA    19     -11.506  46.316  -8.223  1.00  0.00             
ATOM    148  O   ALA    19     -11.247  45.112  -8.218  1.00  0.00             
ATOM    149  CB  ALA    19     -10.979  48.176  -6.642  1.00  0.00             
ATOM    150  N   LYS    20     -12.690  46.799  -8.586  1.00  0.00             
ATOM    151  CA  LYS    20     -13.777  45.926  -9.010  1.00  0.00             
ATOM    152  C   LYS    20     -14.913  46.725  -9.640  1.00  0.00             
ATOM    153  O   LYS    20     -14.754  47.307 -10.713  1.00  0.00             
ATOM    154  CB  LYS    20     -13.266  44.872  -9.995  1.00  0.00             
ATOM    155  CG  LYS    20     -13.888  43.498  -9.812  1.00  0.00             
ATOM    156  CD  LYS    20     -12.990  42.406 -10.370  1.00  0.00             
ATOM    157  CE  LYS    20     -13.793  41.177 -10.763  1.00  0.00             
ATOM    158  NZ  LYS    20     -13.074  40.339 -11.762  1.00  0.00             
ATOM    159  N   VAL    21     -16.058  46.747  -8.967  1.00  0.00             
ATOM    160  CA  VAL    21     -17.249  47.491  -9.470  1.00  0.00             
ATOM    161  C   VAL    21     -18.065  48.070  -8.319  1.00  0.00             
ATOM    162  O   VAL    21     -17.960  47.615  -7.180  1.00  0.00             
ATOM    163  CB  VAL    21     -16.841  48.631 -10.422  1.00  0.00             
ATOM    164  CG1 VAL    21     -17.441  48.412 -11.803  1.00  0.00             
ATOM    165  CG2 VAL    21     -15.326  48.741 -10.503  1.00  0.00             
ATOM    166  N   THR    22     -18.877  49.076  -8.624  1.00  0.00             
ATOM    167  CA  THR    22     -19.731  49.734  -7.593  1.00  0.00             
ATOM    168  C   THR    22     -19.455  51.233  -7.522  1.00  0.00             
ATOM    169  O   THR    22     -19.690  51.963  -8.485  1.00  0.00             
ATOM    170  CB  THR    22     -21.228  49.511  -7.876  1.00  0.00             
ATOM    171  OG1 THR    22     -21.451  49.470  -9.291  1.00  0.00             
ATOM    172  CG2 THR    22     -21.698  48.204  -7.255  1.00  0.00             
ATOM    173  N   VAL    23     -18.954  51.682  -6.377  1.00  0.00             
ATOM    174  CA  VAL    23     -18.637  53.125  -6.174  1.00  0.00             
ATOM    175  C   VAL    23     -17.132  53.357  -6.115  1.00  0.00             
ATOM    176  O   VAL    23     -16.362  52.681  -6.797  1.00  0.00             
ATOM    177  CB  VAL    23     -19.238  53.997  -7.291  1.00  0.00             
ATOM    178  CG1 VAL    23     -20.495  54.701  -6.802  1.00  0.00             
ATOM    179  CG2 VAL    23     -19.534  53.156  -8.523  1.00  0.00             
ATOM    180  N   GLU    24     -16.717  54.316  -5.293  1.00  0.00             
ATOM    181  CA  GLU    24     -15.302  54.638  -5.143  1.00  0.00             
ATOM    182  C   GLU    24     -15.007  55.187  -3.752  1.00  0.00             
ATOM    183  O   GLU    24     -15.909  55.638  -3.047  1.00  0.00             
ATOM    184  CB  GLU    24     -14.440  53.404  -5.417  1.00  0.00             
ATOM    185  CG  GLU    24     -13.726  53.430  -6.758  1.00  0.00             
ATOM    186  CD  GLU    24     -12.749  52.283  -6.921  1.00  0.00             
ATOM    187  OE1 GLU    24     -13.131  51.260  -7.529  1.00  0.00             
ATOM    188  OE2 GLU    24     -11.603  52.406  -6.441  1.00  0.00             
ATOM    189  N   GLN    25     -13.737  55.146  -3.362  1.00  0.00             
ATOM    190  CA  GLN    25     -13.320  55.638  -2.055  1.00  0.00             
ATOM    191  C   GLN    25     -12.987  54.487  -1.112  1.00  0.00             
ATOM    192  O   GLN    25     -11.822  54.253  -0.789  1.00  0.00             
ATOM    193  CB  GLN    25     -12.114  56.571  -2.193  1.00  0.00             
ATOM    194  CG  GLN    25     -12.455  58.047  -2.078  1.00  0.00             
ATOM    195  CD  GLN    25     -11.235  58.938  -2.207  1.00  0.00             
ATOM    196  OE1 GLN    25     -11.308  60.145  -1.971  1.00  0.00             
ATOM    197  NE2 GLN    25     -10.108  58.345  -2.583  1.00  0.00              
TER
END
