
#######################################################
#                                                     #
#                        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   94 (   94),  selected   94 , name T0283TS383_4-D1
# Molecule2: number of CA atoms   97 (  768),  selected   97 , name T0283_D1.pdb
# PARAMETERS: T0283TS383_4-D1.T0283_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      S       2           -
LGA    -       -      F       3           -
LGA    -       -      I       4           -
LGA    S       2      E       5          1.144
LGA    F       3      K       6          2.470
LGA    I       4      M       7          2.305
LGA    E       5      I       8          1.137
LGA    K       6      G       9          1.199
LGA    M       7      S      10          1.771
LGA    I       8      L      11          1.600
LGA    G       9      N      12          1.611
LGA    -       -      D      13           -
LGA    S      10      K      14          1.075
LGA    L      11      R      15          2.675
LGA    N      12      E      16          2.997
LGA    D      13      W      17          1.756
LGA    K      14      K      18          2.449
LGA    R      15      A      19          3.725
LGA    E      16      M      20          3.093
LGA    W      17      E      21          1.934
LGA    K      18      A      22          3.698
LGA    A      19      R      23          4.530
LGA    M      20      A      24          2.570
LGA    E      21      K      25          1.957
LGA    A      22      A      26          4.267
LGA    R      23      L      27          3.963
LGA    A      24      P      28          2.938
LGA    K      25      K      29           #
LGA    A      26      -       -           -
LGA    L      27      -       -           -
LGA    P      28      E      30           #
LGA    -       -      Y      31           -
LGA    -       -      H      32           -
LGA    K      29      H      33          5.001
LGA    E      30      A      34           -
LGA    Y      31      Y      35           -
LGA    H      32      -       -           -
LGA    H      33      -       -           -
LGA    A      34      -       -           -
LGA    Y      35      K      36          4.207
LGA    K      36      -       -           -
LGA    A      37      A      37          4.463
LGA    I      38      I      38          3.820
LGA    Q      39      Q      39          1.811
LGA    K      40      K      40           #
LGA    Y      41      Y      41          5.590
LGA    T      44      M      42          2.563
LGA    S      45      W      43          1.989
LGA    G      46      T      44          4.388
LGA    G      47      S      45          5.160
LGA    P      48      G      46           -
LGA    T      49      G      47           -
LGA    D      50      P      48           -
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      T      49           #
LGA    G      60      D      50          1.249
LGA    I      61      W      51          1.299
LGA    L      62      Q      52          1.804
LGA    D      63      D      53          1.691
LGA    L      64      T      54          1.167
LGA    F      65      K      55          1.881
LGA    E      66      R      56          2.091
LGA    E      67      I      57          0.938
LGA    G      68      F      58          1.778
LGA    A      69      G      59          3.316
LGA    A      70      G      60          2.517
LGA    E      71      I      61          1.015
LGA    G      72      L      62          2.638
LGA    K      73      D      63          3.146
LGA    K      74      L      64          1.523
LGA    V      75      F      65          1.972
LGA    T      76      E      66          3.857
LGA    D      77      E      67          3.389
LGA    L      78      G      68          1.957
LGA    T      79      A      69          3.443
LGA    G      80      A      70          4.492
LGA    E      81      E      71          3.417
LGA    D      82      G      72           #
LGA    V      83      K      73           -
LGA    A      84      K      74           -
LGA    A      85      V      75           -
LGA    F      86      T      76           -
LGA    C      87      D      77           -
LGA    D      88      L      78           -
LGA    E      89      T      79           -
LGA    L      90      G      80           -
LGA    M      91      E      81           -
LGA    K      92      D      82           -
LGA    D      93      V      83           -
LGA    T      94      A      84           -
LGA    K      95      A      85           -
LGA    T      96      F      86           -
LGA    W      97      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)   94   97    5.0     55    2.93    14.55     39.285     1.818

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.562577 * X  +   0.415534 * Y  +   0.714729 * Z  +  -0.826843
  Y_new =   0.411643 * X  +   0.608941 * Y  +  -0.678042 * Z  +  -3.397287
  Z_new =  -0.716977 * X  +   0.675664 * Y  +   0.171525 * Z  +   9.437673 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.322187   -1.819406  [ DEG:    75.7557   -104.2443 ]
  Theta =   0.799457    2.342136  [ DEG:    45.8055    134.1945 ]
  Phi   =   0.631692   -2.509901  [ DEG:    36.1933   -143.8067 ]
 
# 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: T0283TS383_4-D1                               
REMARK     2: T0283_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0283TS383_4-D1.T0283_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   94   97   5.0   55   2.93   14.55  39.285
REMARK  ---------------------------------------------------------- 
MOLECULE T0283TS383_4-D1
PFRMAT TS
TARGET T0283
MODEL 4
PARENT 1ji4A
ATOM      1  CA  SER     2      24.463   8.776  17.146  1.00  0.00
ATOM      2  CA  PHE     3      24.905  12.391  15.947  1.00  0.00
ATOM      3  CA  ILE     4      28.531  11.902  14.824  1.00  0.00
ATOM      4  CA  GLU     5      27.041   9.240  12.608  1.00  0.00
ATOM      5  CA  LYS     6      23.968  11.092  11.369  1.00  0.00
ATOM      6  CA  MET     7      26.012  14.078  10.158  1.00  0.00
ATOM      7  CA  ILE     8      28.301  11.808   8.094  1.00  0.00
ATOM      8  CA  GLY     9      25.160  10.314   6.554  1.00  0.00
ATOM      9  CA  SER    10      27.615  15.294   4.165  1.00  0.00
ATOM     10  CA  LEU    11      27.777  12.200   1.937  1.00  0.00
ATOM     11  CA  ASN    12      24.385  13.299   0.671  1.00  0.00
ATOM     12  CA  ASP    13      25.509  16.895   0.078  1.00  0.00
ATOM     13  CA  LYS    14      28.482  15.593  -1.880  1.00  0.00
ATOM     14  CA  ARG    15      26.040  13.735  -4.150  1.00  0.00
ATOM     15  CA  GLU    16      23.705  16.721  -4.427  1.00  0.00
ATOM     16  CA  TRP    17      26.689  18.922  -5.251  1.00  0.00
ATOM     17  CA  LYS    18      27.588  16.607  -8.133  1.00  0.00
ATOM     18  CA  ALA    19      24.014  16.166  -9.432  1.00  0.00
ATOM     19  CA  MET    20      23.282  19.895  -9.426  1.00  0.00
ATOM     20  CA  GLU    21      26.493  20.617 -11.329  1.00  0.00
ATOM     21  CA  ALA    22      25.867  17.936 -13.939  1.00  0.00
ATOM     22  CA  ARG    23      22.287  19.084 -14.413  1.00  0.00
ATOM     23  CA  ALA    24      23.670  22.561 -15.121  1.00  0.00
ATOM     24  CA  LYS    25      26.042  21.294 -17.828  1.00  0.00
ATOM     25  CA  ALA    26      23.243  19.147 -19.315  1.00  0.00
ATOM     26  CA  LEU    27      21.259  22.386 -19.422  1.00  0.00
ATOM     27  CA  PRO    28      28.504  25.051 -12.969  1.00  0.00
ATOM     28  CA  LYS    29      30.521  26.713 -10.179  1.00  0.00
ATOM     29  CA  GLU    30      34.064  25.340 -10.474  1.00  0.00
ATOM     30  CA  TYR    31      35.860  27.054  -7.576  1.00  0.00
ATOM     31  CA  HIS    32      35.340  27.400  -3.822  1.00  0.00
ATOM     32  CA  HIS    33      35.711  31.150  -4.386  1.00  0.00
ATOM     33  CA  ALA    34      32.647  31.330  -6.686  1.00  0.00
ATOM     34  CA  TYR    35      30.823  29.154  -4.161  1.00  0.00
ATOM     35  CA  LYS    36      31.179  31.436  -1.147  1.00  0.00
ATOM     36  CA  ALA    37      30.267  34.305  -3.440  1.00  0.00
ATOM     37  CA  ILE    38      26.946  32.635  -4.364  1.00  0.00
ATOM     38  CA  GLN    39      25.829  30.899  -1.134  1.00  0.00
ATOM     39  CA  LYS    40      22.876  31.997   0.914  1.00  0.00
ATOM     40  CA  TYR    41      24.275  29.794   3.684  1.00  0.00
ATOM     41  CA  THR    44      25.307  30.876   5.797  1.00  0.00
ATOM     42  CA  SER    45      26.717  31.130   6.386  1.00  0.00
ATOM     43  CA  GLY    46      25.765  30.411   6.853  1.00  0.00
ATOM     44  CA  GLY    47      26.325  31.365   6.463  1.00  0.00
ATOM     45  CA  PRO    48      33.346  29.549  12.470  1.00  0.00
ATOM     46  CA  THR    49      32.896  27.887  15.872  1.00  0.00
ATOM     47  CA  ASP    50      34.812  24.700  16.626  1.00  0.00
ATOM     48  CA  TRP    51      32.887  23.046  19.442  1.00  0.00
ATOM     49  CA  GLN    52      29.212  22.139  19.694  1.00  0.00
ATOM     50  CA  ASP    53      26.615  20.163  21.564  1.00  0.00
ATOM     51  CA  THR    54      23.986  18.014  19.870  1.00  0.00
ATOM     52  CA  LYS    55      21.133  20.525  20.308  1.00  0.00
ATOM     53  CA  ARG    56      22.883  23.452  18.604  1.00  0.00
ATOM     54  CA  ILE    57      24.021  21.253  15.715  1.00  0.00
ATOM     55  CA  PHE    58      20.479  20.080  14.986  1.00  0.00
ATOM     56  CA  GLY    59      19.003  23.577  15.256  1.00  0.00
ATOM     57  CA  GLY    60      21.454  24.809  12.607  1.00  0.00
ATOM     58  CA  ILE    61      20.975  21.843  10.314  1.00  0.00
ATOM     59  CA  LEU    62      17.212  22.356  10.654  1.00  0.00
ATOM     60  CA  ASP    63      17.561  26.033   9.781  1.00  0.00
ATOM     61  CA  LEU    64      19.590  25.210   6.673  1.00  0.00
ATOM     62  CA  PHE    65      17.242  22.390   5.625  1.00  0.00
ATOM     63  CA  GLU    66      14.230  24.709   5.786  1.00  0.00
ATOM     64  CA  GLU    67      16.146  27.159   3.619  1.00  0.00
ATOM     65  CA  GLY    68      16.978  24.430   1.058  1.00  0.00
ATOM     66  CA  ALA    69      13.333  23.382   0.978  1.00  0.00
ATOM     67  CA  ALA    70      12.254  26.885  -0.061  1.00  0.00
ATOM     68  CA  GLU    71      14.923  26.928  -2.766  1.00  0.00
ATOM     69  CA  GLY    72      13.898  23.549  -4.158  1.00  0.00
ATOM     70  CA  LYS    73      10.273  24.699  -4.243  1.00  0.00
ATOM     71  CA  LYS    74      11.323  27.700  -6.345  1.00  0.00
ATOM     72  CA  VAL    75      13.411  25.380  -8.541  1.00  0.00
ATOM     73  CA  THR    76      10.404  23.111  -9.045  1.00  0.00
ATOM     74  CA  ASP    77       8.107  26.047  -9.792  1.00  0.00
ATOM     75  CA  LEU    78      10.290  27.917 -12.246  1.00  0.00
ATOM     76  CA  THR    79      11.522  24.733 -13.956  1.00  0.00
ATOM     77  CA  GLY    80       7.894  23.840 -14.560  1.00  0.00
ATOM     78  CA  GLU    81       7.112  27.195 -16.187  1.00  0.00
ATOM     79  CA  ASP    82      11.888  21.580 -17.841  1.00  0.00
ATOM     80  CA  VAL    83      14.658  19.329 -13.381  1.00  0.00
ATOM     81  CA  ALA    84      11.181  19.404 -11.868  1.00  0.00
ATOM     82  CA  ALA    85      11.258  15.732 -10.888  1.00  0.00
ATOM     83  CA  PHE    86      14.776  16.184  -9.518  1.00  0.00
ATOM     84  CA  CYS    87      13.563  19.112  -7.409  1.00  0.00
ATOM     85  CA  ASP    88      10.508  17.195  -6.173  1.00  0.00
ATOM     86  CA  GLU    89      12.642  14.202  -5.139  1.00  0.00
ATOM     87  CA  LEU    90      14.967  16.388  -3.078  1.00  0.00
ATOM     88  CA  MET    91      11.899  18.054  -1.561  1.00  0.00
ATOM     89  CA  LYS    92      10.697  14.627  -0.415  1.00  0.00
ATOM     90  CA  ASP    93      13.990  13.826   1.321  1.00  0.00
ATOM     91  CA  THR    94      14.202  17.278   2.885  1.00  0.00
ATOM     92  CA  LYS    95      10.672  17.149   4.235  1.00  0.00
ATOM     93  CA  THR    96      11.198  13.765   5.862  1.00  0.00
ATOM     94  CA  TRP    97      14.419  14.942   7.539  1.00  0.00
TER
END
