
#######################################################
#                                                     #
#                        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   95 (   95),  selected   95 , name T0306TS393_4
# Molecule2: number of CA atoms   95 (  694),  selected   95 , name T0306.pdb
# PARAMETERS: T0306TS393_4.T0306.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      M       1           -
LGA    K       2      K       2           -
LGA    L       3      L       3           -
LGA    A       4      A       4           -
LGA    V       5      V       5           -
LGA    V       6      V       6           -
LGA    T       7      T       7           -
LGA    G       8      G       8           -
LGA    Q       9      Q       9           #
LGA    I      10      I      10           -
LGA    -       -      V      11           -
LGA    -       -      C      12           -
LGA    -       -      T      13           -
LGA    -       -      V      14           -
LGA    -       -      R      15           -
LGA    -       -      H      16           -
LGA    -       -      H      17           -
LGA    -       -      G      18           -
LGA    -       -      L      19           -
LGA    -       -      A      20           -
LGA    -       -      H      21           -
LGA    -       -      D      22           -
LGA    -       -      K      23           -
LGA    V      11      L      24          3.399
LGA    C      12      L      25          1.707
LGA    T      13      M      26          2.392
LGA    V      14      V      27          1.363
LGA    R      15      E      28          2.150
LGA    H      16      M      29          4.109
LGA    H      17      I      30          3.651
LGA    -       -      D      31           -
LGA    -       -      P      32           -
LGA    -       -      Q      33           -
LGA    -       -      G      34           -
LGA    -       -      N      35           -
LGA    G      18      P      36          3.589
LGA    L      19      D      37           #
LGA    A      20      G      38           #
LGA    H      21      Q      39           -
LGA    D      22      -       -           -
LGA    K      23      -       -           -
LGA    L      24      C      40           #
LGA    -       -      A      41           -
LGA    L      25      V      42           #
LGA    M      26      A      43           #
LGA    V      27      I      44           #
LGA    E      28      D      45          3.243
LGA    M      29      N      46          3.715
LGA    I      30      -       -           -
LGA    D      31      -       -           -
LGA    P      32      -       -           -
LGA    Q      33      -       -           -
LGA    G      34      -       -           -
LGA    N      35      -       -           -
LGA    P      36      -       -           -
LGA    D      37      -       -           -
LGA    G      38      -       -           -
LGA    Q      39      -       -           -
LGA    C      40      -       -           -
LGA    A      41      -       -           -
LGA    V      42      I      47          0.982
LGA    A      43      G      48          1.576
LGA    I      44      A      49          3.176
LGA    D      45      G      50          3.429
LGA    N      46      T      51          3.014
LGA    I      47      G      52          3.383
LGA    G      48      -       -           -
LGA    A      49      -       -           -
LGA    G      50      -       -           -
LGA    T      51      -       -           -
LGA    G      52      -       -           -
LGA    E      53      -       -           -
LGA    W      54      -       -           -
LGA    V      55      -       -           -
LGA    L      56      E      53          4.735
LGA    L      57      W      54           #
LGA    V      58      V      55           #
LGA    S      59      -       -           -
LGA    G      60      L      56          4.432
LGA    S      61      -       -           -
LGA    S      62      -       -           -
LGA    A      63      L      57          4.947
LGA    R      64      V      58          0.758
LGA    -       -      S      59           -
LGA    -       -      G      60           -
LGA    -       -      S      61           -
LGA    Q      65      S      62          2.646
LGA    A      66      A      63          0.739
LGA    H      67      R      64          0.698
LGA    K      68      Q      65          3.084
LGA    S      69      A      66           -
LGA    E      70      H      67           -
LGA    -       -      K      68           -
LGA    -       -      S      69           -
LGA    -       -      E      70           -
LGA    -       -      T      71           -
LGA    T      71      S      72           #
LGA    S      72      P      73          2.283
LGA    P      73      V      74          2.468
LGA    V      74      D      75           #
LGA    D      75      L      76          2.364
LGA    L      76      C      77          3.594
LGA    C      77      V      78          4.829
LGA    V      78      I      79           #
LGA    I      79      G      80          4.025
LGA    G      80      I      81          1.705
LGA    I      81      V      82          2.686
LGA    V      82      -       -           -
LGA    D      83      -       -           -
LGA    E      84      -       -           -
LGA    V      85      -       -           -
LGA    V      86      -       -           -
LGA    S      87      -       -           -
LGA    G      88      -       -           -
LGA    G      89      -       -           -
LGA    Q      90      -       -           -
LGA    V      91      -       -           -
LGA    I      92      -       -           -
LGA    F      93      -       -           -
LGA    H      94      -       -           -
LGA    K      95      D      83          3.242
LGA    -       -      E      84           -
LGA    -       -      V      85           -
LGA    -       -      V      86           -
LGA    -       -      S      87           -
LGA    -       -      G      88           -
LGA    -       -      G      89           -
LGA    -       -      Q      90           -
LGA    -       -      V      91           -
LGA    -       -      I      92           -
LGA    -       -      F      93           -
LGA    -       -      H      94           -
LGA    -       -      K      95           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   95   95    5.0     33    3.09     6.06     21.434     1.035

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.718542 * X  +  -0.571788 * Y  +  -0.395924 * Z  +  39.483418
  Y_new =  -0.438496 * X  +   0.814331 * Y  +  -0.380244 * Z  +  22.924490
  Z_new =   0.539833 * X  +  -0.099611 * Y  +  -0.835858 * Z  +  60.883854 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.022980    0.118612  [ DEG:  -173.2040      6.7960 ]
  Theta =  -0.570238   -2.571354  [ DEG:   -32.6722   -147.3278 ]
  Phi   =  -2.593665    0.547928  [ DEG:  -148.6060     31.3940 ]
 
# 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: T0306TS393_4                                  
REMARK     2: T0306.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0306TS393_4.T0306.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   95   95   5.0   33   3.09    6.06  21.434
REMARK  ---------------------------------------------------------- 
MOLECULE T0306TS393_4
PFRMAT TS
TARGET T0306
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1      44.833  26.865  45.624  1.00 25.00           C
ATOM      2  CA  LYS     2      42.754  25.828  48.686  1.00 25.00           C
ATOM      3  CA  LEU     3      42.498  24.608  52.230  1.00 25.00           C
ATOM      4  CA  ALA     4      42.921  21.076  53.471  1.00 25.00           C
ATOM      5  CA  VAL     5      40.503  18.265  54.331  1.00 25.00           C
ATOM      6  CA  VAL     6      38.866  15.923  56.844  1.00 25.00           C
ATOM      7  CA  THR     7      38.080  14.733  60.318  1.00 25.00           C
ATOM      8  CA  GLY     8      35.368  13.397  62.696  1.00 25.00           C
ATOM      9  CA  GLN     9      34.967  16.028  65.451  1.00 25.00           C
ATOM     10  CA  ILE    10      34.175  18.471  62.585  1.00 25.00           C
ATOM     11  CA  VAL    11      35.182  21.255  64.929  1.00 25.00           C
ATOM     12  CA  CYS    12      37.617  22.612  67.597  1.00 25.00           C
ATOM     13  CA  THR    13      40.539  23.408  69.952  1.00 25.00           C
ATOM     14  CA  VAL    14      41.630  26.979  70.276  1.00 25.00           C
ATOM     15  CA  ARG    15      44.359  29.462  71.364  1.00 25.00           C
ATOM     16  CA  HIS    16      46.624  29.067  74.392  1.00 25.00           C
ATOM     17  CA  HIS    17      48.979  32.029  73.996  1.00 25.00           C
ATOM     18  CA  GLY    18      52.573  32.302  72.973  1.00 25.00           C
ATOM     19  CA  LEU    19      52.231  29.307  70.684  1.00 25.00           C
ATOM     20  CA  ALA    20      52.709  26.397  73.129  1.00 25.00           C
ATOM     21  CA  HIS    21      51.295  23.740  75.485  1.00 25.00           C
ATOM     22  CA  ASP    22      48.053  23.524  73.398  1.00 25.00           C
ATOM     23  CA  LYS    23      47.667  23.084  69.631  1.00 25.00           C
ATOM     24  CA  LEU    24      45.235  24.734  67.212  1.00 25.00           C
ATOM     25  CA  LEU    25      42.215  24.199  64.999  1.00 25.00           C
ATOM     26  CA  MET    26      39.285  24.311  62.552  1.00 25.00           C
ATOM     27  CA  VAL    27      36.256  24.705  60.309  1.00 25.00           C
ATOM     28  CA  GLU    28      33.421  22.310  59.403  1.00 25.00           C
ATOM     29  CA  MET    29      33.621  18.927  57.573  1.00 25.00           C
ATOM     30  CA  ILE    30      33.158  19.222  53.773  1.00 25.00           C
ATOM     31  CA  ASP    31      29.646  18.528  52.457  1.00 25.00           C
ATOM     32  CA  PRO    32      27.850  15.258  51.535  1.00 25.00           C
ATOM     33  CA  GLN    33      24.341  16.153  52.702  1.00 25.00           C
ATOM     34  CA  GLY    34      22.745  17.262  49.423  1.00 25.00           C
ATOM     35  CA  ASN    35      24.314  20.694  49.563  1.00 25.00           C
ATOM     36  CA  PRO    36      25.473  20.079  46.037  1.00 25.00           C
ATOM     37  CA  ASP    37      29.009  21.393  46.398  1.00 25.00           C
ATOM     38  CA  GLY    38      31.446  24.077  47.438  1.00 25.00           C
ATOM     39  CA  GLN    39      33.299  21.185  49.165  1.00 25.00           C
ATOM     40  CA  CYS    40      36.124  22.814  51.188  1.00 25.00           C
ATOM     41  CA  ALA    41      36.653  24.920  54.312  1.00 25.00           C
ATOM     42  CA  VAL    42      37.629  21.872  56.421  1.00 25.00           C
ATOM     43  CA  ALA    43      38.133  20.091  59.752  1.00 25.00           C
ATOM     44  CA  ILE    44      38.816  19.248  63.368  1.00 25.00           C
ATOM     45  CA  ASP    45      41.218  19.344  66.379  1.00 25.00           C
ATOM     46  CA  ASN    46      44.948  19.902  65.936  1.00 25.00           C
ATOM     47  CA  ILE    47      45.291  16.423  67.443  1.00 25.00           C
ATOM     48  CA  GLY    48      44.486  16.608  71.209  1.00 25.00           C
ATOM     49  CA  ALA    49      40.913  15.503  70.479  1.00 25.00           C
ATOM     50  CA  GLY    50      37.685  14.426  72.141  1.00 25.00           C
ATOM     51  CA  THR    51      36.595  11.238  70.406  1.00 25.00           C
ATOM     52  CA  GLY    52      39.579  10.691  68.131  1.00 25.00           C
ATOM     53  CA  GLU    53      39.988  13.710  65.891  1.00 25.00           C
ATOM     54  CA  TRP    54      42.329  15.304  63.337  1.00 25.00           C
ATOM     55  CA  VAL    55      42.378  17.386  60.186  1.00 25.00           C
ATOM     56  CA  LEU    56      43.274  20.951  61.340  1.00 25.00           C
ATOM     57  CA  LEU    57      42.170  22.809  58.227  1.00 25.00           C
ATOM     58  CA  VAL    58      41.010  26.186  56.805  1.00 25.00           C
ATOM     59  CA  SER    59      40.389  29.338  54.695  1.00 25.00           C
ATOM     60  CA  GLY    60      42.542  31.049  57.275  1.00 25.00           C
ATOM     61  CA  SER    61      39.922  33.836  57.484  1.00 25.00           C
ATOM     62  CA  SER    62      36.446  32.463  56.980  1.00 25.00           C
ATOM     63  CA  ALA    63      36.409  30.745  60.402  1.00 25.00           C
ATOM     64  CA  ARG    64      37.583  33.986  62.070  1.00 25.00           C
ATOM     65  CA  GLN    65      34.825  35.940  60.269  1.00 25.00           C
ATOM     66  CA  ALA    66      32.222  33.381  61.429  1.00 25.00           C
ATOM     67  CA  HIS    67      28.599  33.717  60.382  1.00 25.00           C
ATOM     68  CA  LYS    68      29.839  36.984  58.839  1.00 25.00           C
ATOM     69  CA  SER    69      27.925  39.585  60.908  1.00 25.00           C
ATOM     70  CA  GLU    70      29.505  38.846  64.317  1.00 25.00           C
ATOM     71  CA  THR    71      27.903  35.678  65.696  1.00 25.00           C
ATOM     72  CA  SER    72      25.673  32.652  65.017  1.00 25.00           C
ATOM     73  CA  PRO    73      26.768  29.572  67.072  1.00 25.00           C
ATOM     74  CA  VAL    74      29.653  27.738  65.368  1.00 25.00           C
ATOM     75  CA  ASP    75      32.691  29.759  66.506  1.00 25.00           C
ATOM     76  CA  LEU    76      34.795  26.877  65.190  1.00 25.00           C
ATOM     77  CA  CYS    77      38.294  27.651  66.465  1.00 25.00           C
ATOM     78  CA  VAL    78      40.664  28.948  63.831  1.00 25.00           C
ATOM     79  CA  ILE    79      43.165  27.552  61.394  1.00 25.00           C
ATOM     80  CA  GLY    80      45.779  26.287  58.863  1.00 25.00           C
ATOM     81  CA  ILE    81      48.515  26.670  61.416  1.00 25.00           C
ATOM     82  CA  VAL    82      47.627  23.244  62.798  1.00 25.00           C
ATOM     83  CA  ASP    83      49.416  20.289  61.170  1.00 25.00           C
ATOM     84  CA  GLU    84      47.504  17.291  62.315  1.00 25.00           C
ATOM     85  CA  VAL    85      46.376  14.357  60.220  1.00 25.00           C
ATOM     86  CA  VAL    86      49.092  13.486  57.737  1.00 25.00           C
ATOM     87  CA  SER    87      50.906  10.638  55.919  1.00 25.00           C
ATOM     88  CA  GLY    88      48.033   8.682  54.399  1.00 25.00           C
ATOM     89  CA  GLY    89      44.778   9.228  52.508  1.00 25.00           C
ATOM     90  CA  GLN    90      43.966  11.576  55.316  1.00 25.00           C
ATOM     91  CA  VAL    91      44.542  15.284  55.462  1.00 25.00           C
ATOM     92  CA  ILE    92      45.853  18.593  56.798  1.00 25.00           C
ATOM     93  CA  PHE    93      47.653  21.941  56.767  1.00 25.00           C
ATOM     94  CA  HIS    94      50.778  24.018  57.450  1.00 25.00           C
ATOM     95  CA  LYS    95      53.334  23.352  54.783  1.00 25.00           C
TER
END
