
#######################################################
#                                                     #
#                        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_4
# Molecule2: number of CA atoms   66 ( 1047),  selected   66 , name T0358.pdb
# PARAMETERS: T0358TS168_4.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    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      Y      24           -
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      S      25           #
LGA    N      26      N      26          2.513
LGA    I      27      I      27          2.962
LGA    T      28      T      28          0.221
LGA    L      29      L      29          0.781
LGA    E      30      E      30          3.744
LGA    D      31      D      31          2.706
LGA    D      32      D      32          2.940
LGA    Q      33      Q      33          2.026
LGA    G      34      G      34           #
LGA    -       -      S      35           -
LGA    S      35      H      36          2.346
LGA    H      36      F      37          3.012
LGA    F      37      R      38          1.823
LGA    R      38      L      39          1.825
LGA    L      39      V      40          2.245
LGA    V      40      V      41          2.073
LGA    V      41      R      42          1.881
LGA    R      42      D      43          2.438
LGA    -       -      T      44           -
LGA    D      43      E      45          2.232
LGA    T      44      G      46           #
LGA    E      45      -       -           -
LGA    G      46      -       -           -
LGA    R      47      -       -           -
LGA    M      48      R      47          1.699
LGA    V      49      M      48          3.496
LGA    W      50      V      49          0.786
LGA    R      51      W      50          2.302
LGA    A      52      R      51          3.269
LGA    W      53      A      52          0.412
LGA    N      54      W      53          2.539
LGA    F      55      N      54          2.114
LGA    -       -      F      55           -
LGA    -       -      E      56           -
LGA    -       -      P      57           -
LGA    -       -      D      58           -
LGA    -       -      A      59           -
LGA    E      56      G      60          3.293
LGA    P      57      E      61           -
LGA    D      58      -       -           -
LGA    A      59      -       -           -
LGA    G      60      -       -           -
LGA    E      61      -       -           -
LGA    G      62      G      62           #
LGA    L      63      L      63          1.704
LGA    N      64      -       -           -
LGA    R      65      N      64          2.786
LGA    Y      66      R      65          2.546
LGA    I      67      Y      66          1.643
LGA    R      68      I      67          2.865
LGA    T      69      R      68          2.620
LGA    S      70      T      69          2.649
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     33    2.40    30.30     33.240     1.319

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.979211 * X  +  -0.059277 * Y  +   0.193990 * Z  +  -0.445517
  Y_new =   0.200223 * X  +  -0.435696 * Y  +   0.877542 * Z  +   1.008761
  Z_new =   0.032503 * X  +   0.898140 * Y  +   0.438507 * Z  +   6.633224 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.116602   -2.024991  [ DEG:    63.9766   -116.0234 ]
  Theta =  -0.032508   -3.109084  [ DEG:    -1.8626   -178.1374 ]
  Phi   =   2.939899   -0.201694  [ DEG:   168.4438    -11.5562 ]
 
# 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_4                                  
REMARK     2: T0358.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358TS168_4.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   33   2.40   30.30  33.240
REMARK  ---------------------------------------------------------- 
MOLECULE T0358TS168_4
PFRMAT TS
TARGET T0358
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1      -9.646 -12.016  19.968  1.00 25.00           C
ATOM      2  CA  THR     2      -7.631  -9.769  17.612  1.00 25.00           C
ATOM      3  CA  GLN     3      -6.238  -7.229  15.175  1.00 25.00           C
ATOM      4  CA  SER     4      -5.996  -3.638  13.862  1.00 25.00           C
ATOM      5  CA  VAL     5      -5.429  -2.276  10.336  1.00 25.00           C
ATOM      6  CA  LEU     6      -4.836   1.516  10.758  1.00 25.00           C
ATOM      7  CA  LEU     7      -3.735   5.148  11.112  1.00 25.00           C
ATOM      8  CA  PRO     8      -3.649   6.425  14.696  1.00 25.00           C
ATOM      9  CA  PRO     9      -5.953   8.305  17.033  1.00 25.00           C
ATOM     10  CA  GLY    10      -3.734  11.319  16.276  1.00 25.00           C
ATOM     11  CA  PRO    11      -4.386  13.460  13.219  1.00 25.00           C
ATOM     12  CA  PHE    12      -5.450  10.132  11.672  1.00 25.00           C
ATOM     13  CA  THR    13      -9.069  10.216  12.988  1.00 25.00           C
ATOM     14  CA  ARG    14      -9.650   6.872  11.194  1.00 25.00           C
ATOM     15  CA  ARG    15      -9.409   9.003   8.021  1.00 25.00           C
ATOM     16  CA  GLN    16      -6.313   7.041   6.909  1.00 25.00           C
ATOM     17  CA  ALA    17      -8.155   3.740   7.520  1.00 25.00           C
ATOM     18  CA  GLN    18     -11.137   4.996   5.471  1.00 25.00           C
ATOM     19  CA  ALA    19      -8.786   6.010   2.623  1.00 25.00           C
ATOM     20  CA  VAL    20      -7.147   2.549   2.713  1.00 25.00           C
ATOM     21  CA  THR    21     -10.594   0.886   2.582  1.00 25.00           C
ATOM     22  CA  THR    22     -11.561   3.072  -0.410  1.00 25.00           C
ATOM     23  CA  THR    23      -8.304   2.125  -2.188  1.00 25.00           C
ATOM     24  CA  TYR    24      -8.994  -1.584  -1.527  1.00 25.00           C
ATOM     25  CA  SER    25      -9.917  -4.267  -4.076  1.00 25.00           C
ATOM     26  CA  ASN    26      -7.141  -6.466  -2.584  1.00 25.00           C
ATOM     27  CA  ILE    27      -4.283  -4.560  -4.218  1.00 25.00           C
ATOM     28  CA  THR    28      -4.523  -0.767  -3.945  1.00 25.00           C
ATOM     29  CA  LEU    29      -3.150   2.651  -4.772  1.00 25.00           C
ATOM     30  CA  GLU    30      -2.364   5.440  -7.173  1.00 25.00           C
ATOM     31  CA  ASP    31      -5.272   7.869  -7.122  1.00 25.00           C
ATOM     32  CA  ASP    32      -4.712  11.158  -8.880  1.00 25.00           C
ATOM     33  CA  GLN    33      -2.821  14.492  -8.597  1.00 25.00           C
ATOM     34  CA  GLY    34      -3.597  14.061  -4.863  1.00 25.00           C
ATOM     35  CA  SER    35      -1.150  11.375  -3.735  1.00 25.00           C
ATOM     36  CA  HIS    36      -1.669   8.752  -0.991  1.00 25.00           C
ATOM     37  CA  PHE    37      -2.670   5.115  -0.446  1.00 25.00           C
ATOM     38  CA  ARG    38      -0.082   2.369  -0.308  1.00 25.00           C
ATOM     39  CA  LEU    39      -3.011   0.121   0.795  1.00 25.00           C
ATOM     40  CA  VAL    40      -3.766  -3.593   1.034  1.00 25.00           C
ATOM     41  CA  VAL    41      -6.541  -5.664   2.618  1.00 25.00           C
ATOM     42  CA  ARG    42     -10.192  -6.765   2.053  1.00 25.00           C
ATOM     43  CA  ASP    43     -12.171  -8.087  -0.923  1.00 25.00           C
ATOM     44  CA  THR    44     -15.409  -9.759   0.105  1.00 25.00           C
ATOM     45  CA  GLU    45     -18.714  -8.105  -0.735  1.00 25.00           C
ATOM     46  CA  GLY    46     -19.683  -6.697   2.650  1.00 25.00           C
ATOM     47  CA  ARG    47     -16.675  -4.994   4.183  1.00 25.00           C
ATOM     48  CA  MET    48     -13.413  -3.035   3.933  1.00 25.00           C
ATOM     49  CA  VAL    49     -11.755  -1.486   6.951  1.00 25.00           C
ATOM     50  CA  TRP    50      -8.092  -1.960   5.854  1.00 25.00           C
ATOM     51  CA  ARG    51      -4.430  -1.073   5.449  1.00 25.00           C
ATOM     52  CA  ALA    52      -2.538   2.200   6.130  1.00 25.00           C
ATOM     53  CA  TRP    53      -0.695   4.939   4.156  1.00 25.00           C
ATOM     54  CA  ASN    54       2.402   6.850   3.169  1.00 25.00           C
ATOM     55  CA  PHE    55       5.192   6.439   0.576  1.00 25.00           C
ATOM     56  CA  GLU    56       6.438   3.798   2.960  1.00 25.00           C
ATOM     57  CA  PRO    57       9.476   3.156   0.794  1.00 25.00           C
ATOM     58  CA  ASP    58       9.226  -0.186  -1.041  1.00 25.00           C
ATOM     59  CA  ALA    59       5.758   0.682  -2.433  1.00 25.00           C
ATOM     60  CA  GLY    60       5.276  -3.112  -2.237  1.00 25.00           C
ATOM     61  CA  GLU    61       2.185  -2.249  -0.188  1.00 25.00           C
ATOM     62  CA  GLY    62       4.684  -0.999   2.430  1.00 25.00           C
ATOM     63  CA  LEU    63       1.800   0.029   4.730  1.00 25.00           C
ATOM     64  CA  ASN    64       0.200  -3.425   4.308  1.00 25.00           C
ATOM     65  CA  ARG    65       3.539  -5.102   5.151  1.00 25.00           C
ATOM     66  CA  TYR    66       3.876  -2.913   8.275  1.00 25.00           C
ATOM     67  CA  ILE    67       0.318  -3.843   9.342  1.00 25.00           C
ATOM     68  CA  ARG    68       1.114  -7.557   8.843  1.00 25.00           C
ATOM     69  CA  THR    69       4.293  -7.183  10.945  1.00 25.00           C
ATOM     70  CA  SER    70       5.799 -10.104   8.997  1.00 25.00           C
ATOM     71  CA  GLY    71       7.285 -11.337  12.341  1.00 25.00           C
ATOM     72  CA  ILE    72       8.352  -8.090  14.048  1.00 25.00           C
ATOM     73  CA  ARG    73      11.305  -9.946  15.611  1.00 25.00           C
ATOM     74  CA  THR    74      11.380  -7.146  18.184  1.00 25.00           C
ATOM     75  CA  ASP    75      14.576  -7.959  20.078  1.00 25.00           C
ATOM     76  CA  THR    76      17.720  -6.223  18.919  1.00 25.00           C
ATOM     77  CA  ALA    77      19.766  -4.720  16.144  1.00 25.00           C
ATOM     78  CA  THR    78      18.833  -1.162  17.291  1.00 25.00           C
ATOM     79  CA  ARG    79      20.869   2.000  17.341  1.00 25.00           C
ATOM     80  CA  LEU    80      21.985   4.096  14.374  1.00 25.00           C
ATOM     81  CA  GLU    81      21.290   7.838  14.687  1.00 25.00           C
ATOM     82  CA  HIS    82      18.221   8.067  16.806  1.00 25.00           C
ATOM     83  CA  HIS    83      18.723  11.774  17.344  1.00 25.00           C
ATOM     84  CA  HIS    84      16.713  11.855  20.546  1.00 25.00           C
ATOM     85  CA  HIS    85      14.796  10.587  23.616  1.00 25.00           C
ATOM     86  CA  HIS    86      11.105  10.575  24.490  1.00 25.00           C
ATOM     87  CA  HIS    87      10.560  12.356  21.243  1.00 25.00           C
TER
END
