
#######################################################
#                                                     #
#                        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 T0349TS599_4
# Molecule2: number of CA atoms   75 ( 1131),  selected   75 , name T0349.pdb
# PARAMETERS: T0349TS599_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      E       3           -
LGA    L       4      L       4           -
LGA    L       5      L       5           -
LGA    R       6      R       6           -
LGA    T       7      -       -           -
LGA    N       8      T       7          4.388
LGA    D       9      N       8          2.475
LGA    A      10      D       9          3.147
LGA    -       -      A      10           -
LGA    V      11      V      11          0.889
LGA    L      12      L      12          0.890
LGA    L      13      L      13          0.659
LGA    S      14      S      14          0.483
LGA    A      15      A      15          0.540
LGA    V      16      V      16          0.753
LGA    G      17      G      17          0.752
LGA    A      18      A      18          0.382
LGA    L      19      L      19          0.333
LGA    L      20      L      20          0.613
LGA    D      21      D      21          1.408
LGA    G      22      G      22          1.536
LGA    A      23      A      23          1.021
LGA    D      24      D      24          1.253
LGA    I      25      I      25          1.046
LGA    G      26      G      26          3.134
LGA    H      27      H      27          1.660
LGA    L      28      L      28          3.150
LGA    V      29      V      29          1.670
LGA    L      30      L      30          1.709
LGA    D      31      D      31          1.687
LGA    Q      32      Q      32          2.882
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    N      33      I      44          4.731
LGA    M      34      P      45          3.317
LGA    S      35      R      46          2.772
LGA    I      36      -       -           -
LGA    L      37      R      47          2.248
LGA    E      38      V      48          2.000
LGA    G      39      -       -           -
LGA    S      40      -       -           -
LGA    L      41      L      49          0.341
LGA    G      42      -       -           -
LGA    V      43      -       -           -
LGA    I      44      V      50          4.042
LGA    P      45      H      51          4.343
LGA    -       -      E      52           -
LGA    R      46      D      53          4.338
LGA    R      47      D      54          5.344
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      -       -           -
LGA    R      59      -       -           -
LGA    R      60      -       -           -
LGA    L      61      -       -           -
LGA    L      62      -       -           -
LGA    T      63      -       -           -
LGA    D      64      -       -           -
LGA    A      65      -       -           -
LGA    G      66      -       -           -
LGA    L      67      L      55          3.926
LGA    A      68      -       -           -
LGA    H      69      -       -           -
LGA    E      70      -       -           -
LGA    L      71      A      56          3.926
LGA    -       -      G      57           -
LGA    -       -      A      58           -
LGA    -       -      R      59           -
LGA    -       -      R      60           -
LGA    -       -      L      61           -
LGA    -       -      L      62           -
LGA    -       -      T      63           -
LGA    -       -      D      64           -
LGA    -       -      A      65           -
LGA    -       -      G      66           -
LGA    -       -      L      67           -
LGA    -       -      A      68           -
LGA    -       -      H      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      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     37    2.60    64.86     37.465     1.369

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.849612 * X  +  -0.412024 * Y  +  -0.329234 * Z  +  -0.633198
  Y_new =   0.491775 * X  +  -0.844455 * Y  +  -0.212257 * Z  +   5.324646
  Z_new =  -0.190568 * X  +  -0.342245 * Y  +   0.920083 * Z  +  -0.194683 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.356114    2.785479  [ DEG:   -20.4038    159.5962 ]
  Theta =   0.191741    2.949852  [ DEG:    10.9859    169.0141 ]
  Phi   =   2.616890   -0.524702  [ DEG:   149.9368    -30.0632 ]
 
# 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: T0349TS599_4                                  
REMARK     2: T0349.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS599_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   37   2.60   64.86  37.465
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS599_4
PFRMAT TS                                                                       
TARGET T0349                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      -3.570  -8.464  12.828  1.00  0.00              
ATOM      2  CA  ARG     2      -0.314  -9.795  13.917  1.00  0.00              
ATOM      3  CA  GLU     3      -2.882 -11.607  11.127  1.00  0.00              
ATOM      4  CA  LEU     4      -2.597  -8.675   9.081  1.00  0.00              
ATOM      5  CA  LEU     5       1.252  -8.553   9.168  1.00  0.00              
ATOM      6  CA  ARG     6       1.616 -12.244   8.420  1.00  0.00              
ATOM      7  CA  THR     7      -0.749 -12.254   5.421  1.00  0.00              
ATOM      8  CA  ASN     8       0.390  -8.992   3.963  1.00  0.00              
ATOM      9  CA  ASP     9      -2.785  -7.061   3.576  1.00  0.00              
ATOM     10  CA  ALA    10      -5.530  -6.267   6.051  1.00  0.00              
ATOM     11  CA  VAL    11      -4.255  -4.883   9.358  1.00  0.00              
ATOM     12  CA  LEU    12      -1.491  -2.957   7.567  1.00  0.00              
ATOM     13  CA  LEU    13      -3.758  -1.226   5.010  1.00  0.00              
ATOM     14  CA  SER    14      -6.137  -0.140   7.755  1.00  0.00              
ATOM     15  CA  ALA    15      -3.323   1.193   9.985  1.00  0.00              
ATOM     16  CA  VAL    16      -1.822   3.180   7.076  1.00  0.00              
ATOM     17  CA  GLY    17      -5.264   4.619   6.267  1.00  0.00              
ATOM     18  CA  ALA    18      -5.822   5.623   9.903  1.00  0.00              
ATOM     19  CA  LEU    19      -2.399   7.319  10.045  1.00  0.00              
ATOM     20  CA  LEU    20      -3.166   9.214   6.801  1.00  0.00              
ATOM     21  CA  ASP    21      -6.561  10.307   8.184  1.00  0.00              
ATOM     22  CA  GLY    22      -5.043  11.589  11.445  1.00  0.00              
ATOM     23  CA  ALA    23      -2.469  13.636   9.519  1.00  0.00              
ATOM     24  CA  ASP    24      -4.978  15.199   7.167  1.00  0.00              
ATOM     25  CA  ILE    25      -3.680  13.429   4.055  1.00  0.00              
ATOM     26  CA  GLY    26      -6.252  11.636   2.019  1.00  0.00              
ATOM     27  CA  HIS    27      -4.608   8.659   0.553  1.00  0.00              
ATOM     28  CA  LEU    28      -6.578   5.728  -0.953  1.00  0.00              
ATOM     29  CA  VAL    29      -4.677   3.092  -2.824  1.00  0.00              
ATOM     30  CA  LEU    30      -6.521   1.282  -5.560  1.00  0.00              
ATOM     31  CA  ASP    31      -4.606  -0.741  -8.042  1.00  0.00              
ATOM     32  CA  GLN    32      -5.768  -4.266  -8.738  1.00  0.00              
ATOM     33  CA  ASN    33      -2.960  -5.739  -6.584  1.00  0.00              
ATOM     34  CA  MET    34      -3.935  -3.948  -3.398  1.00  0.00              
ATOM     35  CA  SER    35      -0.742  -4.518  -1.361  1.00  0.00              
ATOM     36  CA  ILE    36       1.419  -3.199  -4.248  1.00  0.00              
ATOM     37  CA  LEU    37      -0.618  -0.013  -4.768  1.00  0.00              
ATOM     38  CA  GLU    38      -0.608   0.718  -1.016  1.00  0.00              
ATOM     39  CA  GLY    39       3.196   0.646  -0.671  1.00  0.00              
ATOM     40  CA  SER    40       3.640   3.036  -3.649  1.00  0.00              
ATOM     41  CA  LEU    41       1.060   5.527  -2.361  1.00  0.00              
ATOM     42  CA  GLY    42       2.682   5.555   1.132  1.00  0.00              
ATOM     43  CA  VAL    43       6.119   6.693  -0.031  1.00  0.00              
ATOM     44  CA  ILE    44       4.618   9.747  -1.740  1.00  0.00              
ATOM     45  CA  PRO    45       2.022  10.992   0.712  1.00  0.00              
ATOM     46  CA  ARG    46       1.663  14.695   1.643  1.00  0.00              
ATOM     47  CA  ARG    47      -1.994  14.765   0.497  1.00  0.00              
ATOM     48  CA  VAL    48      -2.391  12.159  -2.222  1.00  0.00              
ATOM     49  CA  LEU    49      -5.884  11.045  -3.093  1.00  0.00              
ATOM     50  CA  VAL    50      -6.241   7.822  -4.953  1.00  0.00              
ATOM     51  CA  HIS    51      -9.588   6.180  -5.917  1.00  0.00              
ATOM     52  CA  GLU    52      -9.210   3.186  -8.166  1.00  0.00              
ATOM     53  CA  ASP    53     -10.988   4.467 -11.229  1.00  0.00              
ATOM     54  CA  ASP    54      -8.986   7.599 -11.072  1.00  0.00              
ATOM     55  CA  LEU    55      -5.546   5.921 -10.741  1.00  0.00              
ATOM     56  CA  ALA    56      -4.107   8.017 -13.507  1.00  0.00              
ATOM     57  CA  GLY    57      -5.497  11.212 -11.923  1.00  0.00              
ATOM     58  CA  ALA    58      -4.081  10.269  -8.529  1.00  0.00              
ATOM     59  CA  ARG    59      -0.626   9.532  -9.863  1.00  0.00              
ATOM     60  CA  ARG    60      -0.579  12.831 -11.672  1.00  0.00              
ATOM     61  CA  LEU    61      -1.668  14.711  -8.521  1.00  0.00              
ATOM     62  CA  LEU    62       1.012  13.115  -6.372  1.00  0.00              
ATOM     63  CA  THR    63       3.739  13.953  -8.957  1.00  0.00              
ATOM     64  CA  ASP    64       2.446  17.521  -9.295  1.00  0.00              
ATOM     65  CA  ALA    65       2.634  17.909  -5.513  1.00  0.00              
ATOM     66  CA  GLY    66       6.367  16.975  -5.562  1.00  0.00              
ATOM     67  CA  LEU    67       6.397  14.026  -3.385  1.00  0.00              
ATOM     68  CA  ALA    68       9.010  11.561  -4.740  1.00  0.00              
ATOM     69  CA  HIS    69      11.728  14.154  -4.603  1.00  0.00              
ATOM     70  CA  GLU    70      10.849  15.105  -1.039  1.00  0.00              
ATOM     71  CA  LEU    71      10.730  11.533   0.291  1.00  0.00              
ATOM     72  CA  ARG    72      13.887  10.504  -1.515  1.00  0.00              
ATOM     73  CA  SER    73      15.961  14.018  -0.507  1.00  0.00              
ATOM     74  CA  ASP    74      16.283  17.544   0.827  1.00  0.00              
ATOM     75  CA  ASP    75      15.648  13.946   2.876  1.00  0.00              
TER                                                                             
END
