
#######################################################
#                                                     #
#                        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 T0358TS393_3
# Molecule2: number of CA atoms   66 ( 1047),  selected   66 , name T0358.pdb
# PARAMETERS: T0358TS393_3.T0358.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      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    -       -      Q      16           -
LGA    -       -      A      17           -
LGA    -       -      Q      18           -
LGA    -       -      A      19           -
LGA    L       7      V      20           #
LGA    P       8      T      21           #
LGA    P       9      -       -           -
LGA    G      10      -       -           -
LGA    P      11      T      22          4.457
LGA    F      12      T      23          2.368
LGA    T      13      -       -           -
LGA    R      14      Y      24          1.882
LGA    R      15      S      25          2.003
LGA    Q      16      N      26          1.813
LGA    A      17      I      27          1.802
LGA    Q      18      T      28          3.086
LGA    A      19      -       -           -
LGA    V      20      -       -           -
LGA    T      21      L      29          3.063
LGA    T      22      E      30          1.935
LGA    T      23      -       -           -
LGA    Y      24      D      31          3.509
LGA    S      25      D      32           -
LGA    N      26      Q      33           -
LGA    -       -      G      34           -
LGA    -       -      S      35           -
LGA    -       -      H      36           -
LGA    -       -      F      37           -
LGA    -       -      R      38           -
LGA    -       -      L      39           -
LGA    I      27      V      40          4.576
LGA    T      28      -       -           -
LGA    L      29      -       -           -
LGA    E      30      -       -           -
LGA    D      31      -       -           -
LGA    D      32      -       -           -
LGA    Q      33      -       -           -
LGA    G      34      -       -           -
LGA    S      35      -       -           -
LGA    H      36      -       -           -
LGA    F      37      -       -           -
LGA    R      38      -       -           -
LGA    L      39      V      41           #
LGA    V      40      R      42           #
LGA    -       -      D      43           -
LGA    -       -      T      44           -
LGA    -       -      E      45           -
LGA    -       -      G      46           -
LGA    V      41      R      47          3.285
LGA    R      42      M      48           #
LGA    D      43      -       -           -
LGA    T      44      -       -           -
LGA    E      45      -       -           -
LGA    G      46      -       -           -
LGA    R      47      -       -           -
LGA    M      48      -       -           -
LGA    V      49      -       -           -
LGA    W      50      -       -           -
LGA    R      51      V      49          4.536
LGA    A      52      W      50          3.878
LGA    W      53      R      51          1.534
LGA    N      54      A      52          1.682
LGA    F      55      W      53          5.077
LGA    -       -      N      54           -
LGA    -       -      F      55           -
LGA    E      56      E      56          2.965
LGA    P      57      P      57          4.170
LGA    D      58      -       -           -
LGA    A      59      D      58           #
LGA    G      60      A      59          3.058
LGA    E      61      G      60          2.553
LGA    G      62      E      61          2.284
LGA    L      63      G      62          2.160
LGA    N      64      L      63          1.844
LGA    R      65      N      64          0.107
LGA    Y      66      R      65          0.332
LGA    I      67      Y      66          0.786
LGA    R      68      I      67          1.890
LGA    T      69      R      68          2.203
LGA    S      70      T      69           -
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     29    2.86     6.90     28.621     0.980

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.958048 * X  +   0.090476 * Y  +   0.271951 * Z  +  -2.636657
  Y_new =  -0.008437 * X  +  -0.957357 * Y  +   0.288784 * Z  +  -5.863249
  Z_new =   0.286482 * X  +   0.274375 * Y  +   0.917958 * Z  +   4.797248 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.290445   -2.851148  [ DEG:    16.6413   -163.3587 ]
  Theta =  -0.290553   -2.851040  [ DEG:   -16.6475   -163.3525 ]
  Phi   =  -3.132787    0.008806  [ DEG:  -179.4955      0.5045 ]
 
# 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: T0358TS393_3                                  
REMARK     2: T0358.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358TS393_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   29   2.86    6.90  28.621
REMARK  ---------------------------------------------------------- 
MOLECULE T0358TS393_3
PFRMAT TS
TARGET T0358
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      -9.907 -16.841  14.874  1.00 25.00           C
ATOM      2  CA  THR     2      -7.336 -14.804  12.902  1.00 25.00           C
ATOM      3  CA  GLN     3      -8.706 -11.736  11.154  1.00 25.00           C
ATOM      4  CA  SER     4      -9.799  -8.811   8.983  1.00 25.00           C
ATOM      5  CA  VAL     5      -7.547  -6.882   6.656  1.00 25.00           C
ATOM      6  CA  LEU     6      -6.667  -7.326   3.000  1.00 25.00           C
ATOM      7  CA  LEU     7      -3.616  -9.021   1.563  1.00 25.00           C
ATOM      8  CA  PRO     8      -2.387 -11.850  -0.724  1.00 25.00           C
ATOM      9  CA  PRO     9      -2.882 -13.873  -3.972  1.00 25.00           C
ATOM     10  CA  GLY    10      -3.042 -13.934  -7.812  1.00 25.00           C
ATOM     11  CA  PRO    11      -0.795 -10.839  -7.542  1.00 25.00           C
ATOM     12  CA  PHE    12       1.468 -11.373  -4.558  1.00 25.00           C
ATOM     13  CA  THR    13       3.257  -8.014  -4.754  1.00 25.00           C
ATOM     14  CA  ARG    14       0.781  -6.855  -2.074  1.00 25.00           C
ATOM     15  CA  ARG    15      -1.983  -6.449  -4.693  1.00 25.00           C
ATOM     16  CA  GLN    16      -4.423  -5.295  -1.976  1.00 25.00           C
ATOM     17  CA  ALA    17      -1.847  -2.761  -0.706  1.00 25.00           C
ATOM     18  CA  GLN    18      -1.338  -1.455  -4.270  1.00 25.00           C
ATOM     19  CA  ALA    19      -5.126  -1.101  -4.708  1.00 25.00           C
ATOM     20  CA  VAL    20      -5.355   0.810  -1.397  1.00 25.00           C
ATOM     21  CA  THR    21      -2.523   3.134  -2.514  1.00 25.00           C
ATOM     22  CA  THR    22      -4.313   3.756  -5.843  1.00 25.00           C
ATOM     23  CA  THR    23      -7.559   4.557  -3.975  1.00 25.00           C
ATOM     24  CA  TYR    24      -5.678   6.997  -1.701  1.00 25.00           C
ATOM     25  CA  SER    25      -8.450   7.901   0.735  1.00 25.00           C
ATOM     26  CA  ASN    26     -11.508   5.665   0.101  1.00 25.00           C
ATOM     27  CA  ILE    27      -9.097   2.932   1.235  1.00 25.00           C
ATOM     28  CA  THR    28      -8.215   3.274   4.916  1.00 25.00           C
ATOM     29  CA  LEU    29      -8.410   3.837   8.625  1.00 25.00           C
ATOM     30  CA  GLU    30      -8.258   3.086  12.313  1.00 25.00           C
ATOM     31  CA  ASP    31     -10.738   5.957  12.609  1.00 25.00           C
ATOM     32  CA  ASP    32     -11.512   5.499  16.307  1.00 25.00           C
ATOM     33  CA  GLN    33      -9.506   6.819  19.195  1.00 25.00           C
ATOM     34  CA  GLY    34      -7.461   8.505  16.408  1.00 25.00           C
ATOM     35  CA  SER    35      -5.625   7.481  13.206  1.00 25.00           C
ATOM     36  CA  HIS    36      -3.872   5.279  10.582  1.00 25.00           C
ATOM     37  CA  PHE    37      -3.709   2.035   8.658  1.00 25.00           C
ATOM     38  CA  ARG    38      -4.175  -1.783   8.974  1.00 25.00           C
ATOM     39  CA  LEU    39      -7.610  -1.060   7.429  1.00 25.00           C
ATOM     40  CA  VAL    40     -10.936  -1.236   5.709  1.00 25.00           C
ATOM     41  CA  VAL    41     -12.551  -0.763   2.250  1.00 25.00           C
ATOM     42  CA  ARG    42     -14.168  -1.579  -1.093  1.00 25.00           C
ATOM     43  CA  ASP    43     -15.641  -0.144  -4.295  1.00 25.00           C
ATOM     44  CA  THR    44     -19.331   0.184  -4.857  1.00 25.00           C
ATOM     45  CA  GLU    45     -19.745  -2.991  -6.875  1.00 25.00           C
ATOM     46  CA  GLY    46     -19.713  -4.846  -3.523  1.00 25.00           C
ATOM     47  CA  ARG    47     -16.138  -6.072  -2.964  1.00 25.00           C
ATOM     48  CA  MET    48     -12.874  -6.467  -0.938  1.00 25.00           C
ATOM     49  CA  VAL    49      -9.855  -4.274  -0.158  1.00 25.00           C
ATOM     50  CA  TRP    50      -7.562  -2.173   2.037  1.00 25.00           C
ATOM     51  CA  ARG    51      -4.505  -3.085   4.068  1.00 25.00           C
ATOM     52  CA  ALA    52      -2.636   0.218   3.641  1.00 25.00           C
ATOM     53  CA  TRP    53      -3.098   3.934   3.059  1.00 25.00           C
ATOM     54  CA  ASN    54      -0.941   6.659   4.645  1.00 25.00           C
ATOM     55  CA  PHE    55      -0.071  10.059   6.231  1.00 25.00           C
ATOM     56  CA  GLU    56       3.439   8.532   6.526  1.00 25.00           C
ATOM     57  CA  PRO    57       5.424  10.413   3.868  1.00 25.00           C
ATOM     58  CA  ASP    58       3.118   9.658   0.888  1.00 25.00           C
ATOM     59  CA  ALA    59       3.677   6.055   1.974  1.00 25.00           C
ATOM     60  CA  GLY    60       6.799   4.121   2.992  1.00 25.00           C
ATOM     61  CA  GLU    61       4.467   1.181   3.409  1.00 25.00           C
ATOM     62  CA  GLY    62       4.799   1.327   7.221  1.00 25.00           C
ATOM     63  CA  LEU    63       1.151   0.227   7.606  1.00 25.00           C
ATOM     64  CA  ASN    64       1.750  -2.688   5.195  1.00 25.00           C
ATOM     65  CA  ARG    65       4.855  -3.726   7.183  1.00 25.00           C
ATOM     66  CA  TYR    66       2.841  -3.601  10.439  1.00 25.00           C
ATOM     67  CA  ILE    67       0.101  -5.757   8.855  1.00 25.00           C
ATOM     68  CA  ARG    68       2.730  -8.284   7.685  1.00 25.00           C
ATOM     69  CA  THR    69       4.222  -8.401  11.210  1.00 25.00           C
ATOM     70  CA  SER    70       4.561  -6.835  14.615  1.00 25.00           C
ATOM     71  CA  GLY    71       5.120 -10.281  16.088  1.00 25.00           C
ATOM     72  CA  ILE    72       3.454 -13.158  14.309  1.00 25.00           C
ATOM     73  CA  ARG    73       5.631 -15.269  16.672  1.00 25.00           C
ATOM     74  CA  THR    74       8.604 -15.265  14.247  1.00 25.00           C
ATOM     75  CA  ASP    75      11.355 -17.536  12.923  1.00 25.00           C
ATOM     76  CA  THR    76      13.816 -18.766  10.255  1.00 25.00           C
ATOM     77  CA  ALA    77      12.136 -22.184  10.147  1.00 25.00           C
ATOM     78  CA  THR    78       8.876 -24.089  10.173  1.00 25.00           C
ATOM     79  CA  ARG    79      10.427 -27.603  10.485  1.00 25.00           C
ATOM     80  CA  LEU    80      11.648 -31.148   9.885  1.00 25.00           C
ATOM     81  CA  GLU    81       8.397 -33.039   9.291  1.00 25.00           C
ATOM     82  CA  HIS    82       4.928 -33.398  10.933  1.00 25.00           C
ATOM     83  CA  HIS    83       1.204 -32.900  11.570  1.00 25.00           C
ATOM     84  CA  HIS    84       0.454 -31.378   8.185  1.00 25.00           C
ATOM     85  CA  HIS    85       0.922 -30.469   4.536  1.00 25.00           C
ATOM     86  CA  HIS    86      -0.153 -28.292   1.623  1.00 25.00           C
ATOM     87  CA  HIS    87      -3.136 -30.600   1.428  1.00 25.00           C
TER
END
