
#######################################################
#                                                     #
#                        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   76 (   76),  selected   76 , name T0309TS168_2
# Molecule2: number of CA atoms   62 (  501),  selected   62 , name T0309.pdb
# PARAMETERS: T0309TS168_2.T0309.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      A       2           -
LGA    A       2      S       3           -
LGA    S       3      K       4           -
LGA    K       4      K       5           -
LGA    K       5      V       6           -
LGA    -       -      H       7           -
LGA    -       -      Q       8           -
LGA    -       -      I       9           -
LGA    -       -      N      10           -
LGA    -       -      V      11           -
LGA    -       -      K      12           -
LGA    -       -      G      13           -
LGA    -       -      F      14           -
LGA    -       -      F      15           -
LGA    -       -      D      16           -
LGA    -       -      M      17           -
LGA    V       6      D      18           #
LGA    H       7      V      19          1.111
LGA    Q       8      M      20          3.524
LGA    I       9      -       -           -
LGA    N      10      -       -           -
LGA    V      11      -       -           -
LGA    K      12      -       -           -
LGA    G      13      -       -           -
LGA    F      14      -       -           -
LGA    F      15      -       -           -
LGA    D      16      -       -           -
LGA    M      17      -       -           -
LGA    D      18      -       -           -
LGA    V      19      -       -           -
LGA    M      20      -       -           -
LGA    E      21      -       -           -
LGA    V      22      E      21          0.862
LGA    T      23      V      22           #
LGA    E      24      T      23           #
LGA    Q      25      E      24           #
LGA    T      26      Q      25          4.594
LGA    -       -      T      26           -
LGA    -       -      K      27           -
LGA    -       -      E      28           -
LGA    K      27      A      29          2.914
LGA    E      28      E      30          4.873
LGA    A      29      Y      31          4.580
LGA    E      30      -       -           -
LGA    Y      31      -       -           -
LGA    T      32      T      32           #
LGA    Y      33      Y      33          3.950
LGA    D      34      D      34           #
LGA    F      35      F      35          2.362
LGA    K      36      K      36          3.945
LGA    E      37      E      37           #
LGA    I      38      I      38          4.874
LGA    L      39      L      39          2.011
LGA    S      40      S      40          3.072
LGA    -       -      E      41           -
LGA    E      41      F      42          4.098
LGA    F      42      N      43           #
LGA    -       -      G      44           -
LGA    -       -      K      45           -
LGA    -       -      N      46           -
LGA    N      43      V      47          3.264
LGA    G      44      S      48          3.128
LGA    K      45      I      49          3.916
LGA    N      46      T      50          1.959
LGA    V      47      V      51          3.707
LGA    S      48      -       -           -
LGA    I      49      -       -           -
LGA    T      50      -       -           -
LGA    V      51      -       -           -
LGA    K      52      -       -           -
LGA    E      53      -       -           -
LGA    E      54      -       -           -
LGA    N      55      -       -           -
LGA    E      56      -       -           -
LGA    L      57      -       -           -
LGA    P      58      -       -           -
LGA    V      59      -       -           -
LGA    K      60      -       -           -
LGA    G      61      -       -           -
LGA    V      62      -       -           -
LGA    E      63      -       -           -
LGA    M      64      -       -           -
LGA    A      65      -       -           -
LGA    G      66      K      52           #
LGA    D      67      E      53          1.327
LGA    P      68      E      54          1.812
LGA    L      69      N      55          2.708
LGA    E      70      E      56          2.631
LGA    H      71      L      57          1.138
LGA    H      72      P      58          3.278
LGA    H      73      V      59           #
LGA    -       -      K      60           -
LGA    -       -      G      61           -
LGA    H      74      V      62           #
LGA    H      75      E      63           -
LGA    H      76      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   76   62    5.0     25    3.25    36.00     25.656     0.746

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.028814 * X  +   0.724708 * Y  +   0.688453 * Z  +   4.120140
  Y_new =  -0.112071 * X  +   0.686739 * Y  +  -0.718213 * Z  +  -8.324209
  Z_new =  -0.993282 * X  +  -0.056461 * Y  +   0.101007 * Z  +  -6.500515 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.509711    2.631882  [ DEG:   -29.2043    150.7957 ]
  Theta =   1.454821    1.686772  [ DEG:    83.3551     96.6449 ]
  Phi   =  -1.319138    1.822455  [ DEG:   -75.5810    104.4190 ]
 
# 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: T0309TS168_2                                  
REMARK     2: T0309.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0309TS168_2.T0309.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   76   62   5.0   25   3.25   36.00  25.656
REMARK  ---------------------------------------------------------- 
MOLECULE T0309TS168_2
PFRMAT TS
TARGET T0309
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1     -10.936  12.029  -5.336  1.00 25.00           C
ATOM      2  CA  ALA     2     -10.773   9.252  -7.912  1.00 25.00           C
ATOM      3  CA  SER     3      -8.547   6.181  -7.631  1.00 25.00           C
ATOM      4  CA  LYS     4      -6.525   3.311  -6.168  1.00 25.00           C
ATOM      5  CA  LYS     5      -5.007   0.068  -7.274  1.00 25.00           C
ATOM      6  CA  VAL     6      -2.229  -1.060  -9.585  1.00 25.00           C
ATOM      7  CA  HIS     7       1.096  -0.124  -7.929  1.00 25.00           C
ATOM      8  CA  GLN     8       2.635  -1.026  -4.550  1.00 25.00           C
ATOM      9  CA  ILE     9       4.895  -3.364  -2.466  1.00 25.00           C
ATOM     10  CA  ASN    10       5.901  -6.740  -1.011  1.00 25.00           C
ATOM     11  CA  VAL    11       7.202 -10.194  -0.082  1.00 25.00           C
ATOM     12  CA  LYS    12       7.919  -9.093   3.465  1.00 25.00           C
ATOM     13  CA  GLY    13      10.204  -8.654   6.493  1.00 25.00           C
ATOM     14  CA  PHE    14       8.688  -5.198   6.838  1.00 25.00           C
ATOM     15  CA  PHE    15       5.034  -5.976   7.640  1.00 25.00           C
ATOM     16  CA  ASP    16       3.310  -2.769   8.894  1.00 25.00           C
ATOM     17  CA  MET    17       3.034  -1.950   5.154  1.00 25.00           C
ATOM     18  CA  ASP    18       2.104  -5.266   3.514  1.00 25.00           C
ATOM     19  CA  VAL    19       0.947  -7.371   0.515  1.00 25.00           C
ATOM     20  CA  MET    20       0.876  -6.489  -3.184  1.00 25.00           C
ATOM     21  CA  GLU    21      -0.910  -4.359  -5.792  1.00 25.00           C
ATOM     22  CA  VAL    22       0.747  -5.177  -9.085  1.00 25.00           C
ATOM     23  CA  THR    23       0.586  -4.413 -12.766  1.00 25.00           C
ATOM     24  CA  GLU    24      -1.590  -5.888 -15.497  1.00 25.00           C
ATOM     25  CA  GLN    25      -0.942  -7.907 -18.614  1.00 25.00           C
ATOM     26  CA  THR    26       1.009 -10.879 -20.074  1.00 25.00           C
ATOM     27  CA  LYS    27      -2.413 -12.431 -20.855  1.00 25.00           C
ATOM     28  CA  GLU    28      -3.595 -12.283 -17.241  1.00 25.00           C
ATOM     29  CA  ALA    29      -2.184 -15.304 -15.352  1.00 25.00           C
ATOM     30  CA  GLU    30       1.061 -13.307 -15.284  1.00 25.00           C
ATOM     31  CA  TYR    31       3.959 -13.012 -12.797  1.00 25.00           C
ATOM     32  CA  THR    32       3.591  -9.201 -12.781  1.00 25.00           C
ATOM     33  CA  TYR    33      -0.171  -9.542 -12.146  1.00 25.00           C
ATOM     34  CA  ASP    34      -0.461 -12.056  -9.343  1.00 25.00           C
ATOM     35  CA  PHE    35      -2.004  -9.233  -7.221  1.00 25.00           C
ATOM     36  CA  LYS    36      -5.391  -7.718  -6.271  1.00 25.00           C
ATOM     37  CA  GLU    37      -6.612 -11.141  -5.063  1.00 25.00           C
ATOM     38  CA  ILE    38      -3.433 -11.564  -2.970  1.00 25.00           C
ATOM     39  CA  LEU    39      -3.946  -8.091  -1.442  1.00 25.00           C
ATOM     40  CA  SER    40      -7.578  -8.971  -0.604  1.00 25.00           C
ATOM     41  CA  GLU    41      -6.433 -12.235   1.039  1.00 25.00           C
ATOM     42  CA  PHE    42      -3.830 -10.319   3.092  1.00 25.00           C
ATOM     43  CA  ASN    43      -4.351 -13.144   5.576  1.00 25.00           C
ATOM     44  CA  GLY    44      -4.423 -16.272   3.407  1.00 25.00           C
ATOM     45  CA  LYS    45      -2.483 -17.667   0.381  1.00 25.00           C
ATOM     46  CA  ASN    46       0.699 -16.296   1.966  1.00 25.00           C
ATOM     47  CA  VAL    47       1.243 -14.249  -1.173  1.00 25.00           C
ATOM     48  CA  SER    48       1.309 -12.364  -4.460  1.00 25.00           C
ATOM     49  CA  ILE    49       4.373 -10.146  -4.713  1.00 25.00           C
ATOM     50  CA  THR    50       4.983  -6.721  -6.195  1.00 25.00           C
ATOM     51  CA  VAL    51       6.084  -3.296  -7.460  1.00 25.00           C
ATOM     52  CA  LYS    52       6.828  -3.532 -11.155  1.00 25.00           C
ATOM     53  CA  GLU    53       9.478  -1.091 -12.518  1.00 25.00           C
ATOM     54  CA  GLU    54      13.210  -0.516 -12.850  1.00 25.00           C
ATOM     55  CA  ASN    55      14.405   1.727  -9.970  1.00 25.00           C
ATOM     56  CA  GLU    56      12.170   4.317 -11.724  1.00 25.00           C
ATOM     57  CA  LEU    57       8.861   3.675 -10.034  1.00 25.00           C
ATOM     58  CA  PRO    58       9.563   5.030  -6.520  1.00 25.00           C
ATOM     59  CA  VAL    59       8.445   1.684  -5.191  1.00 25.00           C
ATOM     60  CA  LYS    60      11.812  -0.032  -4.934  1.00 25.00           C
ATOM     61  CA  GLY    61      10.034  -3.326  -4.168  1.00 25.00           C
ATOM     62  CA  VAL    62      11.091  -4.089  -7.775  1.00 25.00           C
ATOM     63  CA  GLU    63       9.569  -7.589  -8.089  1.00 25.00           C
ATOM     64  CA  MET    64       8.305  -9.721 -10.979  1.00 25.00           C
ATOM     65  CA  ALA    65       7.967 -12.440  -8.317  1.00 25.00           C
ATOM     66  CA  GLY    66      10.655 -13.956  -5.997  1.00 25.00           C
ATOM     67  CA  ASP    67       8.484 -17.033  -5.355  1.00 25.00           C
ATOM     68  CA  PRO    68      11.570 -19.263  -5.013  1.00 25.00           C
ATOM     69  CA  LEU    69      15.146 -18.728  -6.193  1.00 25.00           C
ATOM     70  CA  GLU    70      17.622 -21.021  -7.948  1.00 25.00           C
ATOM     71  CA  HIS    71      19.531 -24.255  -8.322  1.00 25.00           C
ATOM     72  CA  HIS    72      21.128 -22.764 -11.383  1.00 25.00           C
ATOM     73  CA  HIS    73      19.902 -22.729 -15.035  1.00 25.00           C
ATOM     74  CA  HIS    74      21.109 -26.122 -16.123  1.00 25.00           C
ATOM     75  CA  HIS    75      19.560 -25.430 -19.522  1.00 25.00           C
ATOM     76  CA  HIS    76      16.100 -26.676 -18.580  1.00 25.00           C
TER
END
