
#######################################################
#                                                     #
#                        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   65 (   65),  selected   65 , name T0358TS393_4-D1
# Molecule2: number of CA atoms   65 ( 1035),  selected   65 , name T0358_D1.pdb
# PARAMETERS: T0358TS393_4-D1.T0358_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G      10      G      10           -
LGA    P      11      P      11           -
LGA    F      12      -       -           -
LGA    T      13      -       -           -
LGA    R      14      -       -           -
LGA    R      15      -       -           -
LGA    Q      16      -       -           -
LGA    A      17      -       -           -
LGA    Q      18      -       -           -
LGA    A      19      -       -           -
LGA    V      20      -       -           -
LGA    T      21      -       -           -
LGA    T      22      -       -           -
LGA    T      23      -       -           -
LGA    Y      24      -       -           -
LGA    S      25      F      12           #
LGA    -       -      T      13           -
LGA    -       -      R      14           -
LGA    -       -      R      15           -
LGA    -       -      Q      16           -
LGA    -       -      A      17           -
LGA    -       -      Q      18           -
LGA    -       -      A      19           -
LGA    -       -      V      20           -
LGA    N      26      T      21          4.941
LGA    -       -      T      22           -
LGA    -       -      T      23           -
LGA    -       -      Y      24           -
LGA    -       -      S      25           -
LGA    -       -      N      26           -
LGA    -       -      I      27           -
LGA    I      27      T      28           #
LGA    T      28      L      29          3.904
LGA    L      29      E      30          1.601
LGA    E      30      D      31          0.667
LGA    D      31      D      32          1.097
LGA    D      32      Q      33          3.329
LGA    Q      33      G      34          2.162
LGA    G      34      S      35          3.214
LGA    S      35      H      36          3.023
LGA    H      36      F      37          2.537
LGA    F      37      R      38          4.328
LGA    R      38      L      39           #
LGA    L      39      V      40          3.561
LGA    V      40      V      41          4.587
LGA    V      41      R      42          1.672
LGA    R      42      D      43          1.929
LGA    D      43      T      44          3.162
LGA    T      44      -       -           -
LGA    E      45      -       -           -
LGA    G      46      E      45          4.236
LGA    R      47      G      46          1.924
LGA    M      48      R      47          1.629
LGA    V      49      M      48          1.207
LGA    W      50      V      49          2.651
LGA    R      51      W      50          3.227
LGA    A      52      R      51          2.521
LGA    W      53      A      52          2.395
LGA    N      54      W      53          2.189
LGA    F      55      N      54          2.386
LGA    -       -      F      55           -
LGA    E      56      E      56          1.430
LGA    P      57      P      57          4.405
LGA    D      58      D      58          1.509
LGA    A      59      A      59          3.096
LGA    -       -      G      60           -
LGA    -       -      E      61           -
LGA    G      60      G      62           #
LGA    E      61      L      63           -
LGA    G      62      N      64           -
LGA    L      63      R      65           -
LGA    N      64      Y      66           -
LGA    R      65      I      67           -
LGA    Y      66      R      68           -
LGA    I      67      T      69           -
LGA    R      68      S      70           -
LGA    T      69      G      71           -
LGA    S      70      I      72           -
LGA    G      71      R      73           -
LGA    I      72      T      74           -
LGA    R      73      -       -           -
LGA    T      74      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   65   65    5.0     30    2.91    20.00     29.596     0.998

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.760205 * X  +  -0.130335 * Y  +   0.636475 * Z  +  -7.748408
  Y_new =   0.295795 * X  +   0.802806 * Y  +   0.517694 * Z  +   7.025608
  Z_new =  -0.578440 * X  +   0.581820 * Y  +  -0.571745 * Z  +   7.283608 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.347461   -0.794132  [ DEG:   134.4996    -45.5004 ]
  Theta =   0.616815    2.524777  [ DEG:    35.3409    144.6591 ]
  Phi   =   2.770519   -0.371074  [ DEG:   158.7390    -21.2610 ]
 
# 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: T0358TS393_4-D1                               
REMARK     2: T0358_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358TS393_4-D1.T0358_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   65   65   5.0   30   2.91   20.00  29.596
REMARK  ---------------------------------------------------------- 
MOLECULE T0358TS393_4-D1
PFRMAT TS
TARGET T0358
MODEL 4
PARENT N/A
ATOM     10  CA  GLY    10     -16.854  -2.200  14.351  1.00 25.00           C
ATOM     11  CA  PRO    11     -14.217  -1.940  17.083  1.00 25.00           C
ATOM     12  CA  PHE    12     -11.916   0.505  15.339  1.00 25.00           C
ATOM     13  CA  THR    13      -9.528   0.838  18.300  1.00 25.00           C
ATOM     14  CA  ARG    14      -6.766   1.762  15.877  1.00 25.00           C
ATOM     15  CA  ARG    15      -7.314  -1.792  14.556  1.00 25.00           C
ATOM     16  CA  GLN    16      -7.990  -0.411  11.049  1.00 25.00           C
ATOM     17  CA  ALA    17      -4.787   1.680  11.227  1.00 25.00           C
ATOM     18  CA  GLN    18      -2.802  -1.409  12.313  1.00 25.00           C
ATOM     19  CA  ALA    19      -4.273  -3.410   9.398  1.00 25.00           C
ATOM     20  CA  VAL    20      -3.326  -0.608   6.965  1.00 25.00           C
ATOM     21  CA  THR    21       0.239  -0.564   8.366  1.00 25.00           C
ATOM     22  CA  THR    22       0.475  -4.364   7.953  1.00 25.00           C
ATOM     23  CA  THR    23      -0.750  -4.071   4.336  1.00 25.00           C
ATOM     24  CA  TYR    24       1.861  -1.356   3.646  1.00 25.00           C
ATOM     25  CA  SER    25       2.563  -3.025   0.281  1.00 25.00           C
ATOM     26  CA  ASN    26      -1.171  -3.058  -0.660  1.00 25.00           C
ATOM     27  CA  ILE    27      -2.382   0.153   1.060  1.00 25.00           C
ATOM     28  CA  THR    28      -2.948   2.853  -1.574  1.00 25.00           C
ATOM     29  CA  LEU    29      -4.703   5.499  -3.739  1.00 25.00           C
ATOM     30  CA  GLU    30      -5.090   9.033  -5.092  1.00 25.00           C
ATOM     31  CA  ASP    31      -3.218   8.412  -8.353  1.00 25.00           C
ATOM     32  CA  ASP    32      -4.163  11.352 -10.524  1.00 25.00           C
ATOM     33  CA  GLN    33      -0.552  12.398 -10.361  1.00 25.00           C
ATOM     34  CA  GLY    34       1.654   9.961  -8.475  1.00 25.00           C
ATOM     35  CA  SER    35       0.504   9.281  -4.949  1.00 25.00           C
ATOM     36  CA  HIS    36      -0.772   8.856  -1.348  1.00 25.00           C
ATOM     37  CA  PHE    37      -4.280   9.482   0.076  1.00 25.00           C
ATOM     38  CA  ARG    38      -6.894   6.764   0.575  1.00 25.00           C
ATOM     39  CA  LEU    39      -7.941   3.100   0.162  1.00 25.00           C
ATOM     40  CA  VAL    40      -8.047  -0.701  -0.087  1.00 25.00           C
ATOM     41  CA  VAL    41      -6.066  -3.329   1.763  1.00 25.00           C
ATOM     42  CA  ARG    42      -6.709  -6.601   3.695  1.00 25.00           C
ATOM     43  CA  ASP    43      -6.191  -9.864   1.822  1.00 25.00           C
ATOM     44  CA  THR    44      -9.156 -12.162   1.171  1.00 25.00           C
ATOM     45  CA  GLU    45      -8.535 -12.798  -2.580  1.00 25.00           C
ATOM     46  CA  GLY    46     -10.859  -9.808  -3.004  1.00 25.00           C
ATOM     47  CA  ARG    47     -11.834  -7.811   0.062  1.00 25.00           C
ATOM     48  CA  MET    48     -11.633  -4.329   1.548  1.00 25.00           C
ATOM     49  CA  VAL    49     -10.376  -1.994   4.257  1.00 25.00           C
ATOM     50  CA  TRP    50      -7.500   0.286   5.173  1.00 25.00           C
ATOM     51  CA  ARG    51      -5.627   3.555   4.583  1.00 25.00           C
ATOM     52  CA  ALA    52      -2.533   4.967   2.940  1.00 25.00           C
ATOM     53  CA  TRP    53       0.943   3.712   4.026  1.00 25.00           C
ATOM     54  CA  ASN    54       2.336   6.568   1.959  1.00 25.00           C
ATOM     55  CA  PHE    55       5.760   8.007   0.974  1.00 25.00           C
ATOM     56  CA  GLU    56       6.220   8.688   4.730  1.00 25.00           C
ATOM     57  CA  PRO    57       8.213   5.487   4.669  1.00 25.00           C
ATOM     58  CA  ASP    58       8.556   5.271   8.479  1.00 25.00           C
ATOM     59  CA  ALA    59       4.850   4.580   8.363  1.00 25.00           C
ATOM     60  CA  GLY    60       4.412   8.095   9.701  1.00 25.00           C
ATOM     61  CA  GLU    61       1.506   9.149   7.456  1.00 25.00           C
ATOM     62  CA  GLY    62      -0.415  12.110   5.970  1.00 25.00           C
ATOM     63  CA  LEU    63      -3.332   9.797   5.069  1.00 25.00           C
ATOM     64  CA  ASN    64      -3.350   8.393   8.632  1.00 25.00           C
ATOM     65  CA  ARG    65      -3.380  11.946  10.059  1.00 25.00           C
ATOM     66  CA  TYR    66      -6.304  12.870   7.764  1.00 25.00           C
ATOM     67  CA  ILE    67      -8.211   9.749   8.899  1.00 25.00           C
ATOM     68  CA  ARG    68      -7.578  10.662  12.563  1.00 25.00           C
ATOM     69  CA  THR    69      -8.843  14.220  11.920  1.00 25.00           C
ATOM     70  CA  SER    70      -5.560  16.196  11.766  1.00 25.00           C
ATOM     71  CA  GLY    71      -5.823  19.838  10.610  1.00 25.00           C
ATOM     72  CA  ILE    72      -9.157  19.910   8.773  1.00 25.00           C
ATOM     73  CA  ARG    73     -11.051  22.990  10.006  1.00 25.00           C
ATOM     74  CA  THR    74      -8.876  24.853  12.596  1.00 25.00           C
TER
END
