
#######################################################
#                                                     #
#                        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 T0324TS393_2-D2
# Molecule2: number of CA atoms   65 (  494),  selected   65 , name T0324_D2.pdb
# PARAMETERS: T0324TS393_2-D2.T0324_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S      17      S      17           -
LGA    -       -      Q      18           -
LGA    -       -      P      19           -
LGA    -       -      A      20           -
LGA    -       -      Y      21           -
LGA    -       -      T      22           -
LGA    -       -      T      23           -
LGA    -       -      V      24           -
LGA    -       -      M      25           -
LGA    -       -      R      26           -
LGA    -       -      E      27           -
LGA    -       -      V      28           -
LGA    -       -      L      29           -
LGA    -       -      A      30           -
LGA    -       -      T      31           -
LGA    -       -      Y      32           -
LGA    -       -      G      33           -
LGA    -       -      K      34           -
LGA    Q      18      P      35          4.841
LGA    P      19      F      36          3.933
LGA    A      20      -       -           -
LGA    Y      21      S      37          1.527
LGA    T      22      -       -           -
LGA    T      23      -       -           -
LGA    V      24      P      38          3.243
LGA    M      25      A      39          2.798
LGA    R      26      Q      40          2.944
LGA    E      27      A      41          2.605
LGA    V      28      Q      42          1.144
LGA    L      29      K      43          1.271
LGA    A      30      T      44          2.574
LGA    T      31      F      45          3.743
LGA    Y      32      P      46          1.964
LGA    G      33      M      47           #
LGA    K      34      A      48          5.283
LGA    P      35      A      49           -
LGA    F      36      -       -           -
LGA    S      37      -       -           -
LGA    P      38      -       -           -
LGA    A      39      -       -           -
LGA    Q      40      E      50           #
LGA    A      41      -       -           -
LGA    Q      42      -       -           -
LGA    K      43      Q      51          3.908
LGA    T      44      -       -           -
LGA    F      45      A      52          3.905
LGA    P      46      M      53          3.098
LGA    M      47      T      54          1.531
LGA    -       -      E      55           -
LGA    -       -      L      56           -
LGA    A      48      G      57          4.651
LGA    A      49      I      58          0.702
LGA    E      50      A      59          3.095
LGA    Q      51      A      60           -
LGA    A      52      S      61           -
LGA    M      53      E      62          5.058
LGA    T      54      F      63           #
LGA    -       -      D      64           -
LGA    -       -      H      65           -
LGA    E      55      F      66          3.095
LGA    L      56      Q      67          2.305
LGA    G      57      A      68          1.851
LGA    I      58      Q      69          1.616
LGA    -       -      Y      70           -
LGA    A      59      E      71          3.826
LGA    A      60      D      72          3.389
LGA    S      61      -       -           -
LGA    E      62      V      73          2.158
LGA    F      63      M      74          2.883
LGA    D      64      A      75          2.741
LGA    -       -      S      76           -
LGA    H      65      H      77          3.803
LGA    F      66      Y      78           #
LGA    Q      67      D      79           -
LGA    A      68      Q      80           #
LGA    Q      69      -       -           -
LGA    Y      70      -       -           -
LGA    E      71      I      81           #
LGA    D      72      -       -           -
LGA    V      73      -       -           -
LGA    M      74      -       -           -
LGA    A      75      -       -           -
LGA    S      76      -       -           -
LGA    H      77      -       -           -
LGA    Y      78      -       -           -
LGA    D      79      -       -           -
LGA    Q      80      -       -           -
LGA    I      81      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   65   65    5.0     31    3.17     3.23     28.783     0.947

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.589385 * X  +  -0.796298 * Y  +  -0.136143 * Z  +   8.452196
  Y_new =  -0.485013 * X  +   0.483562 * Y  +  -0.728650 * Z  +  22.286964
  Z_new =   0.646056 * X  +  -0.363424 * Y  +  -0.671219 * Z  +  -4.692873 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.645346    0.496246  [ DEG:  -151.5672     28.4328 ]
  Theta =  -0.702406   -2.439187  [ DEG:   -40.2449   -139.7551 ]
  Phi   =  -2.453035    0.688557  [ DEG:  -140.5486     39.4514 ]
 
# 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: T0324TS393_2-D2                               
REMARK     2: T0324_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0324TS393_2-D2.T0324_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   65   65   5.0   31   3.17    3.23  28.783
REMARK  ---------------------------------------------------------- 
MOLECULE T0324TS393_2-D2
PFRMAT TS
TARGET T0324
MODEL 2
PARENT N/A
ATOM     17  CA  SER    17      11.903  20.899  -2.397  1.00 25.00           C
ATOM     18  CA  GLN    18      13.390  17.397  -2.956  1.00 25.00           C
ATOM     19  CA  PRO    19      13.578  15.126   0.122  1.00 25.00           C
ATOM     20  CA  ALA    20      17.152  16.315   0.812  1.00 25.00           C
ATOM     21  CA  TYR    21      16.023  19.962   0.512  1.00 25.00           C
ATOM     22  CA  THR    22      13.141  19.295   2.943  1.00 25.00           C
ATOM     23  CA  THR    23      15.570  17.669   5.417  1.00 25.00           C
ATOM     24  CA  VAL    24      17.908  20.689   5.144  1.00 25.00           C
ATOM     25  CA  MET    25      14.966  23.056   5.783  1.00 25.00           C
ATOM     26  CA  ARG    26      13.948  21.003   8.852  1.00 25.00           C
ATOM     27  CA  GLU    27      17.544  21.139  10.165  1.00 25.00           C
ATOM     28  CA  VAL    28      17.612  24.934   9.658  1.00 25.00           C
ATOM     29  CA  LEU    29      14.292  25.269  11.539  1.00 25.00           C
ATOM     30  CA  ALA    30      15.677  23.146  14.410  1.00 25.00           C
ATOM     31  CA  THR    31      18.815  25.338  14.550  1.00 25.00           C
ATOM     32  CA  TYR    32      19.730  22.934  17.388  1.00 25.00           C
ATOM     33  CA  GLY    33      18.849  25.149  20.407  1.00 25.00           C
ATOM     34  CA  LYS    34      15.175  24.702  19.660  1.00 25.00           C
ATOM     35  CA  PRO    35      14.911  28.241  21.178  1.00 25.00           C
ATOM     36  CA  PHE    36      13.641  29.335  17.729  1.00 25.00           C
ATOM     37  CA  SER    37      10.680  31.528  18.419  1.00 25.00           C
ATOM     38  CA  PRO    38       9.102  28.280  19.744  1.00 25.00           C
ATOM     39  CA  ALA    39       7.234  25.098  20.768  1.00 25.00           C
ATOM     40  CA  GLN    40       4.831  25.531  17.818  1.00 25.00           C
ATOM     41  CA  ALA    41       7.796  25.983  15.437  1.00 25.00           C
ATOM     42  CA  GLN    42       9.432  22.813  16.831  1.00 25.00           C
ATOM     43  CA  LYS    43       6.160  20.882  16.346  1.00 25.00           C
ATOM     44  CA  THR    44       5.923  22.143  12.737  1.00 25.00           C
ATOM     45  CA  PHE    45       9.538  21.057  12.093  1.00 25.00           C
ATOM     46  CA  PRO    46       8.371  17.440  11.982  1.00 25.00           C
ATOM     47  CA  MET    47       6.924  15.879  15.136  1.00 25.00           C
ATOM     48  CA  ALA    48       4.781  13.231  13.576  1.00 25.00           C
ATOM     49  CA  ALA    49       6.659  12.673  10.337  1.00 25.00           C
ATOM     50  CA  GLU    50       6.474   9.020  11.470  1.00 25.00           C
ATOM     51  CA  GLN    51       9.275   8.095   9.029  1.00 25.00           C
ATOM     52  CA  ALA    52      11.419  10.976  10.358  1.00 25.00           C
ATOM     53  CA  MET    53      10.805   9.807  13.952  1.00 25.00           C
ATOM     54  CA  THR    54      11.806   6.239  12.990  1.00 25.00           C
ATOM     55  CA  GLU    55      15.004   7.554  11.344  1.00 25.00           C
ATOM     56  CA  LEU    56      15.824   9.572  14.493  1.00 25.00           C
ATOM     57  CA  GLY    57      15.532   6.518  16.786  1.00 25.00           C
ATOM     58  CA  ILE    58      18.162   5.065  14.425  1.00 25.00           C
ATOM     59  CA  ALA    59      21.339   3.984  16.337  1.00 25.00           C
ATOM     60  CA  ALA    60      25.145   4.077  16.134  1.00 25.00           C
ATOM     61  CA  SER    61      27.319   4.278  12.988  1.00 25.00           C
ATOM     62  CA  GLU    62      24.189   4.704  10.823  1.00 25.00           C
ATOM     63  CA  PHE    63      22.942   7.493  13.132  1.00 25.00           C
ATOM     64  CA  ASP    64      26.345   9.236  12.906  1.00 25.00           C
ATOM     65  CA  HIS    65      26.250   8.980   9.087  1.00 25.00           C
ATOM     66  CA  PHE    66      22.720  10.463   9.049  1.00 25.00           C
ATOM     67  CA  GLN    67      23.880  13.342  11.293  1.00 25.00           C
ATOM     68  CA  ALA    68      26.847  13.996   8.961  1.00 25.00           C
ATOM     69  CA  GLN    69      24.496  14.028   5.938  1.00 25.00           C
ATOM     70  CA  TYR    70      22.186  16.501   7.731  1.00 25.00           C
ATOM     71  CA  GLU    71      25.178  18.748   8.542  1.00 25.00           C
ATOM     72  CA  ASP    72      26.290  18.632   4.879  1.00 25.00           C
ATOM     73  CA  VAL    73      22.750  19.563   3.750  1.00 25.00           C
ATOM     74  CA  MET    74      22.708  22.493   6.216  1.00 25.00           C
ATOM     75  CA  ALA    75      26.102  23.683   4.898  1.00 25.00           C
ATOM     76  CA  SER    76      24.805  23.477   1.301  1.00 25.00           C
ATOM     77  CA  HIS    77      21.702  25.497   2.279  1.00 25.00           C
ATOM     78  CA  TYR    78      23.916  28.139   3.948  1.00 25.00           C
ATOM     79  CA  ASP    79      26.090  28.340   0.801  1.00 25.00           C
ATOM     80  CA  GLN    80      24.162  30.880  -1.276  1.00 25.00           C
ATOM     81  CA  ILE    81      20.771  29.204  -1.210  1.00 25.00           C
TER
END
