
#######################################################
#                                                     #
#                        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   57 (   57),  selected   57 , name T0349TS393_3-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS393_3-D1.T0349_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    R       2      R       2           -
LGA    E       3      E       3           -
LGA    L       4      L       4           -
LGA    -       -      L       5           -
LGA    -       -      R       6           -
LGA    L       5      T       7          2.874
LGA    R       6      N       8          2.610
LGA    T       7      D       9          2.744
LGA    -       -      A      10           -
LGA    -       -      V      11           -
LGA    N       8      L      12          1.955
LGA    D       9      L      13          2.342
LGA    A      10      S      14          2.408
LGA    V      11      A      15          1.641
LGA    L      12      V      16          0.941
LGA    L      13      G      17          0.978
LGA    S      14      A      18          1.309
LGA    A      15      L      19          1.492
LGA    V      16      L      20          1.214
LGA    G      17      D      21          1.770
LGA    A      18      G      22          2.491
LGA    L      19      A      23          2.885
LGA    L      20      D      24          3.025
LGA    D      21      -       -           -
LGA    G      22      -       -           -
LGA    A      23      -       -           -
LGA    D      24      -       -           -
LGA    I      25      I      25           #
LGA    G      26      -       -           -
LGA    H      27      -       -           -
LGA    L      28      G      26           #
LGA    -       -      H      27           -
LGA    V      29      L      28          2.892
LGA    P      45      V      29           -
LGA    -       -      P      45           -
LGA    -       -      R      46           -
LGA    -       -      R      47           -
LGA    R      46      V      48          5.508
LGA    R      47      -       -           -
LGA    V      48      L      49          5.032
LGA    L      49      V      50          2.027
LGA    V      50      H      51          4.819
LGA    H      51      -       -           -
LGA    E      52      E      52          3.240
LGA    D      53      D      53          2.943
LGA    D      54      D      54          2.336
LGA    L      55      L      55          1.137
LGA    A      56      A      56          1.431
LGA    G      57      G      57          2.055
LGA    A      58      A      58          1.592
LGA    R      59      R      59          0.984
LGA    R      60      R      60          1.906
LGA    L      61      L      61          2.180
LGA    L      62      L      62          1.039
LGA    T      63      T      63          1.833
LGA    D      64      D      64          3.469
LGA    A      65      A      65          3.326
LGA    -       -      G      66           -
LGA    G      66      L      67          2.049
LGA    L      67      A      68           -
LGA    A      68      H      69           -
LGA    H      69      E      70           -
LGA    E      70      L      71           -
LGA    L      71      R      72           -
LGA    R      72      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   57   57    5.0     36    2.59    38.89     44.725     1.338

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.439740 * X  +   0.151956 * Y  +   0.885177 * Z  +   0.532284
  Y_new =   0.062704 * X  +   0.977983 * Y  +  -0.199039 * Z  +   4.524328
  Z_new =  -0.895933 * X  +   0.143030 * Y  +   0.420531 * Z  +   5.819359 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.327844   -2.813749  [ DEG:    18.7841   -161.2159 ]
  Theta =   1.110528    2.031065  [ DEG:    63.6286    116.3714 ]
  Phi   =   0.141639   -2.999954  [ DEG:     8.1153   -171.8847 ]
 
# 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: T0349TS393_3-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS393_3-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   57   57   5.0   36   2.59   38.89  44.725
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS393_3-D1
PFRMAT TS
TARGET T0349
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      -6.142 -16.316   7.781  1.00 25.00           C
ATOM      2  CA  ARG     2      -5.731 -12.732   6.619  1.00 25.00           C
ATOM      3  CA  GLU     3      -4.462 -11.180   3.427  1.00 25.00           C
ATOM      4  CA  LEU     4      -1.541 -10.111   5.661  1.00 25.00           C
ATOM      5  CA  LEU     5      -0.428  -7.563   3.029  1.00 25.00           C
ATOM      6  CA  ARG     6      -3.996  -6.186   2.817  1.00 25.00           C
ATOM      7  CA  THR     7      -4.130  -5.881   6.632  1.00 25.00           C
ATOM      8  CA  ASN     8      -0.775  -4.032   6.627  1.00 25.00           C
ATOM      9  CA  ASP     9      -2.067  -1.647   3.922  1.00 25.00           C
ATOM     10  CA  ALA    10      -5.232  -0.993   5.976  1.00 25.00           C
ATOM     11  CA  VAL    11      -3.102  -0.272   9.075  1.00 25.00           C
ATOM     12  CA  LEU    12      -0.936   2.155   7.054  1.00 25.00           C
ATOM     13  CA  LEU    13      -4.079   3.924   5.764  1.00 25.00           C
ATOM     14  CA  SER    14      -5.413   4.214   9.342  1.00 25.00           C
ATOM     15  CA  ALA    15      -2.067   5.677  10.497  1.00 25.00           C
ATOM     16  CA  VAL    16      -2.155   8.209   7.627  1.00 25.00           C
ATOM     17  CA  GLY    17      -5.731   9.200   8.576  1.00 25.00           C
ATOM     18  CA  ALA    18      -4.661   9.654  12.226  1.00 25.00           C
ATOM     19  CA  LEU    19      -1.717  11.838  11.116  1.00 25.00           C
ATOM     20  CA  LEU    20      -4.069  13.957   8.961  1.00 25.00           C
ATOM     21  CA  ASP    21      -6.456  14.368  11.927  1.00 25.00           C
ATOM     22  CA  GLY    22      -8.621  12.883  14.693  1.00 25.00           C
ATOM     23  CA  ALA    23     -10.865  11.956  11.774  1.00 25.00           C
ATOM     24  CA  ASP    24     -11.476  15.072   9.640  1.00 25.00           C
ATOM     25  CA  ILE    25      -8.736  14.868   7.101  1.00 25.00           C
ATOM     26  CA  GLY    26     -10.051  11.408   6.479  1.00 25.00           C
ATOM     27  CA  HIS    27      -9.533   8.317   4.353  1.00 25.00           C
ATOM     28  CA  LEU    28      -8.534   8.219   0.686  1.00 25.00           C
ATOM     29  CA  VAL    29      -6.104   5.656  -0.759  1.00 25.00           C
ATOM     45  CA  PRO    45       6.045   3.122   4.728  1.00 25.00           C
ATOM     46  CA  ARG    46       2.483   4.235   3.921  1.00 25.00           C
ATOM     47  CA  ARG    47       0.101   6.620   2.164  1.00 25.00           C
ATOM     48  CA  VAL    48      -0.837   9.685   0.205  1.00 25.00           C
ATOM     49  CA  LEU    49       0.894  10.530  -3.032  1.00 25.00           C
ATOM     50  CA  VAL    50       3.316  10.331  -5.960  1.00 25.00           C
ATOM     51  CA  HIS    51       4.001  14.038  -5.443  1.00 25.00           C
ATOM     52  CA  GLU    52       6.916  15.785  -3.844  1.00 25.00           C
ATOM     53  CA  ASP    53       5.443  17.624  -0.824  1.00 25.00           C
ATOM     54  CA  ASP    54       2.580  15.085  -0.645  1.00 25.00           C
ATOM     55  CA  LEU    55       5.096  12.201  -0.780  1.00 25.00           C
ATOM     56  CA  ALA    56       7.133  13.813   2.034  1.00 25.00           C
ATOM     57  CA  GLY    57       3.958  14.211   4.138  1.00 25.00           C
ATOM     58  CA  ALA    58       3.072  10.533   3.539  1.00 25.00           C
ATOM     59  CA  ARG    59       6.602   9.486   4.589  1.00 25.00           C
ATOM     60  CA  ARG    60       6.310  11.599   7.770  1.00 25.00           C
ATOM     61  CA  LEU    61       2.929   9.985   8.561  1.00 25.00           C
ATOM     62  CA  LEU    62       4.444   6.504   8.052  1.00 25.00           C
ATOM     63  CA  THR    63       7.347   7.400  10.383  1.00 25.00           C
ATOM     64  CA  ASP    64       4.872   8.642  13.029  1.00 25.00           C
ATOM     65  CA  ALA    65       2.876   5.388  12.725  1.00 25.00           C
ATOM     66  CA  GLY    66       3.807   1.660  12.571  1.00 25.00           C
ATOM     67  CA  LEU    67       0.934  -0.266  14.216  1.00 25.00           C
ATOM     68  CA  ALA    68       1.582  -0.295  18.008  1.00 25.00           C
ATOM     69  CA  HIS    69       4.480  -0.001  20.410  1.00 25.00           C
ATOM     70  CA  GLU    70       8.021  -1.487  20.800  1.00 25.00           C
ATOM     71  CA  LEU    71       6.589  -4.170  18.463  1.00 25.00           C
ATOM     72  CA  ARG    72       6.726  -6.433  21.447  1.00 25.00           C
TER
END
