
#######################################################
#                                                     #
#                        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   87 (   87),  selected   87 , name T0358TS168_3
# Molecule2: number of CA atoms   66 ( 1047),  selected   66 , name T0358.pdb
# PARAMETERS: T0358TS168_3.T0358.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      G      10           -
LGA    T       2      P      11           -
LGA    Q       3      F      12           -
LGA    S       4      T      13           -
LGA    V       5      R      14           -
LGA    L       6      R      15           -
LGA    L       7      Q      16           -
LGA    P       8      A      17           -
LGA    P       9      Q      18           -
LGA    G      10      A      19           -
LGA    P      11      V      20           -
LGA    F      12      T      21           -
LGA    T      13      T      22           -
LGA    R      14      T      23           -
LGA    R      15      -       -           -
LGA    Q      16      -       -           -
LGA    A      17      -       -           -
LGA    Q      18      -       -           -
LGA    A      19      -       -           -
LGA    V      20      -       -           -
LGA    T      21      -       -           -
LGA    T      22      -       -           -
LGA    T      23      -       -           -
LGA    Y      24      -       -           -
LGA    S      25      Y      24           #
LGA    N      26      S      25           #
LGA    I      27      N      26          4.752
LGA    T      28      I      27          2.337
LGA    L      29      T      28          3.175
LGA    E      30      L      29          1.795
LGA    D      31      E      30          2.024
LGA    D      32      D      31          5.892
LGA    Q      33      D      32          3.064
LGA    G      34      Q      33          3.663
LGA    S      35      G      34           #
LGA    -       -      S      35           -
LGA    -       -      H      36           -
LGA    H      36      F      37          3.340
LGA    F      37      R      38          2.735
LGA    R      38      L      39          3.779
LGA    L      39      V      40          4.489
LGA    V      40      V      41          1.434
LGA    V      41      R      42          1.274
LGA    R      42      D      43          0.986
LGA    D      43      T      44          3.792
LGA    T      44      E      45          2.426
LGA    E      45      G      46           -
LGA    G      46      -       -           -
LGA    R      47      R      47          3.685
LGA    M      48      M      48          3.212
LGA    V      49      V      49          5.379
LGA    W      50      W      50          4.830
LGA    R      51      R      51          1.134
LGA    A      52      -       -           -
LGA    W      53      A      52          1.773
LGA    N      54      W      53          2.900
LGA    F      55      N      54          1.769
LGA    E      56      F      55           #
LGA    P      57      E      56           -
LGA    D      58      P      57           -
LGA    A      59      -       -           -
LGA    G      60      D      58           #
LGA    E      61      A      59          2.129
LGA    -       -      G      60           -
LGA    G      62      E      61          0.620
LGA    L      63      G      62          0.561
LGA    N      64      L      63          0.562
LGA    R      65      N      64          1.255
LGA    Y      66      R      65          1.410
LGA    I      67      Y      66          1.128
LGA    R      68      I      67          0.930
LGA    T      69      R      68          1.032
LGA    S      70      T      69          1.573
LGA    G      71      S      70           -
LGA    I      72      G      71           -
LGA    R      73      I      72           -
LGA    T      74      R      73           -
LGA    D      75      T      74           -
LGA    T      76      D      75           -
LGA    A      77      -       -           -
LGA    T      78      -       -           -
LGA    R      79      -       -           -
LGA    L      80      -       -           -
LGA    E      81      -       -           -
LGA    H      82      -       -           -
LGA    H      83      -       -           -
LGA    H      84      -       -           -
LGA    H      85      -       -           -
LGA    H      86      -       -           -
LGA    H      87      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   87   66    5.0     35    2.87    20.00     34.149     1.179

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.672901 * X  +   0.441624 * Y  +   0.593442 * Z  +   0.090466
  Y_new =   0.293571 * X  +   0.576928 * Y  +  -0.762214 * Z  +  -1.181088
  Z_new =  -0.678985 * X  +   0.687112 * Y  +   0.258567 * Z  +   8.936339 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.210877   -1.930716  [ DEG:    69.3782   -110.6218 ]
  Theta =   0.746379    2.395214  [ DEG:    42.7644    137.2356 ]
  Phi   =   0.411384   -2.730209  [ DEG:    23.5706   -156.4294 ]
 
# 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: T0358TS168_3                                  
REMARK     2: T0358.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358TS168_3.T0358.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   87   66   5.0   35   2.87   20.00  34.149
REMARK  ---------------------------------------------------------- 
MOLECULE T0358TS168_3
PFRMAT TS
TARGET T0358
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      -3.696 -12.131  22.766  1.00 25.00           C
ATOM      2  CA  THR     2      -2.589 -10.308  19.600  1.00 25.00           C
ATOM      3  CA  GLN     3      -2.360  -6.767  18.152  1.00 25.00           C
ATOM      4  CA  SER     4      -1.968  -3.026  17.744  1.00 25.00           C
ATOM      5  CA  VAL     5      -1.981  -1.757  14.152  1.00 25.00           C
ATOM      6  CA  LEU     6      -2.185   1.872  12.948  1.00 25.00           C
ATOM      7  CA  LEU     7      -0.711   5.319  12.334  1.00 25.00           C
ATOM      8  CA  PRO     8      -1.151   7.779  15.250  1.00 25.00           C
ATOM      9  CA  PRO     9      -2.826  10.903  16.669  1.00 25.00           C
ATOM     10  CA  GLY    10      -6.254  10.312  18.200  1.00 25.00           C
ATOM     11  CA  PRO    11      -7.267   6.917  19.450  1.00 25.00           C
ATOM     12  CA  PHE    12      -6.109   4.444  16.855  1.00 25.00           C
ATOM     13  CA  THR    13      -8.120   6.674  14.516  1.00 25.00           C
ATOM     14  CA  ARG    14      -7.871   8.709  11.311  1.00 25.00           C
ATOM     15  CA  ARG    15     -10.812   6.680   9.936  1.00 25.00           C
ATOM     16  CA  GLN    16      -8.774   5.792   6.817  1.00 25.00           C
ATOM     17  CA  ALA    17      -5.840   4.689   9.018  1.00 25.00           C
ATOM     18  CA  GLN    18      -8.198   2.518  11.115  1.00 25.00           C
ATOM     19  CA  ALA    19      -9.614   0.934   7.928  1.00 25.00           C
ATOM     20  CA  VAL    20      -6.065   0.215   6.680  1.00 25.00           C
ATOM     21  CA  THR    21      -5.182  -1.392  10.043  1.00 25.00           C
ATOM     22  CA  THR    22      -8.337  -3.556   9.864  1.00 25.00           C
ATOM     23  CA  THR    23      -7.424  -4.638   6.307  1.00 25.00           C
ATOM     24  CA  TYR    24      -3.886  -5.541   7.463  1.00 25.00           C
ATOM     25  CA  SER    25      -3.274  -7.943   4.642  1.00 25.00           C
ATOM     26  CA  ASN    26      -3.199  -7.235   0.861  1.00 25.00           C
ATOM     27  CA  ILE    27      -1.038  -4.391  -0.519  1.00 25.00           C
ATOM     28  CA  THR    28      -2.751  -1.339  -2.119  1.00 25.00           C
ATOM     29  CA  LEU    29      -4.518   1.956  -2.638  1.00 25.00           C
ATOM     30  CA  GLU    30      -2.326   3.982  -5.085  1.00 25.00           C
ATOM     31  CA  ASP    31      -5.521   4.715  -7.078  1.00 25.00           C
ATOM     32  CA  ASP    32      -6.341   6.795 -10.086  1.00 25.00           C
ATOM     33  CA  GLN    33      -5.929  10.100  -8.160  1.00 25.00           C
ATOM     34  CA  GLY    34      -3.853  11.584  -5.341  1.00 25.00           C
ATOM     35  CA  SER    35      -1.249   8.984  -4.373  1.00 25.00           C
ATOM     36  CA  HIS    36      -1.633   7.620  -0.905  1.00 25.00           C
ATOM     37  CA  PHE    37      -0.308   4.155  -0.149  1.00 25.00           C
ATOM     38  CA  ARG    38       0.500   0.753   1.414  1.00 25.00           C
ATOM     39  CA  LEU    39      -2.317  -0.987   3.322  1.00 25.00           C
ATOM     40  CA  VAL    40      -5.726  -2.052   1.855  1.00 25.00           C
ATOM     41  CA  VAL    41      -8.281  -4.829   1.308  1.00 25.00           C
ATOM     42  CA  ARG    42      -8.415  -8.310   2.841  1.00 25.00           C
ATOM     43  CA  ASP    43     -11.969  -9.222   3.762  1.00 25.00           C
ATOM     44  CA  THR    44     -14.954  -9.483   1.394  1.00 25.00           C
ATOM     45  CA  GLU    45     -17.184  -9.079   4.432  1.00 25.00           C
ATOM     46  CA  GLY    46     -19.220  -6.232   2.901  1.00 25.00           C
ATOM     47  CA  ARG    47     -16.071  -4.053   3.313  1.00 25.00           C
ATOM     48  CA  MET    48     -12.356  -3.392   4.017  1.00 25.00           C
ATOM     49  CA  VAL    49     -10.764  -0.427   2.221  1.00 25.00           C
ATOM     50  CA  TRP    50      -8.118   2.331   2.617  1.00 25.00           C
ATOM     51  CA  ARG    51      -4.503   3.515   2.616  1.00 25.00           C
ATOM     52  CA  ALA    52      -2.256   3.666   5.691  1.00 25.00           C
ATOM     53  CA  TRP    53      -0.538   6.781   4.428  1.00 25.00           C
ATOM     54  CA  ASN    54       2.895   6.576   2.900  1.00 25.00           C
ATOM     55  CA  PHE    55       5.416   7.698   0.302  1.00 25.00           C
ATOM     56  CA  GLU    56       7.661   4.673   0.481  1.00 25.00           C
ATOM     57  CA  PRO    57       9.718   1.969  -1.315  1.00 25.00           C
ATOM     58  CA  ASP    58       8.023  -1.355  -2.216  1.00 25.00           C
ATOM     59  CA  ALA    59       5.467  -0.279   0.388  1.00 25.00           C
ATOM     60  CA  GLY    60       7.871   0.372   3.301  1.00 25.00           C
ATOM     61  CA  GLU    61       5.942   3.001   5.272  1.00 25.00           C
ATOM     62  CA  GLY    62       6.739   1.581   8.737  1.00 25.00           C
ATOM     63  CA  LEU    63       3.022   0.873   9.331  1.00 25.00           C
ATOM     64  CA  ASN    64       2.792  -0.894   5.941  1.00 25.00           C
ATOM     65  CA  ARG    65       5.867  -3.008   6.807  1.00 25.00           C
ATOM     66  CA  TYR    66       4.306  -3.941  10.177  1.00 25.00           C
ATOM     67  CA  ILE    67       1.051  -4.937   8.423  1.00 25.00           C
ATOM     68  CA  ARG    68       3.020  -7.093   5.943  1.00 25.00           C
ATOM     69  CA  THR    69       4.868  -8.782   8.841  1.00 25.00           C
ATOM     70  CA  SER    70       7.373 -10.816   6.882  1.00 25.00           C
ATOM     71  CA  GLY    71      10.115  -9.951   9.448  1.00 25.00           C
ATOM     72  CA  ILE    72       8.079 -10.260  12.639  1.00 25.00           C
ATOM     73  CA  ARG    73       9.516 -13.744  13.180  1.00 25.00           C
ATOM     74  CA  THR    74      12.412 -15.596  14.924  1.00 25.00           C
ATOM     75  CA  ASP    75      16.198 -15.165  14.837  1.00 25.00           C
ATOM     76  CA  THR    76      16.714 -15.209  18.588  1.00 25.00           C
ATOM     77  CA  ALA    77      18.661 -11.959  18.714  1.00 25.00           C
ATOM     78  CA  THR    78      19.127 -10.523  22.191  1.00 25.00           C
ATOM     79  CA  ARG    79      17.017 -10.898  25.306  1.00 25.00           C
ATOM     80  CA  LEU    80      16.470  -8.588  28.291  1.00 25.00           C
ATOM     81  CA  GLU    81      14.659  -6.913  31.150  1.00 25.00           C
ATOM     82  CA  HIS    82      13.352  -3.750  29.380  1.00 25.00           C
ATOM     83  CA  HIS    83      15.963  -2.229  27.089  1.00 25.00           C
ATOM     84  CA  HIS    84      15.150   1.314  25.847  1.00 25.00           C
ATOM     85  CA  HIS    85      13.267   4.444  27.045  1.00 25.00           C
ATOM     86  CA  HIS    86       9.693   5.050  28.090  1.00 25.00           C
ATOM     87  CA  HIS    87       8.659   1.600  29.265  1.00 25.00           C
TER
END
