
#######################################################
#                                                     #
#                        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   88 (   88),  selected   88 , name T0288TS168_5-D1
# Molecule2: number of CA atoms   86 (  617),  selected   86 , name T0288_D1.pdb
# PARAMETERS: T0288TS168_5-D1.T0288_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S       1      S       1           -
LGA    M       2      M       2           -
LGA    V       3      V       3          4.927
LGA    P       4      P       4          2.811
LGA    G       5      G       5          2.014
LGA    K       6      K       6          2.702
LGA    V       7      V       7          1.430
LGA    T       8      T       8          2.727
LGA    L       9      L       9          1.102
LGA    Q      10      Q      10          0.757
LGA    K      11      K      11          0.910
LGA    D      12      D      12          2.261
LGA    A      13      A      13          2.111
LGA    Q      14      Q      14          1.802
LGA    N      15      N      15          0.668
LGA    L      16      L      16          1.370
LGA    I      17      I      17          1.955
LGA    G      18      G      18          2.461
LGA    I      19      I      19          1.506
LGA    S      20      S      20          2.002
LGA    I      21      I      21          1.895
LGA    G      22      G      22          0.638
LGA    G      23      G      23          0.481
LGA    G      24      G      24          1.737
LGA    A      25      A      25          3.753
LGA    Q      26      Q      26          3.356
LGA    Y      27      -       -           -
LGA    C      28      -       -           -
LGA    P      29      P      29          2.000
LGA    C      30      C      30          1.390
LGA    L      31      L      31          1.377
LGA    Y      32      Y      32          2.723
LGA    I      33      I      33          1.409
LGA    V      34      V      34          1.103
LGA    Q      35      Q      35          0.869
LGA    V      36      V      36          0.392
LGA    F      37      F      37          0.936
LGA    D      38      D      38          1.309
LGA    N      39      N      39          1.014
LGA    T      40      T      40          0.773
LGA    P      41      P      41          2.406
LGA    A      42      A      42          2.116
LGA    A      43      A      43          1.156
LGA    L      44      L      44          0.905
LGA    D      45      D      45          0.930
LGA    G      46      G      46          0.737
LGA    T      47      T      47          1.644
LGA    V      48      V      48          0.779
LGA    A      49      A      49          1.012
LGA    A      50      A      50          1.699
LGA    G      51      G      51          1.566
LGA    D      52      D      52          1.786
LGA    E      53      E      53          0.828
LGA    I      54      I      54          1.010
LGA    T      55      T      55          2.222
LGA    G      56      G      56          1.452
LGA    V      57      V      57          2.214
LGA    N      58      N      58          1.242
LGA    G      59      G      59          1.431
LGA    R      60      R      60          1.283
LGA    S      61      S      61          1.122
LGA    I      62      I      62          1.001
LGA    K      63      K      63          2.377
LGA    G      64      G      64          2.473
LGA    K      65      K      65          1.674
LGA    T      66      T      66          1.152
LGA    K      67      K      67          0.830
LGA    V      68      V      68          0.683
LGA    E      69      E      69          0.794
LGA    V      70      V      70          0.934
LGA    A      71      A      71          0.492
LGA    K      72      K      72          0.579
LGA    M      73      M      73          0.820
LGA    I      74      I      74          0.759
LGA    Q      75      Q      75          0.519
LGA    E      76      E      76          1.258
LGA    V      77      V      77          0.944
LGA    K      78      K      78          0.861
LGA    G      79      G      79          1.825
LGA    E      80      E      80          2.123
LGA    V      81      V      81          0.665
LGA    T      82      T      82          0.172
LGA    I      83      I      83          0.342
LGA    H      84      H      84          1.339
LGA    Y      85      Y      85          1.109
LGA    N      86      N      86          0.822
LGA    K      87      K      87          1.509
LGA    L      88      L      88          1.582

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   88   86    5.0     84    1.66   100.00     88.663     4.770

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.242863 * X  +  -0.921351 * Y  +   0.303527 * Z  +  27.590714
  Y_new =  -0.866611 * X  +  -0.065472 * Y  +   0.494670 * Z  +  17.618345
  Z_new =  -0.435892 * X  +  -0.383177 * Y  +  -0.814354 * Z  +  13.329879 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.701798    0.439794  [ DEG:  -154.8017     25.1983 ]
  Theta =   0.451030    2.690563  [ DEG:    25.8421    154.1579 ]
  Phi   =  -1.297561    1.844032  [ DEG:   -74.3447    105.6553 ]
 
# 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: T0288TS168_5-D1                               
REMARK     2: T0288_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0288TS168_5-D1.T0288_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   88   86   5.0   84   1.66  100.00  88.663
REMARK  ---------------------------------------------------------- 
MOLECULE T0288TS168_5-D1
PFRMAT TS
TARGET T0288
MODEL 5
PARENT N/A
ATOM      1  CA  SER     1      25.169   8.521  30.797  1.00 25.00           C
ATOM      2  CA  MET     2      24.394  12.182  30.796  1.00 25.00           C
ATOM      3  CA  VAL     3      25.672  12.819  27.230  1.00 25.00           C
ATOM      4  CA  PRO     4      24.557  13.363  23.619  1.00 25.00           C
ATOM      5  CA  GLY     5      23.792  17.065  24.010  1.00 25.00           C
ATOM      6  CA  LYS     6      20.485  17.660  22.329  1.00 25.00           C
ATOM      7  CA  VAL     7      20.242  20.308  19.661  1.00 25.00           C
ATOM      8  CA  THR     8      20.381  21.582  16.077  1.00 25.00           C
ATOM      9  CA  LEU     9      20.235  24.140  13.264  1.00 25.00           C
ATOM     10  CA  GLN    10      17.258  25.153  11.210  1.00 25.00           C
ATOM     11  CA  LYS    11      19.205  25.872   7.973  1.00 25.00           C
ATOM     12  CA  ASP    12      19.217  29.702   7.950  1.00 25.00           C
ATOM     13  CA  ALA    13      18.353  29.504   4.206  1.00 25.00           C
ATOM     14  CA  GLN    14      21.690  29.667   2.448  1.00 25.00           C
ATOM     15  CA  ASN    15      21.467  25.813   2.433  1.00 25.00           C
ATOM     16  CA  LEU    16      23.687  23.860   4.875  1.00 25.00           C
ATOM     17  CA  ILE    17      25.519  24.249   8.121  1.00 25.00           C
ATOM     18  CA  GLY    18      28.730  26.030   6.974  1.00 25.00           C
ATOM     19  CA  ILE    19      30.557  23.167   8.684  1.00 25.00           C
ATOM     20  CA  SER    20      32.451  21.096   6.115  1.00 25.00           C
ATOM     21  CA  ILE    21      33.495  17.646   7.134  1.00 25.00           C
ATOM     22  CA  GLY    22      36.107  15.216   8.402  1.00 25.00           C
ATOM     23  CA  GLY    23      37.283  12.357  10.664  1.00 25.00           C
ATOM     24  CA  GLY    24      35.645   9.043   9.697  1.00 25.00           C
ATOM     25  CA  ALA    25      37.687   6.388   7.776  1.00 25.00           C
ATOM     26  CA  GLN    26      40.117   5.991  10.686  1.00 25.00           C
ATOM     27  CA  TYR    27      39.480   8.504  13.472  1.00 25.00           C
ATOM     28  CA  CYS    28      37.472   6.152  15.649  1.00 25.00           C
ATOM     29  CA  PRO    29      34.557   5.362  13.313  1.00 25.00           C
ATOM     30  CA  CYS    30      32.863   8.676  14.022  1.00 25.00           C
ATOM     31  CA  LEU    31      31.743  11.560  11.781  1.00 25.00           C
ATOM     32  CA  TYR    32      32.141  15.380  11.498  1.00 25.00           C
ATOM     33  CA  ILE    33      33.720  18.809  12.196  1.00 25.00           C
ATOM     34  CA  VAL    34      36.556  21.318  11.740  1.00 25.00           C
ATOM     35  CA  GLN    35      34.959  24.814  11.710  1.00 25.00           C
ATOM     36  CA  VAL    36      31.546  26.296  12.499  1.00 25.00           C
ATOM     37  CA  PHE    37      32.024  29.480  10.461  1.00 25.00           C
ATOM     38  CA  ASP    38      30.588  32.957  10.144  1.00 25.00           C
ATOM     39  CA  ASN    39      27.315  34.183  11.536  1.00 25.00           C
ATOM     40  CA  THR    40      26.055  30.712  10.682  1.00 25.00           C
ATOM     41  CA  PRO    41      24.830  27.482  12.196  1.00 25.00           C
ATOM     42  CA  ALA    42      27.108  25.986  14.906  1.00 25.00           C
ATOM     43  CA  ALA    43      28.261  29.583  15.585  1.00 25.00           C
ATOM     44  CA  LEU    44      24.902  31.369  15.627  1.00 25.00           C
ATOM     45  CA  ASP    45      23.050  28.477  17.327  1.00 25.00           C
ATOM     46  CA  GLY    46      25.834  27.620  19.783  1.00 25.00           C
ATOM     47  CA  THR    47      24.432  24.147  20.265  1.00 25.00           C
ATOM     48  CA  VAL    48      27.411  22.453  18.503  1.00 25.00           C
ATOM     49  CA  ALA    49      31.129  22.793  17.809  1.00 25.00           C
ATOM     50  CA  ALA    50      34.855  23.418  17.336  1.00 25.00           C
ATOM     51  CA  GLY    51      35.015  19.574  17.105  1.00 25.00           C
ATOM     52  CA  ASP    52      31.725  17.654  17.019  1.00 25.00           C
ATOM     53  CA  GLU    53      31.758  13.890  16.608  1.00 25.00           C
ATOM     54  CA  ILE    54      28.457  14.333  14.801  1.00 25.00           C
ATOM     55  CA  THR    55      26.099  11.397  14.371  1.00 25.00           C
ATOM     56  CA  GLY    56      22.394  11.325  13.614  1.00 25.00           C
ATOM     57  CA  VAL    57      19.774  11.723  10.872  1.00 25.00           C
ATOM     58  CA  ASN    58      17.062  12.640  13.336  1.00 25.00           C
ATOM     59  CA  GLY    59      16.902   9.073  14.781  1.00 25.00           C
ATOM     60  CA  ARG    60      18.771   7.018  12.203  1.00 25.00           C
ATOM     61  CA  SER    61      22.509   6.331  12.767  1.00 25.00           C
ATOM     62  CA  ILE    62      25.360   7.898  10.720  1.00 25.00           C
ATOM     63  CA  LYS    63      28.115   6.323  12.760  1.00 25.00           C
ATOM     64  CA  GLY    64      30.091   3.517  11.058  1.00 25.00           C
ATOM     65  CA  LYS    65      29.769   4.948   7.585  1.00 25.00           C
ATOM     66  CA  THR    66      32.100   7.369   5.839  1.00 25.00           C
ATOM     67  CA  LYS    67      32.532  11.150   6.165  1.00 25.00           C
ATOM     68  CA  VAL    68      31.297  11.649   2.575  1.00 25.00           C
ATOM     69  CA  GLU    69      28.115   9.672   3.369  1.00 25.00           C
ATOM     70  CA  VAL    70      27.533  11.813   6.491  1.00 25.00           C
ATOM     71  CA  ALA    71      27.994  15.001   4.419  1.00 25.00           C
ATOM     72  CA  LYS    72      25.493  13.706   1.824  1.00 25.00           C
ATOM     73  CA  MET    73      22.977  12.921   4.603  1.00 25.00           C
ATOM     74  CA  ILE    74      23.430  16.443   6.040  1.00 25.00           C
ATOM     75  CA  GLN    75      22.866  17.958   2.568  1.00 25.00           C
ATOM     76  CA  GLU    76      19.687  15.865   2.144  1.00 25.00           C
ATOM     77  CA  VAL    77      17.438  17.066   5.009  1.00 25.00           C
ATOM     78  CA  LYS    78      15.962  20.164   3.310  1.00 25.00           C
ATOM     79  CA  GLY    79      13.451  21.596   5.790  1.00 25.00           C
ATOM     80  CA  GLU    80      14.207  20.729   9.433  1.00 25.00           C
ATOM     81  CA  VAL    81      17.652  19.468  10.633  1.00 25.00           C
ATOM     82  CA  THR    82      18.903  17.472  13.640  1.00 25.00           C
ATOM     83  CA  ILE    83      22.436  16.647  14.844  1.00 25.00           C
ATOM     84  CA  HIS    84      23.303  15.403  18.332  1.00 25.00           C
ATOM     85  CA  TYR    85      26.887  16.150  19.363  1.00 25.00           C
ATOM     86  CA  ASN    86      28.907  13.506  21.141  1.00 25.00           C
ATOM     87  CA  LYS    87      31.436  16.035  22.301  1.00 25.00           C
ATOM     88  CA  LEU    88      34.945  16.417  23.844  1.00 25.00           C
TER
END
