
#######################################################
#                                                     #
#                        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   75 (   75),  selected   75 , name T0349TS393_4
# Molecule2: number of CA atoms   75 ( 1131),  selected   75 , name T0349.pdb
# PARAMETERS: T0349TS393_4.T0349.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           -
LGA    -       -      L       4           -
LGA    -       -      L       5           -
LGA    -       -      R       6           -
LGA    -       -      T       7           -
LGA    E       3      N       8           #
LGA    L       4      D       9          1.018
LGA    L       5      A      10          0.789
LGA    R       6      V      11          1.528
LGA    T       7      L      12          1.158
LGA    N       8      L      13          0.520
LGA    D       9      S      14          1.212
LGA    A      10      A      15          1.184
LGA    V      11      V      16          0.867
LGA    L      12      G      17          0.764
LGA    L      13      A      18          0.570
LGA    S      14      L      19          0.545
LGA    A      15      L      20          0.681
LGA    V      16      D      21          0.875
LGA    G      17      G      22          1.841
LGA    A      18      A      23          2.476
LGA    L      19      D      24          2.013
LGA    L      20      -       -           -
LGA    D      21      -       -           -
LGA    G      22      -       -           -
LGA    A      23      -       -           -
LGA    D      24      -       -           -
LGA    I      25      -       -           -
LGA    G      26      -       -           -
LGA    H      27      I      25          5.519
LGA    L      28      G      26          5.283
LGA    V      29      H      27           -
LGA    L      30      -       -           -
LGA    D      31      -       -           -
LGA    Q      32      -       -           -
LGA    N      33      L      28           #
LGA    M      34      -       -           -
LGA    S      35      -       -           -
LGA    I      36      V      29          2.340
LGA    L      37      L      30          4.072
LGA    -       -      D      31           -
LGA    E      38      Q      32          4.162
LGA    G      39      N      33           -
LGA    S      40      M      34           -
LGA    L      41      S      35           -
LGA    G      42      I      36           -
LGA    -       -      L      37           -
LGA    -       -      E      38           -
LGA    -       -      G      39           -
LGA    -       -      S      40           -
LGA    -       -      L      41           -
LGA    -       -      G      42           -
LGA    -       -      V      43           -
LGA    -       -      I      44           -
LGA    V      43      P      45           #
LGA    I      44      R      46           #
LGA    P      45      R      47          5.686
LGA    R      46      V      48          3.686
LGA    R      47      -       -           -
LGA    V      48      -       -           -
LGA    L      49      -       -           -
LGA    V      50      -       -           -
LGA    H      51      -       -           -
LGA    E      52      -       -           -
LGA    D      53      -       -           -
LGA    D      54      -       -           -
LGA    L      55      -       -           -
LGA    A      56      -       -           -
LGA    G      57      -       -           -
LGA    A      58      L      49          4.815
LGA    R      59      V      50          2.814
LGA    R      60      -       -           -
LGA    L      61      H      51          2.710
LGA    L      62      E      52           -
LGA    -       -      D      53           -
LGA    -       -      D      54           -
LGA    T      63      L      55          3.720
LGA    D      64      A      56          3.006
LGA    A      65      G      57          3.060
LGA    G      66      A      58          3.036
LGA    -       -      R      59           -
LGA    -       -      R      60           -
LGA    -       -      L      61           -
LGA    L      67      L      62          2.228
LGA    A      68      T      63          1.450
LGA    H      69      D      64          4.178
LGA    E      70      A      65           -
LGA    -       -      G      66           -
LGA    -       -      L      67           -
LGA    L      71      A      68          5.010
LGA    R      72      H      69           #
LGA    S      73      E      70           -
LGA    D      74      L      71           -
LGA    D      75      R      72           -
LGA    -       -      S      73           -
LGA    -       -      D      74           -
LGA    -       -      D      75           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   75   75    5.0     34    2.96    17.65     31.287     1.110

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.255600 * X  +   0.771745 * Y  +   0.582304 * Z  +  -1.738691
  Y_new =   0.882873 * X  +   0.431765 * Y  +  -0.184698 * Z  +   5.898731
  Z_new =  -0.393958 * X  +   0.466892 * Y  +  -0.791713 * Z  +   3.000136 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.608763   -0.532829  [ DEG:   149.4711    -30.5289 ]
  Theta =   0.404934    2.736659  [ DEG:    23.2010    156.7990 ]
  Phi   =   1.852601   -1.288992  [ DEG:   106.1462    -73.8538 ]
 
# 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_4                                  
REMARK     2: T0349.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS393_4.T0349.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   75   75   5.0   34   2.96   17.65  31.287
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS393_4
PFRMAT TS
TARGET T0349
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1      -1.322 -11.594  13.843  1.00 25.00           C
ATOM      2  CA  ARG     2      -4.076  -9.262  12.673  1.00 25.00           C
ATOM      3  CA  GLU     3      -4.732  -9.638   8.947  1.00 25.00           C
ATOM      4  CA  LEU     4      -3.605  -8.015   5.666  1.00 25.00           C
ATOM      5  CA  LEU     5      -6.946  -6.163   5.407  1.00 25.00           C
ATOM      6  CA  ARG     6      -6.573  -4.933   9.014  1.00 25.00           C
ATOM      7  CA  THR     7      -3.022  -3.716   8.258  1.00 25.00           C
ATOM      8  CA  ASN     8      -4.290  -1.872   5.150  1.00 25.00           C
ATOM      9  CA  ASP     9      -7.061  -0.233   7.223  1.00 25.00           C
ATOM     10  CA  ALA    10      -4.492   0.850   9.847  1.00 25.00           C
ATOM     11  CA  VAL    11      -2.273   2.332   7.101  1.00 25.00           C
ATOM     12  CA  LEU    12      -5.275   4.231   5.667  1.00 25.00           C
ATOM     13  CA  LEU    13      -6.112   5.586   9.149  1.00 25.00           C
ATOM     14  CA  SER    14      -2.481   6.713   9.610  1.00 25.00           C
ATOM     15  CA  ALA    15      -2.566   8.463   6.204  1.00 25.00           C
ATOM     16  CA  VAL    16      -5.827  10.224   7.163  1.00 25.00           C
ATOM     17  CA  GLY    17      -4.272  11.360  10.473  1.00 25.00           C
ATOM     18  CA  ALA    18      -1.210  12.700   8.602  1.00 25.00           C
ATOM     19  CA  LEU    19      -3.491  14.596   6.179  1.00 25.00           C
ATOM     20  CA  LEU    20      -5.421  16.094   9.128  1.00 25.00           C
ATOM     21  CA  ASP    21      -2.131  17.174  10.765  1.00 25.00           C
ATOM     22  CA  GLY    22      -2.662  20.871   9.990  1.00 25.00           C
ATOM     23  CA  ALA    23      -4.483  21.101   6.678  1.00 25.00           C
ATOM     24  CA  ASP    24      -1.120  22.102   5.211  1.00 25.00           C
ATOM     25  CA  ILE    25      -1.276  18.853   3.307  1.00 25.00           C
ATOM     26  CA  GLY    26      -4.807  18.106   2.161  1.00 25.00           C
ATOM     27  CA  HIS    27      -7.494  15.751   3.380  1.00 25.00           C
ATOM     28  CA  LEU    28      -8.916  13.802   0.395  1.00 25.00           C
ATOM     29  CA  VAL    29     -11.321  10.883   1.163  1.00 25.00           C
ATOM     30  CA  LEU    30     -12.228   8.237   3.798  1.00 25.00           C
ATOM     31  CA  ASP    31     -14.657   6.991   1.108  1.00 25.00           C
ATOM     32  CA  GLN    32     -11.555   5.393  -0.353  1.00 25.00           C
ATOM     33  CA  ASN    33     -12.920   5.585  -3.905  1.00 25.00           C
ATOM     34  CA  MET    34     -11.909   1.893  -3.956  1.00 25.00           C
ATOM     35  CA  SER    35      -8.548   0.456  -4.990  1.00 25.00           C
ATOM     36  CA  ILE    36      -6.198   1.771  -2.265  1.00 25.00           C
ATOM     37  CA  LEU    37      -3.422  -0.559  -3.500  1.00 25.00           C
ATOM     38  CA  GLU    38      -3.976  -0.831  -7.291  1.00 25.00           C
ATOM     39  CA  GLY    39      -1.733   1.980  -8.573  1.00 25.00           C
ATOM     40  CA  SER    40       1.835   3.288  -8.674  1.00 25.00           C
ATOM     41  CA  LEU    41       4.366   2.201  -6.120  1.00 25.00           C
ATOM     42  CA  GLY    42       4.620  -1.554  -5.963  1.00 25.00           C
ATOM     43  CA  VAL    43       2.520  -1.470  -2.790  1.00 25.00           C
ATOM     44  CA  ILE    44       1.453  -0.150   0.615  1.00 25.00           C
ATOM     45  CA  PRO    45       2.540   3.421   0.200  1.00 25.00           C
ATOM     46  CA  ARG    46      -0.363   4.138   2.619  1.00 25.00           C
ATOM     47  CA  ARG    47      -2.963   5.208   0.017  1.00 25.00           C
ATOM     48  CA  VAL    48      -6.277   6.860  -1.023  1.00 25.00           C
ATOM     49  CA  LEU    49      -7.730   6.062  -4.415  1.00 25.00           C
ATOM     50  CA  VAL    50      -9.567   4.800  -7.566  1.00 25.00           C
ATOM     51  CA  HIS    51      -7.585   5.769 -10.703  1.00 25.00           C
ATOM     52  CA  GLU    52      -4.186   5.964 -12.270  1.00 25.00           C
ATOM     53  CA  ASP    53      -3.186   9.631 -11.807  1.00 25.00           C
ATOM     54  CA  ASP    54      -5.295   9.830  -8.616  1.00 25.00           C
ATOM     55  CA  LEU    55      -3.634   6.643  -7.292  1.00 25.00           C
ATOM     56  CA  ALA    56      -0.175   8.102  -8.049  1.00 25.00           C
ATOM     57  CA  GLY    57      -1.109  11.332  -6.215  1.00 25.00           C
ATOM     58  CA  ALA    58      -2.316   9.302  -3.201  1.00 25.00           C
ATOM     59  CA  ARG    59       0.965   7.326  -3.187  1.00 25.00           C
ATOM     60  CA  ARG    60       2.960  10.592  -3.311  1.00 25.00           C
ATOM     61  CA  LEU    61       0.914  11.983  -0.388  1.00 25.00           C
ATOM     62  CA  LEU    62       1.556   8.783   1.616  1.00 25.00           C
ATOM     63  CA  THR    63       5.308   9.054   0.892  1.00 25.00           C
ATOM     64  CA  ASP    64       5.289  12.709   2.033  1.00 25.00           C
ATOM     65  CA  ALA    65       3.472  11.719   5.256  1.00 25.00           C
ATOM     66  CA  GLY    66       4.960   8.264   6.061  1.00 25.00           C
ATOM     67  CA  LEU    67       6.182   5.063   7.710  1.00 25.00           C
ATOM     68  CA  ALA    68       9.483   6.079   9.305  1.00 25.00           C
ATOM     69  CA  HIS    69      12.064   7.751  11.446  1.00 25.00           C
ATOM     70  CA  GLU    70      14.478   5.357  13.113  1.00 25.00           C
ATOM     71  CA  LEU    71      11.491   2.958  13.145  1.00 25.00           C
ATOM     72  CA  ARG    72      12.725   1.933  16.613  1.00 25.00           C
ATOM     73  CA  SER    73      12.535   3.570  20.106  1.00 25.00           C
ATOM     74  CA  ASP    74      10.811   1.099  22.440  1.00 25.00           C
ATOM     75  CA  ASP    75       7.614   1.089  24.465  1.00 25.00           C
TER
END
