
#######################################################
#                                                     #
#                        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   97 (   97),  selected   97 , name T0283TS393_3-D1
# Molecule2: number of CA atoms   97 (  768),  selected   97 , name T0283_D1.pdb
# PARAMETERS: T0283TS393_3-D1.T0283_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1          3.994
LGA    S       2      S       2          2.879
LGA    F       3      F       3          2.064
LGA    I       4      I       4          1.025
LGA    E       5      E       5          1.250
LGA    K       6      K       6          1.850
LGA    M       7      M       7          1.597
LGA    I       8      I       8          0.946
LGA    G       9      G       9          1.254
LGA    S      10      S      10          1.805
LGA    L      11      L      11          1.616
LGA    N      12      N      12          0.941
LGA    D      13      D      13          1.244
LGA    K      14      K      14          1.483
LGA    R      15      R      15          1.307
LGA    E      16      E      16          1.008
LGA    W      17      W      17          1.441
LGA    K      18      K      18          1.678
LGA    A      19      A      19          1.189
LGA    M      20      M      20          1.071
LGA    E      21      E      21          1.510
LGA    A      22      A      22          1.404
LGA    R      23      R      23          0.803
LGA    A      24      A      24          1.081
LGA    K      25      K      25          1.600
LGA    A      26      A      26          1.175
LGA    L      27      L      27          1.249
LGA    P      28      P      28          2.380
LGA    K      29      K      29          2.722
LGA    E      30      E      30          4.267
LGA    Y      31      Y      31          3.063
LGA    H      32      H      32           #
LGA    -       -      H      33           -
LGA    -       -      A      34           -
LGA    -       -      Y      35           -
LGA    -       -      K      36           -
LGA    -       -      A      37           -
LGA    -       -      I      38           -
LGA    -       -      Q      39           -
LGA    -       -      K      40           -
LGA    -       -      Y      41           -
LGA    -       -      M      42           -
LGA    -       -      W      43           -
LGA    -       -      T      44           -
LGA    -       -      S      45           -
LGA    -       -      G      46           -
LGA    -       -      G      47           -
LGA    -       -      P      48           -
LGA    -       -      T      49           -
LGA    -       -      D      50           -
LGA    -       -      W      51           -
LGA    -       -      Q      52           -
LGA    -       -      D      53           -
LGA    -       -      T      54           -
LGA    -       -      K      55           -
LGA    -       -      R      56           -
LGA    -       -      I      57           -
LGA    -       -      F      58           -
LGA    -       -      G      59           -
LGA    -       -      G      60           -
LGA    -       -      I      61           -
LGA    -       -      L      62           -
LGA    -       -      D      63           -
LGA    -       -      L      64           -
LGA    -       -      F      65           -
LGA    -       -      E      66           -
LGA    -       -      E      67           -
LGA    -       -      G      68           -
LGA    H      33      A      69          4.747
LGA    A      34      A      70           -
LGA    -       -      E      71           -
LGA    -       -      G      72           -
LGA    -       -      K      73           -
LGA    -       -      K      74           -
LGA    Y      35      V      75          1.209
LGA    K      36      T      76           #
LGA    A      37      -       -           -
LGA    I      38      -       -           -
LGA    Q      39      D      77          3.582
LGA    K      40      L      78          3.310
LGA    Y      41      T      79          4.587
LGA    M      42      -       -           -
LGA    W      43      -       -           -
LGA    T      44      -       -           -
LGA    S      45      -       -           -
LGA    G      46      -       -           -
LGA    G      47      -       -           -
LGA    P      48      -       -           -
LGA    T      49      -       -           -
LGA    D      50      -       -           -
LGA    W      51      -       -           -
LGA    Q      52      -       -           -
LGA    D      53      -       -           -
LGA    T      54      G      80          3.500
LGA    K      55      E      81          2.243
LGA    R      56      D      82          2.256
LGA    I      57      -       -           -
LGA    F      58      V      83          2.047
LGA    G      59      A      84          1.708
LGA    G      60      A      85          1.677
LGA    I      61      F      86          1.469
LGA    L      62      C      87          1.585
LGA    D      63      D      88          2.127
LGA    L      64      E      89          3.029
LGA    F      65      L      90          3.261
LGA    E      66      M      91          3.893
LGA    -       -      K      92           -
LGA    E      67      D      93          5.164
LGA    G      68      T      94          4.213
LGA    A      69      -       -           -
LGA    A      70      K      95          3.699
LGA    E      71      T      96          2.286
LGA    G      72      W      97           #
LGA    K      73      -       -           -
LGA    K      74      -       -           -
LGA    V      75      -       -           -
LGA    T      76      -       -           -
LGA    D      77      -       -           -
LGA    L      78      -       -           -
LGA    T      79      -       -           -
LGA    G      80      -       -           -
LGA    E      81      -       -           -
LGA    D      82      -       -           -
LGA    V      83      -       -           -
LGA    A      84      -       -           -
LGA    A      85      -       -           -
LGA    F      86      -       -           -
LGA    C      87      -       -           -
LGA    D      88      -       -           -
LGA    E      89      -       -           -
LGA    L      90      -       -           -
LGA    M      91      -       -           -
LGA    K      92      -       -           -
LGA    D      93      -       -           -
LGA    T      94      -       -           -
LGA    K      95      -       -           -
LGA    T      96      -       -           -
LGA    W      97      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   97   97    5.0     52    2.48    61.54     38.461     2.012

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.750974 * X  +   0.345165 * Y  +   0.562938 * Z  +  19.262123
  Y_new =  -0.115074 * X  +  -0.907871 * Y  +   0.403148 * Z  +  31.920605
  Z_new =   0.650227 * X  +   0.237975 * Y  +   0.721507 * Z  +   1.403566 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.318594   -2.822999  [ DEG:    18.2541   -161.7459 ]
  Theta =  -0.707883   -2.433709  [ DEG:   -40.5587   -139.4413 ]
  Phi   =  -2.989542    0.152050  [ DEG:  -171.2882      8.7118 ]
 
# 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: T0283TS393_3-D1                               
REMARK     2: T0283_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0283TS393_3-D1.T0283_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   97   97   5.0   52   2.48   61.54  38.461
REMARK  ---------------------------------------------------------- 
MOLECULE T0283TS393_3-D1
PFRMAT TS
TARGET T0283
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      30.303   4.989  24.124  1.00 25.00           C
ATOM      2  CA  SER     2      27.192   6.785  22.791  1.00 25.00           C
ATOM      3  CA  PHE     3      28.153   9.635  20.412  1.00 25.00           C
ATOM      4  CA  ILE     4      27.957   7.032  17.608  1.00 25.00           C
ATOM      5  CA  GLU     5      24.329   8.035  16.899  1.00 25.00           C
ATOM      6  CA  LYS     6      25.350  11.724  16.762  1.00 25.00           C
ATOM      7  CA  MET     7      28.187  10.874  14.334  1.00 25.00           C
ATOM      8  CA  ILE     8      25.745   8.915  12.128  1.00 25.00           C
ATOM      9  CA  GLY     9      23.320  11.879  12.137  1.00 25.00           C
ATOM     10  CA  SER    10      26.168  14.244  11.154  1.00 25.00           C
ATOM     11  CA  LEU    11      27.167  11.894   8.301  1.00 25.00           C
ATOM     12  CA  ASN    12      23.537  11.780   7.090  1.00 25.00           C
ATOM     13  CA  ASP    13      23.362  15.605   7.177  1.00 25.00           C
ATOM     14  CA  LYS    14      26.618  15.825   5.173  1.00 25.00           C
ATOM     15  CA  ARG    15      25.225  13.358   2.595  1.00 25.00           C
ATOM     16  CA  GLU    16      22.017  15.430   2.309  1.00 25.00           C
ATOM     17  CA  TRP    17      24.087  18.611   1.800  1.00 25.00           C
ATOM     18  CA  LYS    18      26.140  16.868  -0.923  1.00 25.00           C
ATOM     19  CA  ALA    19      22.921  15.727  -2.655  1.00 25.00           C
ATOM     20  CA  MET    20      21.550  19.300  -2.516  1.00 25.00           C
ATOM     21  CA  GLU    21      24.809  20.636  -4.017  1.00 25.00           C
ATOM     22  CA  ALA    22      24.612  18.033  -6.821  1.00 25.00           C
ATOM     23  CA  ARG    23      20.985  19.036  -7.530  1.00 25.00           C
ATOM     24  CA  ALA    24      22.006  22.725  -7.667  1.00 25.00           C
ATOM     25  CA  LYS    25      24.842  21.876 -10.096  1.00 25.00           C
ATOM     26  CA  ALA    26      22.400  19.916 -12.301  1.00 25.00           C
ATOM     27  CA  LEU    27      19.378  22.056 -12.874  1.00 25.00           C
ATOM     28  CA  PRO    28      19.351  24.015 -16.184  1.00 25.00           C
ATOM     29  CA  LYS    29      22.818  25.462 -16.770  1.00 25.00           C
ATOM     30  CA  GLU    30      23.514  25.716 -13.012  1.00 25.00           C
ATOM     31  CA  TYR    31      23.399  29.538 -13.224  1.00 25.00           C
ATOM     32  CA  HIS    32      20.066  29.358 -15.102  1.00 25.00           C
ATOM     33  CA  HIS    33      18.660  27.000 -12.432  1.00 25.00           C
ATOM     34  CA  ALA    34      19.804  29.401  -9.675  1.00 25.00           C
ATOM     35  CA  TYR    35      18.134  32.327 -11.497  1.00 25.00           C
ATOM     36  CA  LYS    36      14.893  30.312 -11.814  1.00 25.00           C
ATOM     37  CA  ALA    37      15.011  29.487  -8.076  1.00 25.00           C
ATOM     38  CA  ILE    38      15.533  33.190  -7.251  1.00 25.00           C
ATOM     39  CA  GLN    39      12.556  34.130  -9.469  1.00 25.00           C
ATOM     40  CA  LYS    40      10.390  31.502  -7.718  1.00 25.00           C
ATOM     41  CA  TYR    41      11.441  32.876  -4.302  1.00 25.00           C
ATOM     42  CA  MET    42      10.565  36.428  -5.434  1.00 25.00           C
ATOM     43  CA  TRP    43       7.140  35.222  -6.650  1.00 25.00           C
ATOM     44  CA  THR    44       6.528  33.490  -3.289  1.00 25.00           C
ATOM     45  CA  SER    45       7.110  36.782  -1.474  1.00 25.00           C
ATOM     46  CA  GLY    46       7.242  39.840  -3.633  1.00 25.00           C
ATOM     47  CA  GLY    47       7.322  40.414  -7.374  1.00 25.00           C
ATOM     48  CA  PRO    48       8.963  41.569 -10.638  1.00 25.00           C
ATOM     49  CA  THR    49      11.551  41.410 -13.444  1.00 25.00           C
ATOM     50  CA  ASP    50      15.028  42.482 -14.737  1.00 25.00           C
ATOM     51  CA  TRP    51      17.378  45.006 -13.110  1.00 25.00           C
ATOM     52  CA  GLN    52      17.909  46.671  -9.703  1.00 25.00           C
ATOM     53  CA  ASP    53      14.408  45.580  -8.597  1.00 25.00           C
ATOM     54  CA  THR    54      15.145  41.994  -9.723  1.00 25.00           C
ATOM     55  CA  LYS    55      18.440  42.032  -7.772  1.00 25.00           C
ATOM     56  CA  ARG    56      16.611  43.305  -4.657  1.00 25.00           C
ATOM     57  CA  ILE    57      14.002  40.525  -5.024  1.00 25.00           C
ATOM     58  CA  PHE    58      16.789  37.918  -5.345  1.00 25.00           C
ATOM     59  CA  GLY    59      18.481  39.304  -2.201  1.00 25.00           C
ATOM     60  CA  GLY    60      15.157  39.130  -0.306  1.00 25.00           C
ATOM     61  CA  ILE    61      14.670  35.506  -1.443  1.00 25.00           C
ATOM     62  CA  LEU    62      18.214  34.638  -0.277  1.00 25.00           C
ATOM     63  CA  ASP    63      17.521  36.265   3.120  1.00 25.00           C
ATOM     64  CA  LEU    64      14.269  34.268   3.441  1.00 25.00           C
ATOM     65  CA  PHE    65      16.142  31.036   2.599  1.00 25.00           C
ATOM     66  CA  GLU    66      18.794  31.856   5.236  1.00 25.00           C
ATOM     67  CA  GLU    67      16.051  32.504   7.829  1.00 25.00           C
ATOM     68  CA  GLY    68      14.403  29.159   6.957  1.00 25.00           C
ATOM     69  CA  ALA    69      17.770  27.374   7.333  1.00 25.00           C
ATOM     70  CA  ALA    70      18.301  29.039  10.741  1.00 25.00           C
ATOM     71  CA  GLU    71      20.779  31.835  10.014  1.00 25.00           C
ATOM     72  CA  GLY    72      23.514  31.891   7.403  1.00 25.00           C
ATOM     73  CA  LYS    73      22.685  28.293   6.429  1.00 25.00           C
ATOM     74  CA  LYS    74      22.115  27.875   2.706  1.00 25.00           C
ATOM     75  CA  VAL    75      20.641  29.673  -0.325  1.00 25.00           C
ATOM     76  CA  THR    76      18.138  27.929  -2.641  1.00 25.00           C
ATOM     77  CA  ASP    77      20.542  24.977  -3.055  1.00 25.00           C
ATOM     78  CA  LEU    78      22.615  27.634  -4.917  1.00 25.00           C
ATOM     79  CA  THR    79      25.595  25.653  -3.526  1.00 25.00           C
ATOM     80  CA  GLY    80      29.023  26.058  -5.147  1.00 25.00           C
ATOM     81  CA  GLU    81      31.415  28.146  -3.007  1.00 25.00           C
ATOM     82  CA  ASP    82      30.483  31.289  -4.986  1.00 25.00           C
ATOM     83  CA  VAL    83      26.763  30.529  -4.487  1.00 25.00           C
ATOM     84  CA  ALA    84      27.335  30.071  -0.728  1.00 25.00           C
ATOM     85  CA  ALA    85      29.205  33.410  -0.580  1.00 25.00           C
ATOM     86  CA  PHE    86      26.331  35.129  -2.438  1.00 25.00           C
ATOM     87  CA  CYS    87      23.807  33.612   0.011  1.00 25.00           C
ATOM     88  CA  ASP    88      25.906  34.840   2.971  1.00 25.00           C
ATOM     89  CA  GLU    89      26.049  38.350   1.446  1.00 25.00           C
ATOM     90  CA  LEU    90      22.249  38.324   0.968  1.00 25.00           C
ATOM     91  CA  MET    91      21.774  37.242   4.611  1.00 25.00           C
ATOM     92  CA  LYS    92      24.087  40.065   5.776  1.00 25.00           C
ATOM     93  CA  ASP    93      22.107  42.586   3.681  1.00 25.00           C
ATOM     94  CA  THR    94      18.829  41.308   5.196  1.00 25.00           C
ATOM     95  CA  LYS    95      20.296  41.651   8.718  1.00 25.00           C
ATOM     96  CA  THR    96      21.411  45.229   7.931  1.00 25.00           C
ATOM     97  CA  TRP    97      17.906  46.063   6.635  1.00 25.00           C
TER
END
