
#######################################################
#                                                     #
#                        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   68 (   68),  selected   68 , name T0348TS393_1
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS393_1.T0348.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      D       2           -
LGA    D       2      A       3           -
LGA    -       -      K       4           -
LGA    -       -      F       5           -
LGA    A       3      L       6          2.949
LGA    K       4      E       7          3.609
LGA    F       5      I       8          1.644
LGA    L       6      -       -           -
LGA    E       7      -       -           -
LGA    I       8      -       -           -
LGA    L       9      L       9          4.386
LGA    V      10      V      10          2.061
LGA    C      11      C      11          1.229
LGA    P      12      P      12           #
LGA    L      13      -       -           -
LGA    C      14      L      13          4.600
LGA    K      15      C      14          3.382
LGA    G      16      -       -           -
LGA    P      17      K      15          2.192
LGA    L      18      G      16          2.797
LGA    V      19      -       -           -
LGA    F      20      -       -           -
LGA    D      21      P      17          1.401
LGA    K      22      L      18          3.017
LGA    S      23      V      19          2.684
LGA    -       -      F      20           -
LGA    -       -      D      21           -
LGA    -       -      K      22           -
LGA    -       -      S      23           -
LGA    -       -      K      24           -
LGA    -       -      D      25           -
LGA    -       -      E      26           -
LGA    -       -      L      27           -
LGA    -       -      I      28           -
LGA    -       -      C      29           -
LGA    K      24      K      30          2.862
LGA    D      25      G      31          3.551
LGA    E      26      D      32          3.298
LGA    -       -      R      33           -
LGA    L      27      L      34          1.399
LGA    I      28      A      35          3.044
LGA    C      29      F      36          4.434
LGA    -       -      P      37           -
LGA    -       -      I      38           -
LGA    -       -      K      39           -
LGA    -       -      D      40           -
LGA    -       -      G      41           -
LGA    -       -      I      42           -
LGA    -       -      P      43           -
LGA    -       -      M      44           -
LGA    -       -      M      45           -
LGA    -       -      L      46           -
LGA    K      30      E      47          3.655
LGA    G      31      S      48          4.500
LGA    D      32      -       -           -
LGA    R      33      -       -           -
LGA    L      34      -       -           -
LGA    A      35      -       -           -
LGA    F      36      -       -           -
LGA    P      37      E      49          3.453
LGA    I      38      A      50           #
LGA    K      39      R      51           #
LGA    -       -      E      52           -
LGA    D      40      L      53           #
LGA    G      41      A      54           -
LGA    I      42      P      55           -
LGA    P      43      E      56           -
LGA    M      44      E      57           -
LGA    M      45      E      58           -
LGA    L      46      V      59           -
LGA    E      47      K      60           -
LGA    S      48      L      61           -
LGA    E      49      E      62           -
LGA    A      50      -       -           -
LGA    R      51      -       -           -
LGA    E      52      -       -           -
LGA    L      53      -       -           -
LGA    A      54      -       -           -
LGA    P      55      -       -           -
LGA    E      56      -       -           -
LGA    E      57      -       -           -
LGA    E      58      -       -           -
LGA    V      59      -       -           -
LGA    K      60      -       -           -
LGA    L      61      -       -           -
LGA    E      62      -       -           -
LGA    H      63      -       -           -
LGA    H      64      -       -           -
LGA    H      65      -       -           -
LGA    H      66      -       -           -
LGA    H      67      -       -           -
LGA    H      68      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   68   61    5.0     22    3.17    22.73     22.291     0.673

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.635653 * X  +   0.751193 * Y  +   0.177920 * Z  +  12.463850
  Y_new =   0.039463 * X  +   0.261792 * Y  +  -0.964317 * Z  +  32.647045
  Z_new =  -0.770966 * X  +  -0.605949 * Y  +  -0.196053 * Z  +  49.406578 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.883713    1.257879  [ DEG:  -107.9288     72.0712 ]
  Theta =   0.880357    2.261236  [ DEG:    50.4407    129.5593 ]
  Phi   =   3.079589   -0.062003  [ DEG:   176.4475     -3.5525 ]
 
# 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: T0348TS393_1                                  
REMARK     2: T0348.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0348TS393_1.T0348.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   68   61   5.0   22   3.17   22.73  22.291
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS393_1
PFRMAT TS
TARGET T0348
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1       5.741  35.814  46.078  1.00 25.00           C
ATOM      2  CA  ASP     2       4.889  37.114  49.543  1.00 25.00           C
ATOM      3  CA  ALA     3       4.547  39.149  52.683  1.00 25.00           C
ATOM      4  CA  LYS     4       8.283  39.043  53.520  1.00 25.00           C
ATOM      5  CA  PHE     5       7.546  36.969  56.655  1.00 25.00           C
ATOM      6  CA  LEU     6       5.420  34.549  54.583  1.00 25.00           C
ATOM      7  CA  GLU     7       8.249  34.216  52.023  1.00 25.00           C
ATOM      8  CA  ILE     8      10.745  33.505  54.839  1.00 25.00           C
ATOM      9  CA  LEU     9       8.403  30.837  56.275  1.00 25.00           C
ATOM     10  CA  VAL    10       6.821  32.457  59.286  1.00 25.00           C
ATOM     11  CA  CYS    11       6.074  28.921  60.478  1.00 25.00           C
ATOM     12  CA  PRO    12       9.757  28.339  61.238  1.00 25.00           C
ATOM     13  CA  LEU    13      10.497  27.785  64.878  1.00 25.00           C
ATOM     14  CA  CYS    14       7.316  25.636  65.102  1.00 25.00           C
ATOM     15  CA  LYS    15       3.573  26.396  64.810  1.00 25.00           C
ATOM     16  CA  GLY    16       3.933  29.514  67.035  1.00 25.00           C
ATOM     17  CA  PRO    17       4.845  32.147  64.488  1.00 25.00           C
ATOM     18  CA  LEU    18       8.664  32.642  64.237  1.00 25.00           C
ATOM     19  CA  VAL    19       9.362  35.892  62.322  1.00 25.00           C
ATOM     20  CA  PHE    20      11.921  33.875  60.471  1.00 25.00           C
ATOM     21  CA  ASP    21      13.741  31.323  62.703  1.00 25.00           C
ATOM     22  CA  LYS    22      15.742  30.563  59.560  1.00 25.00           C
ATOM     23  CA  SER    23      13.647  28.279  57.309  1.00 25.00           C
ATOM     24  CA  LYS    24      14.162  25.367  59.742  1.00 25.00           C
ATOM     25  CA  ASP    25      11.269  23.534  61.397  1.00 25.00           C
ATOM     26  CA  GLU    26       8.019  22.266  60.030  1.00 25.00           C
ATOM     27  CA  LEU    27       9.111  21.453  56.498  1.00 25.00           C
ATOM     28  CA  ILE    28       8.399  25.167  55.895  1.00 25.00           C
ATOM     29  CA  CYS    29       4.660  24.569  56.474  1.00 25.00           C
ATOM     30  CA  LYS    30       2.940  24.744  59.892  1.00 25.00           C
ATOM     31  CA  GLY    31       0.145  26.288  57.791  1.00 25.00           C
ATOM     32  CA  ASP    32      -0.954  27.698  61.213  1.00 25.00           C
ATOM     33  CA  ARG    33      -1.889  30.685  59.035  1.00 25.00           C
ATOM     34  CA  LEU    34       1.860  31.328  59.152  1.00 25.00           C
ATOM     35  CA  ALA    35       3.539  29.676  56.191  1.00 25.00           C
ATOM     36  CA  PHE    36       5.098  28.274  53.000  1.00 25.00           C
ATOM     37  CA  PRO    37       2.933  26.548  50.414  1.00 25.00           C
ATOM     38  CA  ILE    38       6.149  26.692  48.356  1.00 25.00           C
ATOM     39  CA  LYS    39       6.422  23.048  47.139  1.00 25.00           C
ATOM     40  CA  ASP    40      10.215  22.492  46.952  1.00 25.00           C
ATOM     41  CA  GLY    41      13.029  21.260  44.691  1.00 25.00           C
ATOM     42  CA  ILE    42      13.016  24.031  42.029  1.00 25.00           C
ATOM     43  CA  PRO    43      12.002  24.348  38.377  1.00 25.00           C
ATOM     44  CA  MET    44      11.790  28.025  37.399  1.00 25.00           C
ATOM     45  CA  MET    45      15.410  27.530  36.449  1.00 25.00           C
ATOM     46  CA  LEU    46      15.810  31.127  37.481  1.00 25.00           C
ATOM     47  CA  GLU    47      13.592  32.854  34.939  1.00 25.00           C
ATOM     48  CA  SER    48      15.693  32.561  31.821  1.00 25.00           C
ATOM     49  CA  GLU    49      15.231  34.230  28.390  1.00 25.00           C
ATOM     50  CA  ALA    50      12.197  36.481  27.712  1.00 25.00           C
ATOM     51  CA  ARG    51       9.926  38.428  30.061  1.00 25.00           C
ATOM     52  CA  GLU    52      11.421  41.649  31.502  1.00 25.00           C
ATOM     53  CA  LEU    53      14.969  42.412  32.665  1.00 25.00           C
ATOM     54  CA  ALA    54      14.935  46.125  31.981  1.00 25.00           C
ATOM     55  CA  PRO    55      16.846  46.456  35.311  1.00 25.00           C
ATOM     56  CA  GLU    56      19.705  47.902  33.272  1.00 25.00           C
ATOM     57  CA  GLU    57      22.780  45.676  33.567  1.00 25.00           C
ATOM     58  CA  GLU    58      25.331  47.845  35.478  1.00 25.00           C
ATOM     59  CA  VAL    59      26.810  44.576  36.760  1.00 25.00           C
ATOM     60  CA  LYS    60      29.920  42.486  36.210  1.00 25.00           C
ATOM     61  CA  LEU    61      32.156  39.703  37.480  1.00 25.00           C
ATOM     62  CA  GLU    62      31.265  39.646  41.166  1.00 25.00           C
ATOM     63  CA  HIS    63      31.695  35.936  41.756  1.00 25.00           C
ATOM     64  CA  HIS    64      29.924  33.629  44.223  1.00 25.00           C
ATOM     65  CA  HIS    65      30.017  34.372  47.923  1.00 25.00           C
ATOM     66  CA  HIS    66      27.345  37.106  48.408  1.00 25.00           C
ATOM     67  CA  HIS    67      28.276  38.305  51.881  1.00 25.00           C
ATOM     68  CA  HIS    68      24.848  40.025  51.704  1.00 25.00           C
TER
END
