
#######################################################
#                                                     #
#                        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 T0306TS168_4
# Molecule2: number of CA atoms   95 (  694),  selected   95 , name T0306.pdb
# PARAMETERS: T0306TS168_4.T0306.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    K       2      -       -           -
LGA    L       3      -       -           -
LGA    A       4      -       -           -
LGA    V       5      -       -           -
LGA    V       6      -       -           -
LGA    T       7      -       -           -
LGA    G       8      -       -           -
LGA    Q       9      -       -           -
LGA    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      M       1           #
LGA    D      22      K       2          5.222
LGA    K      23      L       3          1.611
LGA    L      24      A       4          1.698
LGA    L      25      V       5          1.777
LGA    M      26      V       6          2.729
LGA    V      27      T       7          3.357
LGA    E      28      G       8          2.365
LGA    M      29      Q       9          1.800
LGA    I      30      I      10          1.381
LGA    D      31      V      11          2.974
LGA    P      32      C      12          4.946
LGA    Q      33      -       -           -
LGA    G      34      -       -           -
LGA    N      35      -       -           -
LGA    P      36      T      13          2.630
LGA    D      37      V      14          4.529
LGA    G      38      R      15           #
LGA    Q      39      H      16           -
LGA    -       -      H      17           -
LGA    -       -      G      18           -
LGA    -       -      L      19           -
LGA    -       -      A      20           -
LGA    -       -      H      21           -
LGA    -       -      D      22           -
LGA    C      40      K      23          2.058
LGA    A      41      L      24          0.956
LGA    V      42      L      25          1.717
LGA    A      43      M      26          1.680
LGA    I      44      V      27          2.122
LGA    D      45      E      28          2.123
LGA    N      46      M      29          4.182
LGA    I      47      I      30           -
LGA    G      48      D      31           -
LGA    A      49      P      32           -
LGA    -       -      Q      33           -
LGA    -       -      G      34           -
LGA    -       -      N      35           -
LGA    -       -      P      36           -
LGA    G      50      D      37           #
LGA    T      51      G      38          1.609
LGA    G      52      Q      39          4.749
LGA    E      53      C      40          1.669
LGA    W      54      A      41          1.490
LGA    V      55      V      42          3.679
LGA    L      56      A      43          3.836
LGA    L      57      I      44          3.672
LGA    V      58      D      45          3.639
LGA    S      59      N      46           #
LGA    G      60      I      47          0.846
LGA    S      61      G      48          1.794
LGA    S      62      A      49          2.464
LGA    A      63      G      50          1.539
LGA    R      64      -       -           -
LGA    Q      65      -       -           -
LGA    A      66      -       -           -
LGA    H      67      -       -           -
LGA    K      68      -       -           -
LGA    S      69      -       -           -
LGA    E      70      -       -           -
LGA    T      71      -       -           -
LGA    S      72      -       -           -
LGA    P      73      T      51           #
LGA    V      74      G      52          4.107
LGA    D      75      -       -           -
LGA    L      76      E      53          2.837
LGA    C      77      W      54          1.953
LGA    V      78      V      55          3.993
LGA    I      79      -       -           -
LGA    G      80      L      56          3.620
LGA    I      81      L      57          1.744
LGA    V      82      V      58          4.102
LGA    D      83      S      59          3.006
LGA    E      84      -       -           -
LGA    V      85      G      60          2.370
LGA    V      86      S      61          3.909
LGA    S      87      S      62          3.912
LGA    G      88      A      63           #
LGA    -       -      R      64           -
LGA    -       -      Q      65           -
LGA    -       -      A      66           -
LGA    -       -      H      67           -
LGA    -       -      K      68           -
LGA    -       -      S      69           -
LGA    -       -      E      70           -
LGA    -       -      T      71           -
LGA    -       -      S      72           -
LGA    G      89      P      73          4.393
LGA    Q      90      V      74          3.939
LGA    V      91      D      75          2.788
LGA    I      92      L      76          1.563
LGA    F      93      C      77          1.268
LGA    -       -      V      78           -
LGA    H      94      I      79          3.370
LGA    K      95      G      80           -
LGA    -       -      I      81           -
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           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   95   95    5.0     49    3.00    10.20     29.623     1.579

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.924011 * X  +  -0.360220 * Y  +  -0.128238 * Z  +  39.341557
  Y_new =   0.113084 * X  +   0.062932 * Y  +  -0.991590 * Z  +  24.753340
  Z_new =   0.365261 * X  +  -0.930742 * Y  +  -0.017415 * Z  +  66.795349 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.589505    1.552088  [ DEG:   -91.0719     88.9281 ]
  Theta =  -0.373913   -2.767680  [ DEG:   -21.4236   -158.5764 ]
  Phi   =   3.019815   -0.121778  [ DEG:   173.0226     -6.9774 ]
 
# 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: T0306TS168_4                                  
REMARK     2: T0306.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0306TS168_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   49   3.00   10.20  29.623
REMARK  ---------------------------------------------------------- 
MOLECULE T0306TS168_4
PFRMAT TS
TARGET T0306
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1      41.271  20.108  81.634  1.00 25.00           C
ATOM      2  CA  LYS     2      39.185  21.643  78.865  1.00 25.00           C
ATOM      3  CA  LEU     3      38.355  23.828  75.836  1.00 25.00           C
ATOM      4  CA  ALA     4      34.907  23.983  74.392  1.00 25.00           C
ATOM      5  CA  VAL     5      33.356  26.417  71.992  1.00 25.00           C
ATOM      6  CA  VAL     6      33.373  26.207  68.211  1.00 25.00           C
ATOM      7  CA  THR     7      30.842  25.358  65.505  1.00 25.00           C
ATOM      8  CA  GLY     8      32.324  23.802  62.354  1.00 25.00           C
ATOM      9  CA  GLN     9      34.004  20.812  60.745  1.00 25.00           C
ATOM     10  CA  ILE    10      37.087  20.696  62.969  1.00 25.00           C
ATOM     11  CA  VAL    11      40.373  22.455  63.519  1.00 25.00           C
ATOM     12  CA  CYS    12      41.355  26.083  63.063  1.00 25.00           C
ATOM     13  CA  THR    13      44.634  27.909  63.475  1.00 25.00           C
ATOM     14  CA  VAL    14      48.447  28.155  63.844  1.00 25.00           C
ATOM     15  CA  ARG    15      52.090  29.426  63.779  1.00 25.00           C
ATOM     16  CA  HIS    16      53.108  32.613  65.671  1.00 25.00           C
ATOM     17  CA  HIS    17      56.186  32.634  63.387  1.00 25.00           C
ATOM     18  CA  GLY    18      56.421  35.135  60.558  1.00 25.00           C
ATOM     19  CA  LEU    19      52.660  34.765  60.077  1.00 25.00           C
ATOM     20  CA  ALA    20      50.903  37.856  58.658  1.00 25.00           C
ATOM     21  CA  HIS    21      48.828  38.957  61.643  1.00 25.00           C
ATOM     22  CA  ASP    22      48.665  35.454  63.210  1.00 25.00           C
ATOM     23  CA  LYS    23      47.198  32.799  65.527  1.00 25.00           C
ATOM     24  CA  LEU    24      45.458  30.391  67.898  1.00 25.00           C
ATOM     25  CA  LEU    25      45.689  26.769  68.868  1.00 25.00           C
ATOM     26  CA  MET    26      42.611  24.871  67.816  1.00 25.00           C
ATOM     27  CA  VAL    27      41.998  21.335  69.082  1.00 25.00           C
ATOM     28  CA  GLU    28      39.454  18.596  69.790  1.00 25.00           C
ATOM     29  CA  MET    29      36.302  19.672  71.526  1.00 25.00           C
ATOM     30  CA  ILE    30      32.475  19.535  71.892  1.00 25.00           C
ATOM     31  CA  ASP    31      29.477  18.113  73.803  1.00 25.00           C
ATOM     32  CA  PRO    32      28.258  14.552  74.598  1.00 25.00           C
ATOM     33  CA  GLN    33      29.138  11.424  76.522  1.00 25.00           C
ATOM     34  CA  GLY    34      25.655  10.321  75.276  1.00 25.00           C
ATOM     35  CA  ASN    35      26.155  10.357  71.472  1.00 25.00           C
ATOM     36  CA  PRO    36      23.712  13.191  71.275  1.00 25.00           C
ATOM     37  CA  ASP    37      23.003  15.469  68.257  1.00 25.00           C
ATOM     38  CA  GLY    38      26.561  14.802  67.095  1.00 25.00           C
ATOM     39  CA  GLN    39      28.098  18.231  66.503  1.00 25.00           C
ATOM     40  CA  CYS    40      31.841  18.260  66.357  1.00 25.00           C
ATOM     41  CA  ALA    41      33.920  21.341  67.076  1.00 25.00           C
ATOM     42  CA  VAL    42      37.425  22.787  67.626  1.00 25.00           C
ATOM     43  CA  ALA    43      38.522  24.536  70.842  1.00 25.00           C
ATOM     44  CA  ILE    44      41.654  25.859  72.672  1.00 25.00           C
ATOM     45  CA  ASP    45      42.736  29.467  72.091  1.00 25.00           C
ATOM     46  CA  ASN    46      41.133  32.416  70.294  1.00 25.00           C
ATOM     47  CA  ILE    47      39.721  35.925  70.355  1.00 25.00           C
ATOM     48  CA  GLY    48      37.834  35.455  73.641  1.00 25.00           C
ATOM     49  CA  ALA    49      41.252  34.621  75.046  1.00 25.00           C
ATOM     50  CA  GLY    50      42.555  34.634  78.638  1.00 25.00           C
ATOM     51  CA  THR    51      44.827  31.524  78.637  1.00 25.00           C
ATOM     52  CA  GLY    52      41.835  29.525  79.975  1.00 25.00           C
ATOM     53  CA  GLU    53      40.086  29.681  76.590  1.00 25.00           C
ATOM     54  CA  TRP    54      37.906  29.986  73.439  1.00 25.00           C
ATOM     55  CA  VAL    55      37.121  29.284  69.783  1.00 25.00           C
ATOM     56  CA  LEU    56      38.902  28.039  66.654  1.00 25.00           C
ATOM     57  CA  LEU    57      36.643  26.360  64.137  1.00 25.00           C
ATOM     58  CA  VAL    58      36.861  25.996  60.398  1.00 25.00           C
ATOM     59  CA  SER    59      39.402  23.774  58.678  1.00 25.00           C
ATOM     60  CA  GLY    60      37.281  21.536  56.507  1.00 25.00           C
ATOM     61  CA  SER    61      38.304  17.933  57.374  1.00 25.00           C
ATOM     62  CA  SER    62      41.495  19.212  59.082  1.00 25.00           C
ATOM     63  CA  ALA    63      41.744  17.727  62.603  1.00 25.00           C
ATOM     64  CA  ARG    64      40.157  14.469  61.367  1.00 25.00           C
ATOM     65  CA  GLN    65      42.644  14.330  58.459  1.00 25.00           C
ATOM     66  CA  ALA    66      45.552  14.883  60.888  1.00 25.00           C
ATOM     67  CA  HIS    67      44.521  12.754  63.867  1.00 25.00           C
ATOM     68  CA  LYS    68      44.412   8.938  63.531  1.00 25.00           C
ATOM     69  CA  SER    69      46.528   9.109  60.368  1.00 25.00           C
ATOM     70  CA  GLU    70      49.905   8.455  61.925  1.00 25.00           C
ATOM     71  CA  THR    71      49.428  10.098  65.379  1.00 25.00           C
ATOM     72  CA  SER    72      49.872  10.725  69.098  1.00 25.00           C
ATOM     73  CA  PRO    73      46.550  12.220  70.206  1.00 25.00           C
ATOM     74  CA  VAL    74      46.089  16.036  69.921  1.00 25.00           C
ATOM     75  CA  ASP    75      48.977  18.439  69.279  1.00 25.00           C
ATOM     76  CA  LEU    76      46.748  20.509  67.024  1.00 25.00           C
ATOM     77  CA  CYS    77      46.337  23.270  64.461  1.00 25.00           C
ATOM     78  CA  VAL    78      44.887  23.099  60.962  1.00 25.00           C
ATOM     79  CA  ILE    79      43.922  25.936  58.654  1.00 25.00           C
ATOM     80  CA  GLY    80      41.423  28.811  58.823  1.00 25.00           C
ATOM     81  CA  ILE    81      40.395  30.930  61.775  1.00 25.00           C
ATOM     82  CA  VAL    82      40.695  32.636  65.216  1.00 25.00           C
ATOM     83  CA  ASP    83      37.317  33.649  66.606  1.00 25.00           C
ATOM     84  CA  GLU    84      34.382  35.084  68.626  1.00 25.00           C
ATOM     85  CA  VAL    85      33.014  35.719  65.090  1.00 25.00           C
ATOM     86  CA  VAL    86      31.075  34.808  61.986  1.00 25.00           C
ATOM     87  CA  SER    87      28.787  37.812  61.337  1.00 25.00           C
ATOM     88  CA  GLY    88      27.364  37.114  64.759  1.00 25.00           C
ATOM     89  CA  GLY    89      25.124  34.958  66.920  1.00 25.00           C
ATOM     90  CA  GLN    90      28.278  33.785  68.728  1.00 25.00           C
ATOM     91  CA  VAL    91      31.163  31.260  68.821  1.00 25.00           C
ATOM     92  CA  ILE    92      33.223  30.552  65.672  1.00 25.00           C
ATOM     93  CA  PHE    93      35.027  30.790  62.327  1.00 25.00           C
ATOM     94  CA  HIS    94      36.050  30.839  58.647  1.00 25.00           C
ATOM     95  CA  LYS    95      34.051  30.941  55.366  1.00 25.00           C
TER
END
