
#######################################################
#                                                     #
#                        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 T0348TS168_5
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS168_5.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    -       -      D       2           -
LGA    -       -      A       3           -
LGA    M       1      K       4           #
LGA    D       2      F       5          3.954
LGA    A       3      L       6          3.117
LGA    K       4      E       7          2.561
LGA    F       5      I       8           #
LGA    L       6      L       9          2.161
LGA    E       7      V      10          3.352
LGA    I       8      C      11          3.816
LGA    L       9      P      12           -
LGA    V      10      L      13           -
LGA    C      11      C      14           -
LGA    P      12      K      15           -
LGA    L      13      G      16           -
LGA    C      14      P      17          4.208
LGA    K      15      L      18          2.908
LGA    G      16      -       -           -
LGA    P      17      -       -           -
LGA    L      18      V      19          2.783
LGA    V      19      -       -           -
LGA    F      20      -       -           -
LGA    D      21      -       -           -
LGA    K      22      F      20          4.246
LGA    S      23      D      21          3.983
LGA    K      24      K      22          3.240
LGA    D      25      S      23          3.966
LGA    E      26      K      24          4.440
LGA    L      27      D      25          3.329
LGA    I      28      E      26          4.204
LGA    C      29      L      27          4.517
LGA    K      30      I      28          4.288
LGA    -       -      C      29           -
LGA    -       -      K      30           -
LGA    -       -      G      31           -
LGA    -       -      D      32           -
LGA    G      31      R      33          4.099
LGA    D      32      L      34          3.582
LGA    R      33      A      35          4.610
LGA    L      34      F      36          4.414
LGA    A      35      P      37          4.808
LGA    -       -      I      38           -
LGA    -       -      K      39           -
LGA    -       -      D      40           -
LGA    -       -      G      41           -
LGA    -       -      I      42           -
LGA    F      36      P      43          2.194
LGA    P      37      M      44          1.665
LGA    I      38      M      45           #
LGA    K      39      L      46           -
LGA    D      40      E      47           -
LGA    G      41      S      48           -
LGA    I      42      E      49           -
LGA    P      43      A      50           -
LGA    M      44      R      51           -
LGA    M      45      E      52           -
LGA    L      46      L      53           -
LGA    E      47      A      54           -
LGA    S      48      P      55           -
LGA    E      49      E      56           -
LGA    A      50      E      57           -
LGA    R      51      E      58           -
LGA    E      52      V      59           -
LGA    L      53      K      60           -
LGA    A      54      L      61           -
LGA    P      55      E      62           -
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     25    3.71     8.00     21.479     0.656

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.345957 * X  +   0.734712 * Y  +  -0.583534 * Z  +   8.650333
  Y_new =  -0.421746 * X  +  -0.433791 * Y  +  -0.796213 * Z  +  36.259628
  Z_new =  -0.838119 * X  +   0.521559 * Y  +   0.159789 * Z  +  44.767006 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.273508   -1.868085  [ DEG:    72.9666   -107.0334 ]
  Theta =   0.993827    2.147766  [ DEG:    56.9421    123.0579 ]
  Phi   =  -0.883801    2.257792  [ DEG:   -50.6381    129.3619 ]
 
# 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: T0348TS168_5                                  
REMARK     2: T0348.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0348TS168_5.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   25   3.71    8.00  21.479
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS168_5
PFRMAT TS
TARGET T0348
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1       3.130  38.270  47.286  1.00 25.00           C
ATOM      2  CA  ASP     2       4.837  39.125  50.593  1.00 25.00           C
ATOM      3  CA  ALA     3       5.857  39.816  54.154  1.00 25.00           C
ATOM      4  CA  LYS     4       3.791  36.701  54.990  1.00 25.00           C
ATOM      5  CA  PHE     5       6.342  34.494  53.176  1.00 25.00           C
ATOM      6  CA  LEU     6       9.195  36.147  55.125  1.00 25.00           C
ATOM      7  CA  GLU     7       7.326  35.552  58.414  1.00 25.00           C
ATOM      8  CA  ILE     8       6.795  31.877  57.476  1.00 25.00           C
ATOM      9  CA  LEU     9      10.521  31.520  56.665  1.00 25.00           C
ATOM     10  CA  VAL    10      12.379  31.480  53.335  1.00 25.00           C
ATOM     11  CA  CYS    11      13.770  28.260  51.881  1.00 25.00           C
ATOM     12  CA  PRO    12      15.740  25.597  53.797  1.00 25.00           C
ATOM     13  CA  LEU    13      14.414  25.243  57.278  1.00 25.00           C
ATOM     14  CA  CYS    14      13.223  27.730  59.825  1.00 25.00           C
ATOM     15  CA  LYS    15      14.712  31.195  60.167  1.00 25.00           C
ATOM     16  CA  GLY    16      18.472  31.341  60.710  1.00 25.00           C
ATOM     17  CA  PRO    17      18.770  28.510  58.170  1.00 25.00           C
ATOM     18  CA  LEU    18      17.002  30.759  55.687  1.00 25.00           C
ATOM     19  CA  VAL    19      16.082  34.449  55.741  1.00 25.00           C
ATOM     20  CA  PHE    20      17.045  34.427  52.098  1.00 25.00           C
ATOM     21  CA  ASP    21      14.827  33.171  49.297  1.00 25.00           C
ATOM     22  CA  LYS    22      17.472  30.508  48.889  1.00 25.00           C
ATOM     23  CA  SER    23      19.411  28.736  51.676  1.00 25.00           C
ATOM     24  CA  LYS    24      20.073  25.760  49.358  1.00 25.00           C
ATOM     25  CA  ASP    25      16.338  25.214  48.662  1.00 25.00           C
ATOM     26  CA  GLU    26      13.593  27.237  46.852  1.00 25.00           C
ATOM     27  CA  LEU    27      10.225  25.387  46.919  1.00 25.00           C
ATOM     28  CA  ILE    28       8.534  23.264  49.620  1.00 25.00           C
ATOM     29  CA  CYS    29      11.706  23.414  51.759  1.00 25.00           C
ATOM     30  CA  LYS    30      13.015  21.124  54.541  1.00 25.00           C
ATOM     31  CA  GLY    31      10.165  21.858  56.917  1.00 25.00           C
ATOM     32  CA  ASP    32       7.363  21.858  54.335  1.00 25.00           C
ATOM     33  CA  ARG    33       5.639  24.360  56.664  1.00 25.00           C
ATOM     34  CA  LEU    34       8.521  26.826  56.878  1.00 25.00           C
ATOM     35  CA  ALA    35       8.933  27.833  53.195  1.00 25.00           C
ATOM     36  CA  PHE    36       7.528  29.920  50.323  1.00 25.00           C
ATOM     37  CA  PRO    37       3.891  28.939  49.814  1.00 25.00           C
ATOM     38  CA  ILE    38       3.072  31.362  47.062  1.00 25.00           C
ATOM     39  CA  LYS    39       2.123  28.866  44.405  1.00 25.00           C
ATOM     40  CA  ASP    40       4.586  29.892  41.692  1.00 25.00           C
ATOM     41  CA  GLY    41       5.401  29.275  38.026  1.00 25.00           C
ATOM     42  CA  ILE    42       5.256  32.469  36.055  1.00 25.00           C
ATOM     43  CA  PRO    43       1.733  32.468  34.513  1.00 25.00           C
ATOM     44  CA  MET    44      -0.862  35.130  35.434  1.00 25.00           C
ATOM     45  CA  MET    45       1.841  37.861  35.615  1.00 25.00           C
ATOM     46  CA  LEU    46       2.252  37.013  31.959  1.00 25.00           C
ATOM     47  CA  GLU    47      -1.083  38.938  31.689  1.00 25.00           C
ATOM     48  CA  SER    48      -2.079  40.767  28.469  1.00 25.00           C
ATOM     49  CA  GLU    49      -4.164  43.519  29.925  1.00 25.00           C
ATOM     50  CA  ALA    50      -7.358  44.084  31.995  1.00 25.00           C
ATOM     51  CA  ARG    51      -5.115  44.917  34.950  1.00 25.00           C
ATOM     52  CA  GLU    52      -5.805  48.442  36.204  1.00 25.00           C
ATOM     53  CA  LEU    53      -3.315  51.047  35.176  1.00 25.00           C
ATOM     54  CA  ALA    54      -2.497  53.850  37.585  1.00 25.00           C
ATOM     55  CA  PRO    55       1.302  54.343  37.670  1.00 25.00           C
ATOM     56  CA  GLU    56       1.401  56.844  34.782  1.00 25.00           C
ATOM     57  CA  GLU    57       3.575  56.060  31.689  1.00 25.00           C
ATOM     58  CA  GLU    58       7.237  56.019  32.747  1.00 25.00           C
ATOM     59  CA  VAL    59       8.383  54.200  29.606  1.00 25.00           C
ATOM     60  CA  LYS    60       9.140  52.928  26.125  1.00 25.00           C
ATOM     61  CA  LEU    61      12.680  51.497  26.156  1.00 25.00           C
ATOM     62  CA  GLU    62      14.921  51.383  29.210  1.00 25.00           C
ATOM     63  CA  HIS    63      16.148  47.876  28.319  1.00 25.00           C
ATOM     64  CA  HIS    64      18.455  44.831  28.809  1.00 25.00           C
ATOM     65  CA  HIS    65      19.303  45.639  32.464  1.00 25.00           C
ATOM     66  CA  HIS    66      17.938  43.838  35.537  1.00 25.00           C
ATOM     67  CA  HIS    67      19.963  46.065  37.924  1.00 25.00           C
ATOM     68  CA  HIS    68      17.262  45.681  40.617  1.00 25.00           C
TER
END
