
#######################################################
#                                                     #
#                        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_5
# Molecule2: number of CA atoms   95 (  694),  selected   95 , name T0306.pdb
# PARAMETERS: T0306TS393_5.T0306.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      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          2.216
LGA    G       8      G       8          4.836
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      -       -           -
LGA    D      22      -       -           -
LGA    K      23      -       -           -
LGA    L      24      -       -           -
LGA    L      25      -       -           -
LGA    M      26      -       -           -
LGA    V      27      -       -           -
LGA    E      28      -       -           -
LGA    M      29      Q       9          4.426
LGA    I      30      I      10          3.393
LGA    D      31      V      11          0.691
LGA    P      32      C      12          4.849
LGA    Q      33      T      13          2.831
LGA    G      34      V      14          5.069
LGA    N      35      R      15           -
LGA    P      36      H      16           -
LGA    D      37      H      17           -
LGA    G      38      G      18           -
LGA    Q      39      L      19           -
LGA    -       -      A      20           -
LGA    -       -      H      21           -
LGA    C      40      D      22          4.489
LGA    A      41      K      23          1.620
LGA    V      42      L      24          3.633
LGA    A      43      L      25          1.994
LGA    -       -      M      26           -
LGA    I      44      V      27          2.304
LGA    D      45      E      28          3.763
LGA    N      46      M      29           #
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    G      50      P      36          0.771
LGA    T      51      D      37          2.668
LGA    -       -      G      38           -
LGA    G      52      Q      39          2.164
LGA    E      53      C      40           #
LGA    W      54      A      41           -
LGA    V      55      V      42           -
LGA    L      56      A      43           -
LGA    L      57      I      44           #
LGA    V      58      D      45          1.362
LGA    S      59      N      46          2.356
LGA    G      60      I      47          4.718
LGA    S      61      G      48           -
LGA    S      62      A      49           -
LGA    -       -      G      50           -
LGA    -       -      T      51           -
LGA    -       -      G      52           -
LGA    -       -      E      53           -
LGA    -       -      W      54           -
LGA    -       -      V      55           -
LGA    -       -      L      56           -
LGA    -       -      L      57           -
LGA    -       -      V      58           -
LGA    -       -      S      59           -
LGA    -       -      G      60           -
LGA    -       -      S      61           -
LGA    -       -      S      62           -
LGA    -       -      A      63           -
LGA    -       -      R      64           -
LGA    -       -      Q      65           -
LGA    A      63      A      66           #
LGA    R      64      H      67          1.418
LGA    Q      65      K      68          1.680
LGA    A      66      -       -           -
LGA    H      67      -       -           -
LGA    K      68      S      69          2.252
LGA    S      69      E      70          2.206
LGA    E      70      -       -           -
LGA    T      71      T      71          1.221
LGA    S      72      S      72          3.004
LGA    P      73      P      73          3.953
LGA    V      74      V      74          2.078
LGA    D      75      D      75          1.767
LGA    L      76      L      76          1.068
LGA    C      77      C      77          2.102
LGA    V      78      V      78          2.498
LGA    I      79      I      79          2.395
LGA    G      80      G      80          2.594
LGA    I      81      I      81          2.032
LGA    V      82      V      82          1.969
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          4.243
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     37    2.93    40.54     24.127     1.222

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.405745 * X  +  -0.758285 * Y  +  -0.510270 * Z  +  38.315781
  Y_new =  -0.408783 * X  +  -0.649896 * Y  +   0.640728 * Z  +  25.276743
  Z_new =  -0.817476 * X  +  -0.051382 * Y  +  -0.573666 * Z  +  65.138062 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.052263    0.089330  [ DEG:  -174.8818      5.1182 ]
  Theta =   0.957015    2.184577  [ DEG:    54.8329    125.1671 ]
  Phi   =  -0.789128    2.352464  [ DEG:   -45.2137    134.7863 ]
 
# 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_5                                  
REMARK     2: T0306.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0306TS393_5.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   37   2.93   40.54  24.127
REMARK  ---------------------------------------------------------- 
MOLECULE T0306TS393_5
PFRMAT TS
TARGET T0306
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1      38.109  12.713  55.275  1.00 25.00           C
ATOM      2  CA  LYS     2      38.480  15.500  57.838  1.00 25.00           C
ATOM      3  CA  LEU     3      40.071  17.761  60.471  1.00 25.00           C
ATOM      4  CA  ALA     4      39.006  17.505  64.110  1.00 25.00           C
ATOM      5  CA  VAL     5      39.729  17.226  67.787  1.00 25.00           C
ATOM      6  CA  VAL     6      39.999  18.046  71.452  1.00 25.00           C
ATOM      7  CA  THR     7      41.679  21.209  72.741  1.00 25.00           C
ATOM      8  CA  GLY     8      38.264  22.466  73.856  1.00 25.00           C
ATOM      9  CA  GLN     9      34.976  24.251  74.178  1.00 25.00           C
ATOM     10  CA  ILE    10      36.235  27.589  72.744  1.00 25.00           C
ATOM     11  CA  VAL    11      35.837  29.755  69.610  1.00 25.00           C
ATOM     12  CA  CYS    12      38.238  32.078  67.702  1.00 25.00           C
ATOM     13  CA  THR    13      41.688  33.463  68.366  1.00 25.00           C
ATOM     14  CA  VAL    14      41.481  35.022  64.842  1.00 25.00           C
ATOM     15  CA  ARG    15      41.930  37.550  61.991  1.00 25.00           C
ATOM     16  CA  HIS    16      44.551  39.276  64.040  1.00 25.00           C
ATOM     17  CA  HIS    17      43.250  42.590  62.585  1.00 25.00           C
ATOM     18  CA  GLY    18      45.784  43.951  60.096  1.00 25.00           C
ATOM     19  CA  LEU    19      46.544  40.275  59.479  1.00 25.00           C
ATOM     20  CA  ALA    20      45.004  39.142  56.257  1.00 25.00           C
ATOM     21  CA  HIS    21      47.363  36.185  56.113  1.00 25.00           C
ATOM     22  CA  ASP    22      48.298  35.061  59.655  1.00 25.00           C
ATOM     23  CA  LYS    23      47.266  32.789  62.549  1.00 25.00           C
ATOM     24  CA  LEU    24      44.115  30.616  63.058  1.00 25.00           C
ATOM     25  CA  LEU    25      41.889  28.930  65.653  1.00 25.00           C
ATOM     26  CA  MET    26      38.464  27.408  64.990  1.00 25.00           C
ATOM     27  CA  VAL    27      34.974  26.350  65.996  1.00 25.00           C
ATOM     28  CA  GLU    28      33.818  24.795  69.286  1.00 25.00           C
ATOM     29  CA  MET    29      33.844  21.122  70.219  1.00 25.00           C
ATOM     30  CA  ILE    30      33.359  17.525  69.026  1.00 25.00           C
ATOM     31  CA  ASP    31      30.759  16.059  71.461  1.00 25.00           C
ATOM     32  CA  PRO    32      28.438  14.225  73.909  1.00 25.00           C
ATOM     33  CA  GLN    33      24.894  13.965  72.526  1.00 25.00           C
ATOM     34  CA  GLY    34      21.870  13.286  70.252  1.00 25.00           C
ATOM     35  CA  ASN    35      24.269  10.881  68.539  1.00 25.00           C
ATOM     36  CA  PRO    36      27.276   9.587  70.491  1.00 25.00           C
ATOM     37  CA  ASP    37      29.131   9.433  67.206  1.00 25.00           C
ATOM     38  CA  GLY    38      27.932  12.084  64.818  1.00 25.00           C
ATOM     39  CA  GLN    39      31.186  13.824  65.686  1.00 25.00           C
ATOM     40  CA  CYS    40      32.316  16.786  63.643  1.00 25.00           C
ATOM     41  CA  ALA    41      33.127  20.527  63.993  1.00 25.00           C
ATOM     42  CA  VAL    42      36.328  21.497  65.876  1.00 25.00           C
ATOM     43  CA  ALA    43      38.703  22.086  68.789  1.00 25.00           C
ATOM     44  CA  ILE    44      39.409  25.821  69.270  1.00 25.00           C
ATOM     45  CA  ASP    45      40.820  29.036  70.751  1.00 25.00           C
ATOM     46  CA  ASN    46      41.195  27.516  74.186  1.00 25.00           C
ATOM     47  CA  ILE    47      44.402  25.539  73.379  1.00 25.00           C
ATOM     48  CA  GLY    48      47.086  26.772  75.766  1.00 25.00           C
ATOM     49  CA  ALA    49      49.436  26.897  72.773  1.00 25.00           C
ATOM     50  CA  GLY    50      50.560  30.185  74.443  1.00 25.00           C
ATOM     51  CA  THR    51      48.078  31.534  77.000  1.00 25.00           C
ATOM     52  CA  GLY    52      44.837  32.264  75.185  1.00 25.00           C
ATOM     53  CA  GLU    53      45.633  30.276  72.059  1.00 25.00           C
ATOM     54  CA  TRP    54      45.709  28.070  68.975  1.00 25.00           C
ATOM     55  CA  VAL    55      44.225  24.850  67.661  1.00 25.00           C
ATOM     56  CA  LEU    56      41.851  23.702  64.907  1.00 25.00           C
ATOM     57  CA  LEU    57      39.397  22.876  62.156  1.00 25.00           C
ATOM     58  CA  VAL    58      35.828  24.063  61.329  1.00 25.00           C
ATOM     59  CA  SER    59      35.704  22.683  57.802  1.00 25.00           C
ATOM     60  CA  GLY    60      34.412  25.813  55.987  1.00 25.00           C
ATOM     61  CA  SER    61      31.198  23.714  55.768  1.00 25.00           C
ATOM     62  CA  SER    62      30.751  24.407  59.448  1.00 25.00           C
ATOM     63  CA  ALA    63      31.717  27.486  61.510  1.00 25.00           C
ATOM     64  CA  ARG    64      31.677  29.646  58.349  1.00 25.00           C
ATOM     65  CA  GLN    65      28.216  28.287  57.433  1.00 25.00           C
ATOM     66  CA  ALA    66      26.949  29.068  60.962  1.00 25.00           C
ATOM     67  CA  HIS    67      27.564  32.686  59.858  1.00 25.00           C
ATOM     68  CA  LYS    68      27.196  33.154  56.135  1.00 25.00           C
ATOM     69  CA  SER    69      23.743  34.560  56.798  1.00 25.00           C
ATOM     70  CA  GLU    70      21.917  31.207  56.953  1.00 25.00           C
ATOM     71  CA  THR    71      22.009  31.454  60.780  1.00 25.00           C
ATOM     72  CA  SER    72      23.375  32.267  64.264  1.00 25.00           C
ATOM     73  CA  PRO    73      25.672  34.531  66.288  1.00 25.00           C
ATOM     74  CA  VAL    74      28.474  32.281  67.587  1.00 25.00           C
ATOM     75  CA  ASP    75      30.989  34.483  65.656  1.00 25.00           C
ATOM     76  CA  LEU    76      33.605  31.700  65.566  1.00 25.00           C
ATOM     77  CA  CYS    77      36.311  31.412  62.881  1.00 25.00           C
ATOM     78  CA  VAL    78      36.467  28.892  60.037  1.00 25.00           C
ATOM     79  CA  ILE    79      40.268  28.980  60.145  1.00 25.00           C
ATOM     80  CA  GLY    80      40.258  25.767  58.167  1.00 25.00           C
ATOM     81  CA  ILE    81      43.425  24.966  60.029  1.00 25.00           C
ATOM     82  CA  VAL    82      47.237  24.847  59.488  1.00 25.00           C
ATOM     83  CA  ASP    83      47.316  26.647  62.790  1.00 25.00           C
ATOM     84  CA  GLU    84      47.638  23.191  64.336  1.00 25.00           C
ATOM     85  CA  VAL    85      48.868  21.416  67.485  1.00 25.00           C
ATOM     86  CA  VAL    86      49.945  18.447  65.488  1.00 25.00           C
ATOM     87  CA  SER    87      52.606  15.764  65.515  1.00 25.00           C
ATOM     88  CA  GLY    88      51.725  14.878  69.084  1.00 25.00           C
ATOM     89  CA  GLY    89      49.137  12.654  70.833  1.00 25.00           C
ATOM     90  CA  GLN    90      46.404  14.746  69.242  1.00 25.00           C
ATOM     91  CA  VAL    91      45.093  18.099  68.014  1.00 25.00           C
ATOM     92  CA  ILE    92      43.949  19.093  64.585  1.00 25.00           C
ATOM     93  CA  PHE    93      44.526  20.116  61.016  1.00 25.00           C
ATOM     94  CA  HIS    94      45.108  19.598  57.296  1.00 25.00           C
ATOM     95  CA  LYS    95      48.381  20.810  55.760  1.00 25.00           C
TER
END
