
#######################################################
#                                                     #
#                        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_3
# Molecule2: number of CA atoms   75 ( 1131),  selected   75 , name T0349.pdb
# PARAMETERS: T0349TS393_3.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      E       3           -
LGA    -       -      L       4           -
LGA    -       -      L       5           -
LGA    -       -      R       6           -
LGA    -       -      T       7           -
LGA    L       4      N       8           #
LGA    L       5      D       9          0.927
LGA    R       6      A      10          1.595
LGA    T       7      V      11          1.131
LGA    N       8      L      12          0.192
LGA    D       9      L      13          0.904
LGA    A      10      S      14          0.870
LGA    V      11      A      15          0.420
LGA    L      12      V      16          0.428
LGA    L      13      G      17          0.900
LGA    S      14      A      18          0.714
LGA    A      15      L      19          1.298
LGA    V      16      L      20          1.498
LGA    G      17      D      21          2.461
LGA    A      18      G      22          2.857
LGA    L      19      A      23          3.097
LGA    L      20      D      24          3.531
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    V      29      H      27          4.653
LGA    L      30      L      28          4.039
LGA    D      31      V      29           #
LGA    Q      32      L      30           #
LGA    N      33      -       -           -
LGA    M      34      D      31           #
LGA    -       -      Q      32           -
LGA    -       -      N      33           -
LGA    -       -      M      34           -
LGA    -       -      S      35           -
LGA    -       -      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    -       -      P      45           -
LGA    -       -      R      46           -
LGA    S      35      R      47          4.213
LGA    I      36      V      48          2.236
LGA    L      37      L      49          3.084
LGA    E      38      -       -           -
LGA    G      39      -       -           -
LGA    S      40      -       -           -
LGA    L      41      -       -           -
LGA    G      42      -       -           -
LGA    V      43      -       -           -
LGA    I      44      -       -           -
LGA    P      45      -       -           -
LGA    R      46      -       -           -
LGA    R      47      -       -           -
LGA    V      48      V      50          2.559
LGA    L      49      H      51          2.764
LGA    V      50      -       -           -
LGA    H      51      -       -           -
LGA    E      52      E      52          3.119
LGA    D      53      D      53          3.340
LGA    D      54      D      54          2.578
LGA    L      55      L      55          1.653
LGA    A      56      A      56          1.343
LGA    G      57      G      57          1.905
LGA    A      58      A      58          1.526
LGA    R      59      R      59          0.613
LGA    R      60      R      60          1.542
LGA    L      61      L      61          1.936
LGA    L      62      L      62          0.831
LGA    T      63      T      63          1.724
LGA    D      64      D      64          3.201
LGA    A      65      A      65          2.799
LGA    -       -      G      66           -
LGA    G      66      L      67          2.709
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      S      73           -
LGA    S      73      D      74           -
LGA    D      74      D      75           -
LGA    D      75      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   75   75    5.0     38    2.33    44.74     37.403     1.564

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.394136 * X  +   0.254102 * Y  +   0.883227 * Z  +   0.101364
  Y_new =  -0.043989 * X  +   0.965133 * Y  +  -0.258037 * Z  +   4.801687
  Z_new =  -0.917999 * X  +   0.062849 * Y  +   0.391571 * Z  +   6.480776 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.159148   -2.982444  [ DEG:     9.1185   -170.8815 ]
  Theta =   1.163005    1.978588  [ DEG:    66.6353    113.3647 ]
  Phi   =  -0.111148    3.030444  [ DEG:    -6.3683    173.6317 ]
 
# 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                                  
REMARK     2: T0349.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS393_3.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   38   2.33   44.74  37.403
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS393_3
PFRMAT TS
TARGET T0349
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      -8.454 -15.072  10.295  1.00 25.00           C
ATOM      2  CA  ARG     2      -7.760 -11.637   8.853  1.00 25.00           C
ATOM      3  CA  GLU     3      -6.523 -10.445   5.498  1.00 25.00           C
ATOM      4  CA  LEU     4      -3.394  -9.525   7.505  1.00 25.00           C
ATOM      5  CA  LEU     5      -2.183  -7.290   4.641  1.00 25.00           C
ATOM      6  CA  ARG     6      -5.606  -5.577   4.498  1.00 25.00           C
ATOM      7  CA  THR     7      -5.501  -4.998   8.283  1.00 25.00           C
ATOM      8  CA  ASN     8      -1.988  -3.502   7.981  1.00 25.00           C
ATOM      9  CA  ASP     9      -3.186  -1.192   5.171  1.00 25.00           C
ATOM     10  CA  ALA    10      -6.156  -0.080   7.319  1.00 25.00           C
ATOM     11  CA  VAL    11      -3.799   0.634  10.252  1.00 25.00           C
ATOM     12  CA  LEU    12      -1.521   2.683   7.955  1.00 25.00           C
ATOM     13  CA  LEU    13      -4.542   4.668   6.690  1.00 25.00           C
ATOM     14  CA  SER    14      -5.645   5.338  10.295  1.00 25.00           C
ATOM     15  CA  ALA    15      -2.114   6.531  11.179  1.00 25.00           C
ATOM     16  CA  VAL    16      -2.111   8.855   8.136  1.00 25.00           C
ATOM     17  CA  GLY    17      -5.516  10.265   9.179  1.00 25.00           C
ATOM     18  CA  ALA    18      -4.210  10.860  12.730  1.00 25.00           C
ATOM     19  CA  LEU    19      -1.131  12.653  11.323  1.00 25.00           C
ATOM     20  CA  LEU    20      -3.380  14.845   9.131  1.00 25.00           C
ATOM     21  CA  ASP    21      -5.551  15.699  12.168  1.00 25.00           C
ATOM     22  CA  GLY    22      -7.695  14.635  15.136  1.00 25.00           C
ATOM     23  CA  ALA    23     -10.175  13.740  12.404  1.00 25.00           C
ATOM     24  CA  ASP    24     -10.595  16.747  10.076  1.00 25.00           C
ATOM     25  CA  ILE    25      -8.031  16.093   7.432  1.00 25.00           C
ATOM     26  CA  GLY    26      -9.709  12.749   7.131  1.00 25.00           C
ATOM     27  CA  HIS    27      -9.611   9.482   5.217  1.00 25.00           C
ATOM     28  CA  LEU    28      -8.829   9.031   1.525  1.00 25.00           C
ATOM     29  CA  VAL    29      -6.743   6.142   0.160  1.00 25.00           C
ATOM     30  CA  LEU    30      -7.269   4.073  -2.968  1.00 25.00           C
ATOM     31  CA  ASP    31      -8.381   7.367  -4.511  1.00 25.00           C
ATOM     32  CA  GLN    32      -4.813   8.576  -4.384  1.00 25.00           C
ATOM     33  CA  ASN    33      -3.764   5.636  -6.528  1.00 25.00           C
ATOM     34  CA  MET    34      -0.573   5.378  -4.529  1.00 25.00           C
ATOM     35  CA  SER    35       1.949   2.486  -4.423  1.00 25.00           C
ATOM     36  CA  ILE    36       2.206   2.908  -0.626  1.00 25.00           C
ATOM     37  CA  LEU    37       3.605   6.443  -1.089  1.00 25.00           C
ATOM     38  CA  GLU    38       6.585   7.279  -3.395  1.00 25.00           C
ATOM     39  CA  GLY    39       7.968   3.760  -2.706  1.00 25.00           C
ATOM     40  CA  SER    40       9.813   5.512   0.160  1.00 25.00           C
ATOM     41  CA  LEU    41      11.495   2.901   2.319  1.00 25.00           C
ATOM     42  CA  GLY    42      11.729  -0.739   1.218  1.00 25.00           C
ATOM     43  CA  VAL    43       7.908  -0.518   1.314  1.00 25.00           C
ATOM     44  CA  ILE    44       4.440  -0.024   2.783  1.00 25.00           C
ATOM     45  CA  PRO    45       5.383   2.777   5.236  1.00 25.00           C
ATOM     46  CA  ARG    46       1.908   4.186   4.518  1.00 25.00           C
ATOM     47  CA  ARG    47      -0.323   6.673   2.705  1.00 25.00           C
ATOM     48  CA  VAL    48      -1.063   9.675   0.571  1.00 25.00           C
ATOM     49  CA  LEU    49       0.562  10.115  -2.798  1.00 25.00           C
ATOM     50  CA  VAL    50       2.790   9.471  -5.815  1.00 25.00           C
ATOM     51  CA  HIS    51       3.860  13.117  -5.607  1.00 25.00           C
ATOM     52  CA  GLU    52       7.014  14.666  -4.282  1.00 25.00           C
ATOM     53  CA  ASP    53       5.895  16.848  -1.340  1.00 25.00           C
ATOM     54  CA  ASP    54       2.812  14.631  -0.837  1.00 25.00           C
ATOM     55  CA  LEU    55       5.023  11.504  -0.879  1.00 25.00           C
ATOM     56  CA  ALA    56       7.359  13.093   1.708  1.00 25.00           C
ATOM     57  CA  GLY    57       4.357  13.953   3.926  1.00 25.00           C
ATOM     58  CA  ALA    58       3.086  10.351   3.644  1.00 25.00           C
ATOM     59  CA  ARG    59       6.550   9.028   4.599  1.00 25.00           C
ATOM     60  CA  ARG    60       6.639  11.374   7.625  1.00 25.00           C
ATOM     61  CA  LEU    61       3.164  10.168   8.693  1.00 25.00           C
ATOM     62  CA  LEU    62       4.303   6.525   8.372  1.00 25.00           C
ATOM     63  CA  THR    63       7.403   7.282  10.490  1.00 25.00           C
ATOM     64  CA  ASP    64       5.209   8.947  13.152  1.00 25.00           C
ATOM     65  CA  ALA    65       2.892   5.898  13.184  1.00 25.00           C
ATOM     66  CA  GLY    66       3.445   2.093  13.263  1.00 25.00           C
ATOM     67  CA  LEU    67       0.492   0.586  15.181  1.00 25.00           C
ATOM     68  CA  ALA    68       1.341   0.753  18.929  1.00 25.00           C
ATOM     69  CA  HIS    69       4.381   0.917  21.162  1.00 25.00           C
ATOM     70  CA  GLU    70       7.776  -0.888  21.493  1.00 25.00           C
ATOM     71  CA  LEU    71       5.964  -3.568  19.432  1.00 25.00           C
ATOM     72  CA  ARG    72       6.042  -5.622  22.565  1.00 25.00           C
ATOM     73  CA  SER    73       4.174  -5.556  25.926  1.00 25.00           C
ATOM     74  CA  ASP    74       4.080  -9.357  25.895  1.00 25.00           C
ATOM     75  CA  ASP    75       4.165 -12.912  24.701  1.00 25.00           C
TER
END
