
#######################################################
#                                                     #
#                        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   65 (   65),  selected   65 , name T0358TS599_1-D1
# Molecule2: number of CA atoms   65 ( 1035),  selected   65 , name T0358_D1.pdb
# PARAMETERS: T0358TS599_1-D1.T0358_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G      10      G      10           -
LGA    P      11      P      11           -
LGA    F      12      F      12           -
LGA    T      13      T      13           -
LGA    R      14      R      14           -
LGA    R      15      R      15           -
LGA    Q      16      Q      16           -
LGA    A      17      A      17           -
LGA    Q      18      Q      18           -
LGA    A      19      A      19           -
LGA    V      20      V      20           -
LGA    T      21      T      21           -
LGA    T      22      T      22           -
LGA    T      23      -       -           -
LGA    Y      24      -       -           -
LGA    S      25      -       -           -
LGA    N      26      -       -           -
LGA    I      27      T      23           #
LGA    T      28      Y      24          3.734
LGA    -       -      S      25           -
LGA    -       -      N      26           -
LGA    L      29      I      27          1.822
LGA    E      30      T      28          2.274
LGA    D      31      L      29          3.196
LGA    D      32      E      30          4.096
LGA    -       -      D      31           -
LGA    -       -      D      32           -
LGA    -       -      Q      33           -
LGA    -       -      G      34           -
LGA    -       -      S      35           -
LGA    -       -      H      36           -
LGA    Q      33      F      37          1.211
LGA    G      34      R      38          1.667
LGA    S      35      L      39          1.721
LGA    H      36      V      40          1.285
LGA    F      37      V      41          1.299
LGA    R      38      R      42          1.473
LGA    L      39      D      43          1.056
LGA    V      40      T      44          0.668
LGA    V      41      -       -           -
LGA    R      42      -       -           -
LGA    D      43      -       -           -
LGA    T      44      -       -           -
LGA    E      45      -       -           -
LGA    G      46      -       -           -
LGA    R      47      -       -           -
LGA    M      48      -       -           -
LGA    V      49      E      45          3.843
LGA    W      50      G      46          3.571
LGA    R      51      R      47          2.060
LGA    A      52      M      48          1.552
LGA    W      53      V      49          2.270
LGA    N      54      W      50          3.665
LGA    F      55      R      51          1.296
LGA    E      56      A      52          2.530
LGA    P      57      W      53          5.756
LGA    D      58      N      54           #
LGA    A      59      F      55          3.861
LGA    G      60      E      56          3.203
LGA    E      61      P      57          3.909
LGA    G      62      D      58          4.853
LGA    L      63      A      59          3.272
LGA    N      64      G      60          1.961
LGA    R      65      E      61          1.546
LGA    -       -      G      62           -
LGA    -       -      L      63           -
LGA    Y      66      N      64          1.888
LGA    I      67      R      65           -
LGA    R      68      Y      66           -
LGA    -       -      I      67           -
LGA    T      69      R      68          4.430
LGA    S      70      T      69          3.022
LGA    G      71      S      70           -
LGA    I      72      G      71           -
LGA    R      73      I      72           -
LGA    T      74      R      73           -
LGA    -       -      T      74           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   65   65    5.0     32    2.91     6.25     31.766     1.063

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.295922 * X  +  -0.723146 * Y  +   0.624091 * Z  +   0.348884
  Y_new =  -0.354946 * X  +   0.689818 * Y  +   0.631003 * Z  +  -5.781471
  Z_new =  -0.886816 * X  +  -0.034791 * Y  +  -0.460810 * Z  +   2.190661 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.066236    0.075356  [ DEG:  -175.6824      4.3176 ]
  Theta =   1.090410    2.051183  [ DEG:    62.4759    117.5241 ]
  Phi   =  -2.265757    0.875836  [ DEG:  -129.8183     50.1817 ]
 
# 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: T0358TS599_1-D1                               
REMARK     2: T0358_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358TS599_1-D1.T0358_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   65   65   5.0   32   2.91    6.25  31.766
REMARK  ---------------------------------------------------------- 
MOLECULE T0358TS599_1-D1
PFRMAT TS                                                                       
TARGET T0358                                                                    
MODEL  1                                                                        
PARENT N/A                                                                      
ATOM     10  CA  GLY    10       2.288 -15.027   7.779  1.00  0.00              
ATOM     11  CA  PRO    11       5.349 -17.158   7.491  1.00  0.00              
ATOM     12  CA  PHE    12       3.898 -20.642   7.517  1.00  0.00              
ATOM     13  CA  THR    13       4.888 -23.658   9.621  1.00  0.00              
ATOM     14  CA  ARG    14       2.820 -26.662   8.487  1.00  0.00              
ATOM     15  CA  ARG    15       0.297 -26.775  11.357  1.00  0.00              
ATOM     16  CA  GLN    16      -0.052 -22.996  11.500  1.00  0.00              
ATOM     17  CA  ALA    17      -0.124 -22.773   7.675  1.00  0.00              
ATOM     18  CA  GLN    18      -3.177 -25.055   7.641  1.00  0.00              
ATOM     19  CA  ALA    19      -4.828 -22.725  10.179  1.00  0.00              
ATOM     20  CA  VAL    20      -3.936 -19.688   8.056  1.00  0.00              
ATOM     21  CA  THR    21      -5.357 -21.410   4.929  1.00  0.00              
ATOM     22  CA  THR    22      -8.636 -21.590   6.762  1.00  0.00              
ATOM     23  CA  THR    23      -8.490 -17.851   7.534  1.00  0.00              
ATOM     24  CA  TYR    24      -7.375 -16.315   4.226  1.00  0.00              
ATOM     25  CA  SER    25      -5.247 -13.292   5.037  1.00  0.00              
ATOM     26  CA  ASN    26      -4.056 -11.933   1.890  1.00  0.00              
ATOM     27  CA  ILE    27      -3.138  -8.471   2.006  1.00  0.00              
ATOM     28  CA  THR    28      -3.144  -6.429  -1.148  1.00  0.00              
ATOM     29  CA  LEU    29      -1.402  -3.120  -1.286  1.00  0.00              
ATOM     30  CA  GLU    30      -2.091  -0.800  -4.013  1.00  0.00              
ATOM     31  CA  ASP    31       0.176   2.101  -4.649  1.00  0.00              
ATOM     32  CA  ASP    32      -1.511   4.968  -6.162  1.00  0.00              
ATOM     33  CA  GLN    33      -0.220   7.977  -4.333  1.00  0.00              
ATOM     34  CA  GLY    34      -2.478   7.750  -1.224  1.00  0.00              
ATOM     35  CA  SER    35      -2.008   4.166  -0.324  1.00  0.00              
ATOM     36  CA  HIS    36      -4.809   1.723  -0.751  1.00  0.00              
ATOM     37  CA  PHE    37      -4.981  -1.308   1.417  1.00  0.00              
ATOM     38  CA  ARG    38      -7.077  -4.196   0.634  1.00  0.00              
ATOM     39  CA  LEU    39      -7.612  -7.039   2.948  1.00  0.00              
ATOM     40  CA  VAL    40      -9.140 -10.200   1.941  1.00  0.00              
ATOM     41  CA  VAL    41     -10.364 -12.561   4.408  1.00  0.00              
ATOM     42  CA  ARG    42     -11.468 -16.043   3.467  1.00  0.00              
ATOM     43  CA  ASP    43     -13.457 -17.991   5.972  1.00  0.00              
ATOM     44  CA  THR    44     -13.164 -21.770   6.107  1.00  0.00              
ATOM     45  CA  GLU    45     -16.573 -22.032   4.415  1.00  0.00              
ATOM     46  CA  GLY    46     -15.555 -20.049   1.380  1.00  0.00              
ATOM     47  CA  ARG    47     -17.183 -16.804   2.432  1.00  0.00              
ATOM     48  CA  MET    48     -15.243 -13.826   1.347  1.00  0.00              
ATOM     49  CA  VAL    49     -14.802 -10.985   3.551  1.00  0.00              
ATOM     50  CA  TRP    50     -13.359  -7.844   2.146  1.00  0.00              
ATOM     51  CA  ARG    51     -11.811  -5.338   4.359  1.00  0.00              
ATOM     52  CA  ALA    52     -10.806  -2.155   3.036  1.00  0.00              
ATOM     53  CA  TRP    53      -8.178  -0.438   4.868  1.00  0.00              
ATOM     54  CA  ASN    54      -7.071   3.131   4.001  1.00  0.00              
ATOM     55  CA  PHE    55      -3.328   3.628   4.472  1.00  0.00              
ATOM     56  CA  GLU    56      -2.268   7.228   4.537  1.00  0.00              
ATOM     57  CA  PRO    57       0.202   7.582   7.462  1.00  0.00              
ATOM     58  CA  ASP    58       2.550  10.094   5.801  1.00  0.00              
ATOM     59  CA  ALA    59       3.107   8.323   2.481  1.00  0.00              
ATOM     60  CA  GLY    60       6.753   7.339   3.039  1.00  0.00              
ATOM     61  CA  GLU    61       6.618   6.261   6.693  1.00  0.00              
ATOM     62  CA  GLY    62       3.628   3.891   6.590  1.00  0.00              
ATOM     63  CA  LEU    63       4.737   2.254   3.316  1.00  0.00              
ATOM     64  CA  ASN    64       8.189   1.752   4.758  1.00  0.00              
ATOM     65  CA  ARG    65       6.762   0.156   7.950  1.00  0.00              
ATOM     66  CA  TYR    66       4.546  -2.159   5.991  1.00  0.00              
ATOM     67  CA  ILE    67       7.332  -3.321   3.730  1.00  0.00              
ATOM     68  CA  ARG    68       9.635  -4.012   6.599  1.00  0.00              
ATOM     69  CA  THR    69       7.139  -6.049   8.552  1.00  0.00              
ATOM     70  CA  SER    70       6.383  -8.160   5.539  1.00  0.00              
ATOM     71  CA  GLY    71       9.972  -8.969   4.766  1.00  0.00              
ATOM     72  CA  ILE    72      10.616  -6.561   1.841  1.00  0.00              
ATOM     73  CA  ARG    73      14.230  -5.517   1.724  1.00  0.00              
ATOM     74  CA  THR    74      15.823  -2.115   1.905  1.00  0.00              
TER                                                                             
END
