
#######################################################
#                                                     #
#                        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 T0349TS168_1
# Molecule2: number of CA atoms   75 ( 1131),  selected   75 , name T0349.pdb
# PARAMETERS: T0349TS168_1.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    E       3      T       7          6.193
LGA    L       4      N       8          2.725
LGA    L       5      D       9          3.083
LGA    R       6      A      10          2.758
LGA    -       -      V      11           -
LGA    T       7      L      12          2.284
LGA    N       8      L      13          2.496
LGA    D       9      S      14          2.383
LGA    A      10      A      15          1.737
LGA    V      11      V      16          1.515
LGA    L      12      G      17          1.402
LGA    L      13      A      18          1.014
LGA    S      14      L      19          0.836
LGA    A      15      L      20          0.457
LGA    V      16      D      21          0.968
LGA    G      17      G      22          1.624
LGA    A      18      A      23          1.627
LGA    L      19      D      24          1.594
LGA    L      20      I      25           -
LGA    D      21      G      26           -
LGA    G      22      H      27           -
LGA    A      23      L      28           -
LGA    D      24      -       -           -
LGA    I      25      -       -           -
LGA    G      26      -       -           -
LGA    H      27      -       -           -
LGA    L      28      -       -           -
LGA    V      29      -       -           -
LGA    L      30      -       -           -
LGA    D      31      -       -           -
LGA    Q      32      -       -           -
LGA    N      33      -       -           -
LGA    M      34      -       -           -
LGA    S      35      V      29          2.776
LGA    I      36      L      30           -
LGA    L      37      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    -       -      R      47           -
LGA    -       -      V      48           -
LGA    -       -      L      49           -
LGA    E      38      V      50           #
LGA    G      39      H      51          2.827
LGA    S      40      E      52          2.541
LGA    L      41      D      53          2.022
LGA    G      42      D      54           -
LGA    V      43      -       -           -
LGA    I      44      -       -           -
LGA    P      45      -       -           -
LGA    R      46      -       -           -
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      L      55          3.897
LGA    A      58      A      56           -
LGA    R      59      G      57           -
LGA    R      60      A      58          3.912
LGA    L      61      -       -           -
LGA    L      62      R      59          4.939
LGA    T      63      R      60          4.168
LGA    D      64      L      61          1.490
LGA    A      65      L      62          4.510
LGA    G      66      T      63          5.311
LGA    -       -      D      64           -
LGA    -       -      A      65           -
LGA    L      67      G      66          2.360
LGA    A      68      L      67          2.986
LGA    H      69      A      68           #
LGA    E      70      H      69           -
LGA    L      71      E      70           -
LGA    R      72      L      71           -
LGA    S      73      R      72           -
LGA    D      74      S      73           -
LGA    D      75      D      74           -
LGA    -       -      D      75           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   75   75    5.0     30    2.95    13.33     29.264     0.982

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.503165 * X  +  -0.700376 * Y  +   0.506259 * Z  +  -1.530510
  Y_new =   0.858486 * X  +  -0.337897 * Y  +   0.385781 * Z  +   5.914451
  Z_new =  -0.099128 * X  +   0.628728 * Y  +   0.771281 * Z  +   5.456235 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.683925   -2.457668  [ DEG:    39.1860   -140.8140 ]
  Theta =   0.099291    3.042302  [ DEG:     5.6890    174.3111 ]
  Phi   =   2.100938   -1.040655  [ DEG:   120.3749    -59.6251 ]
 
# 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: T0349TS168_1                                  
REMARK     2: T0349.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS168_1.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   30   2.95   13.33  29.264
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS168_1
PFRMAT TS
TARGET T0349
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1      -2.974 -13.843  10.768  1.00 25.00           C
ATOM      2  CA  ARG     2      -3.677 -11.116   8.190  1.00 25.00           C
ATOM      3  CA  GLU     3      -1.292  -9.226   5.870  1.00 25.00           C
ATOM      4  CA  LEU     4      -0.621  -6.874   2.924  1.00 25.00           C
ATOM      5  CA  LEU     5      -4.249  -5.653   3.041  1.00 25.00           C
ATOM      6  CA  ARG     6      -3.944  -5.027   6.807  1.00 25.00           C
ATOM      7  CA  THR     7      -0.705  -3.063   6.243  1.00 25.00           C
ATOM      8  CA  ASN     8      -2.419  -0.968   3.533  1.00 25.00           C
ATOM      9  CA  ASP     9      -5.346  -0.258   5.898  1.00 25.00           C
ATOM     10  CA  ALA    10      -2.899   0.803   8.647  1.00 25.00           C
ATOM     11  CA  VAL    11      -1.106   3.127   6.188  1.00 25.00           C
ATOM     12  CA  LEU    12      -4.460   4.661   5.154  1.00 25.00           C
ATOM     13  CA  LEU    13      -5.372   5.207   8.833  1.00 25.00           C
ATOM     14  CA  SER    14      -1.986   6.886   9.449  1.00 25.00           C
ATOM     15  CA  ALA    15      -2.533   9.160   6.416  1.00 25.00           C
ATOM     16  CA  VAL    16      -6.013  10.093   7.714  1.00 25.00           C
ATOM     17  CA  GLY    17      -4.541  10.897  11.157  1.00 25.00           C
ATOM     18  CA  ALA    18      -1.855  13.086   9.524  1.00 25.00           C
ATOM     19  CA  LEU    19      -4.544  14.925   7.509  1.00 25.00           C
ATOM     20  CA  LEU    20      -6.579  15.500  10.702  1.00 25.00           C
ATOM     21  CA  ASP    21      -3.468  16.864  12.469  1.00 25.00           C
ATOM     22  CA  GLY    22      -3.982  16.444  16.242  1.00 25.00           C
ATOM     23  CA  ALA    23      -7.613  15.443  15.805  1.00 25.00           C
ATOM     24  CA  ASP    24      -7.338  12.786  18.500  1.00 25.00           C
ATOM     25  CA  ILE    25      -6.329  10.278  15.872  1.00 25.00           C
ATOM     26  CA  GLY    26      -9.422  10.062  13.688  1.00 25.00           C
ATOM     27  CA  HIS    27     -10.720  10.247  10.062  1.00 25.00           C
ATOM     28  CA  LEU    28     -12.870   8.927   7.176  1.00 25.00           C
ATOM     29  CA  VAL    29     -11.616   5.943   5.247  1.00 25.00           C
ATOM     30  CA  LEU    30     -11.822   2.852   3.022  1.00 25.00           C
ATOM     31  CA  ASP    31     -12.956   3.478  -0.546  1.00 25.00           C
ATOM     32  CA  GLN    32     -10.547   0.683  -1.559  1.00 25.00           C
ATOM     33  CA  ASN    33      -7.345   1.288  -3.396  1.00 25.00           C
ATOM     34  CA  MET    34      -7.070   4.435  -1.368  1.00 25.00           C
ATOM     35  CA  SER    35      -3.401   5.350  -1.175  1.00 25.00           C
ATOM     36  CA  ILE    36      -4.213   8.468   0.895  1.00 25.00           C
ATOM     37  CA  LEU    37      -2.367  10.664  -1.642  1.00 25.00           C
ATOM     38  CA  GLU    38      -3.256  11.631  -5.209  1.00 25.00           C
ATOM     39  CA  GLY    39      -0.639  14.396  -4.975  1.00 25.00           C
ATOM     40  CA  SER    40       1.845  14.553  -2.120  1.00 25.00           C
ATOM     41  CA  LEU    41       0.787  18.029  -0.992  1.00 25.00           C
ATOM     42  CA  GLY    42      -2.017  19.878  -2.701  1.00 25.00           C
ATOM     43  CA  VAL    43      -4.091  16.880  -1.676  1.00 25.00           C
ATOM     44  CA  ILE    44      -3.911  14.800   1.469  1.00 25.00           C
ATOM     45  CA  PRO    45      -6.888  12.709   0.245  1.00 25.00           C
ATOM     46  CA  ARG    46      -8.947   9.576  -0.671  1.00 25.00           C
ATOM     47  CA  ARG    47     -10.486   7.538  -3.542  1.00 25.00           C
ATOM     48  CA  VAL    48      -7.209   7.352  -5.520  1.00 25.00           C
ATOM     49  CA  LEU    49      -5.115   4.717  -7.248  1.00 25.00           C
ATOM     50  CA  VAL    50      -2.653   2.082  -6.017  1.00 25.00           C
ATOM     51  CA  HIS    51       0.020   4.003  -7.970  1.00 25.00           C
ATOM     52  CA  GLU    52       3.815   4.145  -8.074  1.00 25.00           C
ATOM     53  CA  ASP    53       4.633   7.763  -7.122  1.00 25.00           C
ATOM     54  CA  ASP    54       1.294   8.058  -5.271  1.00 25.00           C
ATOM     55  CA  LEU    55       2.019   4.798  -3.396  1.00 25.00           C
ATOM     56  CA  ALA    56       5.489   6.097  -2.429  1.00 25.00           C
ATOM     57  CA  GLY    57       3.943   9.366  -1.171  1.00 25.00           C
ATOM     58  CA  ALA    58       1.393   7.393   0.896  1.00 25.00           C
ATOM     59  CA  ARG    59       4.208   5.270   2.389  1.00 25.00           C
ATOM     60  CA  ARG    60       6.164   8.441   3.274  1.00 25.00           C
ATOM     61  CA  LEU    61       3.052   9.924   4.943  1.00 25.00           C
ATOM     62  CA  LEU    62       2.561   6.699   6.947  1.00 25.00           C
ATOM     63  CA  THR    63       6.227   6.797   8.052  1.00 25.00           C
ATOM     64  CA  ASP    64       5.829  10.450   9.133  1.00 25.00           C
ATOM     65  CA  ALA    65       2.684   9.543  11.123  1.00 25.00           C
ATOM     66  CA  GLY    66       3.402   5.916  12.160  1.00 25.00           C
ATOM     67  CA  LEU    67       4.846   2.393  11.877  1.00 25.00           C
ATOM     68  CA  ALA    68       7.578   1.869  14.466  1.00 25.00           C
ATOM     69  CA  HIS    69      11.038   2.537  15.770  1.00 25.00           C
ATOM     70  CA  GLU    70      10.628   3.228  19.450  1.00 25.00           C
ATOM     71  CA  LEU    71       7.349   1.296  19.462  1.00 25.00           C
ATOM     72  CA  ARG    72       7.291  -0.209  22.956  1.00 25.00           C
ATOM     73  CA  SER    73       8.319  -3.795  22.528  1.00 25.00           C
ATOM     74  CA  ASP    74      11.752  -5.529  22.606  1.00 25.00           C
ATOM     75  CA  ASP    75      12.268  -9.194  21.654  1.00 25.00           C
TER
END
