
#######################################################
#                                                     #
#                        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   61 (   61),  selected   61 , name T0381TS168_3-D1
# Molecule2: number of CA atoms   61 (  477),  selected   61 , name T0381_D1.pdb
# PARAMETERS: T0381TS168_3-D1.T0381_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    V      17      V      17           -
LGA    Q      18      Q      18           -
LGA    S      19      S      19           -
LGA    L      20      L      20           -
LGA    A      21      A      21           -
LGA    R      22      R      22           -
LGA    G      23      G      23           -
LGA    L      24      L      24           -
LGA    A      25      A      25           -
LGA    V      26      V      26           #
LGA    I      27      -       -           -
LGA    R      28      I      27           #
LGA    C      29      R      28          4.309
LGA    F      30      C      29          3.031
LGA    D      31      F      30          2.353
LGA    H      32      D      31          2.401
LGA    R      33      H      32           #
LGA    N      34      R      33           #
LGA    Q      35      N      34           #
LGA    R      36      Q      35           -
LGA    R      37      R      36           -
LGA    T      38      R      37           -
LGA    L      39      T      38           -
LGA    S      40      L      39           -
LGA    -       -      S      40           -
LGA    D      41      D      41           #
LGA    V      42      V      42           #
LGA    A      43      A      43          3.991
LGA    R      44      R      44          3.482
LGA    -       -      A      45           -
LGA    -       -      T      46           -
LGA    A      45      D      47          3.648
LGA    T      46      L      48          4.447
LGA    D      47      T      49          3.154
LGA    L      48      R      50          3.284
LGA    T      49      A      51          0.684
LGA    R      50      T      52          2.983
LGA    A      51      -       -           -
LGA    T      52      A      53          3.913
LGA    A      53      R      54          2.468
LGA    R      54      R      55          0.918
LGA    R      55      F      56          1.770
LGA    F      56      L      57          1.706
LGA    L      57      L      58          1.008
LGA    L      58      T      59          0.629
LGA    T      59      L      60          0.468
LGA    L      60      V      61          1.717
LGA    V      61      E      62          2.127
LGA    E      62      L      63          1.728
LGA    L      63      G      64          2.493
LGA    G      64      Y      65          3.632
LGA    Y      65      V      66          3.692
LGA    V      66      A      67           -
LGA    A      67      T      68           -
LGA    T      68      D      69           -
LGA    D      69      G      70           -
LGA    G      70      S      71           -
LGA    S      71      A      72           -
LGA    A      72      F      73           -
LGA    F      73      -       -           -
LGA    W      74      -       -           -
LGA    L      75      -       -           -
LGA    T      76      W      74           #
LGA    P      77      L      75          2.530
LGA    -       -      T      76           -
LGA    -       -      P      77           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   61   61    5.0     27    2.79    14.81     32.318     0.934

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.624882 * X  +   0.673434 * Y  +  -0.394980 * Z  +   6.568996
  Y_new =   0.710172 * X  +  -0.280145 * Y  +   0.645891 * Z  +  56.855556
  Z_new =   0.324313 * X  +  -0.684109 * Y  +  -0.653311 * Z  +  -3.487342 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.333171    0.808422  [ DEG:  -133.6809     46.3191 ]
  Theta =  -0.330286   -2.811307  [ DEG:   -18.9240   -161.0760 ]
  Phi   =   0.849197   -2.292396  [ DEG:    48.6554   -131.3446 ]
 
# 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: T0381TS168_3-D1                               
REMARK     2: T0381_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0381TS168_3-D1.T0381_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   61   61   5.0   27   2.79   14.81  32.318
REMARK  ---------------------------------------------------------- 
MOLECULE T0381TS168_3-D1
PFRMAT TS
TARGET T0381
MODEL 3
PARENT N/A
ATOM     17  CA  VAL    17      14.354  68.113   8.829  1.00 25.00           C
ATOM     18  CA  GLN    18      12.670  67.946  12.264  1.00 25.00           C
ATOM     19  CA  SER    19       9.473  66.580  10.659  1.00 25.00           C
ATOM     20  CA  LEU    20      11.514  63.934   8.788  1.00 25.00           C
ATOM     21  CA  ALA    21      13.249  62.930  12.052  1.00 25.00           C
ATOM     22  CA  ARG    22       9.853  62.637  13.796  1.00 25.00           C
ATOM     23  CA  GLY    23       8.544  60.453  10.934  1.00 25.00           C
ATOM     24  CA  LEU    24      11.642  58.217  11.191  1.00 25.00           C
ATOM     25  CA  ALA    25      11.122  57.888  14.972  1.00 25.00           C
ATOM     26  CA  VAL    26       7.451  56.951  14.409  1.00 25.00           C
ATOM     27  CA  ILE    27       8.493  54.316  11.832  1.00 25.00           C
ATOM     28  CA  ARG    28      11.049  52.880  14.297  1.00 25.00           C
ATOM     29  CA  CYS    29       8.366  52.725  17.026  1.00 25.00           C
ATOM     30  CA  PHE    30       5.989  50.927  14.621  1.00 25.00           C
ATOM     31  CA  ASP    31       8.744  48.417  13.736  1.00 25.00           C
ATOM     32  CA  HIS    32       8.037  44.853  12.664  1.00 25.00           C
ATOM     33  CA  ARG    33       8.133  42.509  15.680  1.00 25.00           C
ATOM     34  CA  ASN    34       4.814  43.468  17.383  1.00 25.00           C
ATOM     35  CA  GLN    35       2.098  45.911  18.565  1.00 25.00           C
ATOM     36  CA  ARG    36       1.633  45.214  22.285  1.00 25.00           C
ATOM     37  CA  ARG    37       4.720  47.172  23.469  1.00 25.00           C
ATOM     38  CA  THR    38       2.063  49.303  25.162  1.00 25.00           C
ATOM     39  CA  LEU    39       3.216  51.989  22.716  1.00 25.00           C
ATOM     40  CA  SER    40      -0.506  52.071  21.818  1.00 25.00           C
ATOM     41  CA  ASP    41      -1.074  54.911  24.323  1.00 25.00           C
ATOM     42  CA  VAL    42       1.862  56.857  22.821  1.00 25.00           C
ATOM     43  CA  ALA    43       0.427  56.356  19.306  1.00 25.00           C
ATOM     44  CA  ARG    44      -2.994  57.598  20.497  1.00 25.00           C
ATOM     45  CA  ALA    45      -1.354  60.682  22.067  1.00 25.00           C
ATOM     46  CA  THR    46       0.514  61.383  18.799  1.00 25.00           C
ATOM     47  CA  ASP    47      -0.387  65.049  18.811  1.00 25.00           C
ATOM     48  CA  LEU    48       1.309  65.695  22.107  1.00 25.00           C
ATOM     49  CA  THR    49       4.062  68.273  21.740  1.00 25.00           C
ATOM     50  CA  ARG    50       4.860  67.458  25.335  1.00 25.00           C
ATOM     51  CA  ALA    51       7.158  65.332  27.539  1.00 25.00           C
ATOM     52  CA  THR    52       6.610  62.315  25.244  1.00 25.00           C
ATOM     53  CA  ALA    53       7.437  64.463  22.183  1.00 25.00           C
ATOM     54  CA  ARG    54      10.633  65.708  23.888  1.00 25.00           C
ATOM     55  CA  ARG    55      11.631  62.102  24.705  1.00 25.00           C
ATOM     56  CA  PHE    56      11.024  61.083  21.063  1.00 25.00           C
ATOM     57  CA  LEU    57      13.170  64.017  19.859  1.00 25.00           C
ATOM     58  CA  LEU    58      15.967  62.990  22.265  1.00 25.00           C
ATOM     59  CA  THR    59      15.783  59.387  20.981  1.00 25.00           C
ATOM     60  CA  LEU    60      15.985  60.639  17.367  1.00 25.00           C
ATOM     61  CA  VAL    61      19.033  62.782  18.253  1.00 25.00           C
ATOM     62  CA  GLU    62      20.707  59.760  19.906  1.00 25.00           C
ATOM     63  CA  LEU    63      23.927  58.163  18.541  1.00 25.00           C
ATOM     64  CA  GLY    64      22.018  55.195  17.030  1.00 25.00           C
ATOM     65  CA  TYR    65      18.372  54.857  18.060  1.00 25.00           C
ATOM     66  CA  VAL    66      17.605  54.584  21.805  1.00 25.00           C
ATOM     67  CA  ALA    67      15.197  52.546  23.943  1.00 25.00           C
ATOM     68  CA  THR    68      15.728  50.233  26.880  1.00 25.00           C
ATOM     69  CA  ASP    69      16.995  48.957  30.287  1.00 25.00           C
ATOM     70  CA  GLY    70      14.610  46.301  31.584  1.00 25.00           C
ATOM     71  CA  SER    71      11.202  46.965  30.020  1.00 25.00           C
ATOM     72  CA  ALA    72       9.580  47.118  26.526  1.00 25.00           C
ATOM     73  CA  PHE    73       9.455  48.962  23.194  1.00 25.00           C
ATOM     74  CA  TRP    74      11.798  49.768  20.331  1.00 25.00           C
ATOM     75  CA  LEU    75      14.215  48.015  17.997  1.00 25.00           C
ATOM     76  CA  THR    76      17.701  49.423  17.504  1.00 25.00           C
ATOM     77  CA  PRO    77      16.687  51.328  14.399  1.00 25.00           C
TER
END
