
#######################################################
#                                                     #
#                        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_2-D1
# Molecule2: number of CA atoms   97 (  768),  selected   97 , name T0283_D1.pdb
# PARAMETERS: T0283TS393_2-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          6.806
LGA    S       2      S       2          5.247
LGA    F       3      F       3          2.215
LGA    I       4      I       4          1.650
LGA    E       5      E       5          1.812
LGA    K       6      K       6          2.026
LGA    M       7      M       7          1.565
LGA    I       8      I       8          1.211
LGA    G       9      G       9          1.330
LGA    S      10      S      10          1.448
LGA    L      11      L      11          0.947
LGA    N      12      N      12          0.557
LGA    D      13      D      13          0.721
LGA    K      14      K      14          0.830
LGA    R      15      R      15          0.492
LGA    E      16      E      16          0.459
LGA    W      17      W      17          0.679
LGA    K      18      K      18          0.790
LGA    A      19      A      19          0.612
LGA    M      20      M      20          0.527
LGA    E      21      E      21          0.663
LGA    A      22      A      22          0.889
LGA    R      23      R      23          0.688
LGA    A      24      A      24          0.705
LGA    K      25      K      25          0.807
LGA    A      26      A      26          0.813
LGA    L      27      L      27          0.965
LGA    P      28      P      28          0.930
LGA    K      29      K      29          1.330
LGA    E      30      E      30          3.794
LGA    -       -      Y      31           -
LGA    Y      31      H      32          4.718
LGA    H      32      H      33           #
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    A      69      -       -           -
LGA    A      70      -       -           -
LGA    E      71      -       -           -
LGA    G      72      -       -           -
LGA    K      73      A      34          4.340
LGA    K      74      Y      35          3.928
LGA    V      75      K      36          4.493
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    T      76      F      58          4.863
LGA    D      77      G      59           #
LGA    -       -      G      60           -
LGA    L      78      I      61          4.294
LGA    T      79      L      62          4.448
LGA    G      80      D      63          3.289
LGA    E      81      L      64          5.148
LGA    D      82      F      65           -
LGA    V      83      E      66           #
LGA    A      84      E      67           #
LGA    A      85      G      68           -
LGA    F      86      A      69           -
LGA    C      87      A      70           -
LGA    -       -      E      71           -
LGA    -       -      G      72           -
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    D      88      L      90          4.242
LGA    E      89      -       -           -
LGA    L      90      -       -           -
LGA    M      91      -       -           -
LGA    K      92      M      91          3.240
LGA    D      93      K      92           -
LGA    T      94      D      93           -
LGA    -       -      T      94           -
LGA    K      95      K      95           #
LGA    T      96      T      96          1.726
LGA    W      97      W      97          3.116

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   97   97    5.0     43    2.81    74.42     33.472     1.477

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.062902 * X  +   0.091423 * Y  +   0.993824 * Z  +  21.417610
  Y_new =   0.864878 * X  +   0.491922 * Y  +  -0.099993 * Z  +  29.015472
  Z_new =  -0.498025 * X  +   0.865826 * Y  +  -0.048127 * Z  +   1.608564 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.626324   -1.515268  [ DEG:    93.1815    -86.8185 ]
  Theta =   0.521320    2.620273  [ DEG:    29.8694    150.1306 ]
  Phi   =   1.498195   -1.643398  [ DEG:    85.8402    -94.1598 ]
 
# 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_2-D1                               
REMARK     2: T0283_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0283TS393_2-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   43   2.81   74.42  33.472
REMARK  ---------------------------------------------------------- 
MOLECULE T0283TS393_2-D1
PFRMAT TS
TARGET T0283
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1      32.611   8.966  23.266  1.00 25.00           C
ATOM      2  CA  SER     2      30.524   5.967  22.357  1.00 25.00           C
ATOM      3  CA  PHE     3      28.111   8.400  20.748  1.00 25.00           C
ATOM      4  CA  ILE     4      27.523   5.809  17.989  1.00 25.00           C
ATOM      5  CA  GLU     5      24.018   7.225  17.371  1.00 25.00           C
ATOM      6  CA  LYS     6      25.460  10.766  17.154  1.00 25.00           C
ATOM      7  CA  MET     7      28.102   9.564  14.655  1.00 25.00           C
ATOM      8  CA  ILE     8      25.379   7.882  12.549  1.00 25.00           C
ATOM      9  CA  GLY     9      23.321  11.112  12.588  1.00 25.00           C
ATOM     10  CA  SER    10      26.395  13.115  11.489  1.00 25.00           C
ATOM     11  CA  LEU    11      27.023  10.632   8.641  1.00 25.00           C
ATOM     12  CA  ASN    12      23.368  10.934   7.537  1.00 25.00           C
ATOM     13  CA  ASP    13      23.646  14.754   7.577  1.00 25.00           C
ATOM     14  CA  LYS    14      26.842  14.568   5.476  1.00 25.00           C
ATOM     15  CA  ARG    15      25.091  12.256   2.974  1.00 25.00           C
ATOM     16  CA  GLU    16      22.141  14.688   2.754  1.00 25.00           C
ATOM     17  CA  TRP    17      24.553  17.598   2.141  1.00 25.00           C
ATOM     18  CA  LYS    18      26.303  15.599  -0.618  1.00 25.00           C
ATOM     19  CA  ALA    19      22.920  14.825  -2.237  1.00 25.00           C
ATOM     20  CA  MET    20      21.982  18.536  -2.109  1.00 25.00           C
ATOM     21  CA  GLU    21      25.328  19.463  -3.724  1.00 25.00           C
ATOM     22  CA  ALA    22      24.741  16.872  -6.484  1.00 25.00           C
ATOM     23  CA  ARG    23      21.237  18.288  -7.100  1.00 25.00           C
ATOM     24  CA  ALA    24      22.677  21.829  -7.318  1.00 25.00           C
ATOM     25  CA  LYS    25      25.319  20.628  -9.817  1.00 25.00           C
ATOM     26  CA  ALA    26      22.598  18.946 -11.922  1.00 25.00           C
ATOM     27  CA  LEU    27      21.482  22.490 -12.587  1.00 25.00           C
ATOM     28  CA  PRO    28      21.176  25.174 -15.315  1.00 25.00           C
ATOM     29  CA  LYS    29      24.182  27.594 -15.336  1.00 25.00           C
ATOM     30  CA  GLU    30      23.211  27.092 -11.666  1.00 25.00           C
ATOM     31  CA  TYR    31      24.165  30.718 -10.892  1.00 25.00           C
ATOM     32  CA  HIS    32      22.056  31.930 -13.850  1.00 25.00           C
ATOM     33  CA  HIS    33      19.086  29.851 -12.616  1.00 25.00           C
ATOM     34  CA  ALA    34      19.478  31.331  -9.105  1.00 25.00           C
ATOM     35  CA  TYR    35      19.563  34.865 -10.577  1.00 25.00           C
ATOM     36  CA  LYS    36      16.392  34.127 -12.595  1.00 25.00           C
ATOM     37  CA  ALA    37      14.659  32.819  -9.441  1.00 25.00           C
ATOM     38  CA  ILE    38      15.682  35.980  -7.537  1.00 25.00           C
ATOM     39  CA  GLN    39      14.312  38.160 -10.371  1.00 25.00           C
ATOM     40  CA  LYS    40      11.015  36.211 -10.309  1.00 25.00           C
ATOM     41  CA  TYR    41      10.783  36.677  -6.515  1.00 25.00           C
ATOM     42  CA  MET    42      11.410  40.433  -6.914  1.00 25.00           C
ATOM     43  CA  TRP    43       8.677  40.631  -9.588  1.00 25.00           C
ATOM     44  CA  THR    44       6.249  38.775  -7.279  1.00 25.00           C
ATOM     45  CA  SER    45       5.976  35.533  -5.233  1.00 25.00           C
ATOM     46  CA  GLY    46       8.199  34.693  -2.227  1.00 25.00           C
ATOM     47  CA  GLY    47       7.331  36.649   0.893  1.00 25.00           C
ATOM     48  CA  PRO    48       8.187  35.834   4.515  1.00 25.00           C
ATOM     49  CA  THR    49       8.252  39.487   5.657  1.00 25.00           C
ATOM     50  CA  ASP    50       6.295  41.630   3.206  1.00 25.00           C
ATOM     51  CA  TRP    51       6.317  41.399  -0.628  1.00 25.00           C
ATOM     52  CA  GLN    52       8.936  43.037  -2.891  1.00 25.00           C
ATOM     53  CA  ASP    53      11.102  43.847   0.162  1.00 25.00           C
ATOM     54  CA  THR    54      10.812  40.221   1.361  1.00 25.00           C
ATOM     55  CA  LYS    55      11.826  38.966  -2.113  1.00 25.00           C
ATOM     56  CA  ARG    56      14.846  41.323  -2.110  1.00 25.00           C
ATOM     57  CA  ILE    57      15.863  40.055   1.358  1.00 25.00           C
ATOM     58  CA  PHE    58      15.571  36.433   0.146  1.00 25.00           C
ATOM     59  CA  GLY    59      17.735  37.253  -2.905  1.00 25.00           C
ATOM     60  CA  GLY    60      20.356  38.885  -0.638  1.00 25.00           C
ATOM     61  CA  ILE    61      20.361  35.792   1.621  1.00 25.00           C
ATOM     62  CA  LEU    62      20.820  33.530  -1.435  1.00 25.00           C
ATOM     63  CA  ASP    63      23.735  35.703  -2.637  1.00 25.00           C
ATOM     64  CA  LEU    64      25.345  35.505   0.833  1.00 25.00           C
ATOM     65  CA  PHE    65      24.951  31.696   0.825  1.00 25.00           C
ATOM     66  CA  GLU    66      26.558  31.511  -2.646  1.00 25.00           C
ATOM     67  CA  GLU    67      29.475  33.680  -1.437  1.00 25.00           C
ATOM     68  CA  GLY    68      29.935  31.406   1.610  1.00 25.00           C
ATOM     69  CA  ALA    69      29.939  28.322  -0.661  1.00 25.00           C
ATOM     70  CA  ALA    70      32.558  29.961  -2.924  1.00 25.00           C
ATOM     71  CA  GLU    71      31.774  31.997  -6.058  1.00 25.00           C
ATOM     72  CA  GLY    72      29.797  31.309  -9.231  1.00 25.00           C
ATOM     73  CA  LYS    73      27.033  33.230  -7.561  1.00 25.00           C
ATOM     74  CA  LYS    74      23.651  32.109  -6.341  1.00 25.00           C
ATOM     75  CA  VAL    75      22.355  28.602  -5.625  1.00 25.00           C
ATOM     76  CA  THR    76      21.483  25.746  -3.227  1.00 25.00           C
ATOM     77  CA  ASP    77      19.082  24.269  -5.820  1.00 25.00           C
ATOM     78  CA  LEU    78      16.159  26.296  -7.171  1.00 25.00           C
ATOM     79  CA  THR    79      13.222  24.078  -7.919  1.00 25.00           C
ATOM     80  CA  GLY    80      10.156  21.913  -7.078  1.00 25.00           C
ATOM     81  CA  GLU    81       8.313  23.846  -4.332  1.00 25.00           C
ATOM     82  CA  ASP    82       9.946  21.648  -1.655  1.00 25.00           C
ATOM     83  CA  VAL    83      13.389  22.269  -3.212  1.00 25.00           C
ATOM     84  CA  ALA    84      12.729  26.042  -3.229  1.00 25.00           C
ATOM     85  CA  ALA    85      11.682  25.900   0.453  1.00 25.00           C
ATOM     86  CA  PHE    86      14.875  23.968   1.311  1.00 25.00           C
ATOM     87  CA  CYS    87      16.981  26.570  -0.550  1.00 25.00           C
ATOM     88  CA  ASP    88      15.225  29.389   1.357  1.00 25.00           C
ATOM     89  CA  GLU    89      15.897  27.598   4.675  1.00 25.00           C
ATOM     90  CA  LEU    90      19.588  27.191   3.735  1.00 25.00           C
ATOM     91  CA  MET    91      19.802  30.914   2.863  1.00 25.00           C
ATOM     92  CA  LYS    92      18.205  31.818   6.225  1.00 25.00           C
ATOM     93  CA  ASP    93      20.714  29.572   8.048  1.00 25.00           C
ATOM     94  CA  THR    94      23.607  31.238   6.172  1.00 25.00           C
ATOM     95  CA  LYS    95      22.262  34.696   7.119  1.00 25.00           C
ATOM     96  CA  THR    96      22.004  33.619  10.786  1.00 25.00           C
ATOM     97  CA  TRP    97      25.607  32.325  10.684  1.00 25.00           C
TER
END
