
#######################################################
#                                                     #
#                        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 T0288TS393_2-D1
# Molecule2: number of CA atoms   86 (  617),  selected   86 , name T0288_D1.pdb
# PARAMETERS: T0288TS393_2-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          5.890
LGA    P       4      P       4          2.821
LGA    G       5      G       5          2.266
LGA    K       6      K       6          1.013
LGA    V       7      V       7          2.170
LGA    T       8      T       8          2.763
LGA    L       9      L       9          1.259
LGA    Q      10      Q      10          1.561
LGA    K      11      K      11          1.432
LGA    D      12      D      12          2.418
LGA    A      13      A      13          1.061
LGA    Q      14      Q      14          3.412
LGA    N      15      N      15          3.173
LGA    L      16      L      16          1.360
LGA    I      17      I      17          0.855
LGA    G      18      G      18          1.674
LGA    I      19      I      19          1.571
LGA    S      20      S      20          1.577
LGA    I      21      I      21          1.325
LGA    G      22      G      22          1.362
LGA    G      23      G      23          0.942
LGA    G      24      G      24          2.998
LGA    A      25      A      25          3.590
LGA    Q      26      Q      26          1.678
LGA    Y      27      -       -           -
LGA    C      28      -       -           -
LGA    P      29      P      29          2.611
LGA    C      30      C      30          1.917
LGA    L      31      L      31          0.528
LGA    Y      32      Y      32          1.348
LGA    I      33      I      33          0.906
LGA    V      34      V      34          0.812
LGA    Q      35      Q      35          0.838
LGA    V      36      V      36          2.396
LGA    F      37      F      37          1.768
LGA    D      38      D      38          1.268
LGA    N      39      N      39          0.730
LGA    T      40      T      40          1.075
LGA    P      41      P      41          0.537
LGA    A      42      A      42          0.438
LGA    A      43      A      43          1.049
LGA    L      44      L      44          1.152
LGA    D      45      D      45          0.674
LGA    G      46      G      46          0.849
LGA    T      47      T      47          1.561
LGA    V      48      V      48          1.922
LGA    A      49      A      49          1.008
LGA    A      50      A      50          1.349
LGA    G      51      G      51          1.111
LGA    D      52      D      52          0.770
LGA    E      53      E      53          0.622
LGA    I      54      I      54          0.560
LGA    T      55      T      55          0.780
LGA    G      56      G      56          0.617
LGA    V      57      V      57          1.819
LGA    N      58      N      58          0.961
LGA    G      59      G      59          1.606
LGA    R      60      R      60          1.583
LGA    S      61      S      61          1.713
LGA    I      62      I      62          1.394
LGA    K      63      K      63          1.953
LGA    G      64      G      64          1.844
LGA    K      65      K      65          1.260
LGA    T      66      T      66          2.497
LGA    K      67      K      67          0.755
LGA    V      68      V      68          0.747
LGA    E      69      E      69          0.685
LGA    V      70      V      70          0.852
LGA    A      71      A      71          0.682
LGA    K      72      K      72          0.612
LGA    M      73      M      73          0.898
LGA    I      74      I      74          1.249
LGA    Q      75      Q      75          0.718
LGA    E      76      E      76          0.807
LGA    V      77      V      77          0.959
LGA    K      78      K      78          1.983
LGA    G      79      G      79          2.810
LGA    E      80      E      80          2.329
LGA    V      81      V      81          1.297
LGA    T      82      T      82          0.729
LGA    I      83      I      83          1.060
LGA    H      84      H      84          1.874
LGA    Y      85      Y      85          1.463
LGA    N      86      N      86          0.590
LGA    K      87      K      87          0.947
LGA    L      88      L      88          0.914

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   88   86    5.0     84    1.70   100.00     88.800     4.655

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.536038 * X  +   0.320685 * Y  +  -0.780912 * Z  +  27.530050
  Y_new =  -0.551998 * X  +  -0.833032 * Y  +   0.036817 * Z  +  17.240908
  Z_new =  -0.638718 * X  +   0.450798 * Y  +   0.623555 * Z  +  13.319961 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.625962   -2.515631  [ DEG:    35.8650   -144.1350 ]
  Theta =   0.692831    2.448761  [ DEG:    39.6963    140.3037 ]
  Phi   =  -2.341527    0.800066  [ DEG:  -134.1596     45.8404 ]
 
# 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: T0288TS393_2-D1                               
REMARK     2: T0288_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0288TS393_2-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   1.70  100.00  88.800
REMARK  ---------------------------------------------------------- 
MOLECULE T0288TS393_2-D1
PFRMAT TS
TARGET T0288
MODEL 2
PARENT N/A
ATOM      1  CA  SER     1      23.659   8.145  32.857  1.00 25.00           C
ATOM      2  CA  MET     2      24.359  10.341  29.807  1.00 25.00           C
ATOM      3  CA  VAL     3      22.796  13.058  27.661  1.00 25.00           C
ATOM      4  CA  PRO     4      23.804  13.950  24.064  1.00 25.00           C
ATOM      5  CA  GLY     5      22.774  17.626  24.088  1.00 25.00           C
ATOM      6  CA  LYS     6      20.989  16.831  20.829  1.00 25.00           C
ATOM      7  CA  VAL     7      22.238  19.884  19.032  1.00 25.00           C
ATOM      8  CA  THR     8      19.099  21.564  17.802  1.00 25.00           C
ATOM      9  CA  LEU     9      19.460  23.295  14.432  1.00 25.00           C
ATOM     10  CA  GLN    10      18.002  25.812  11.979  1.00 25.00           C
ATOM     11  CA  LYS    11      18.276  26.122   8.246  1.00 25.00           C
ATOM     12  CA  ASP    12      17.581  29.349   6.272  1.00 25.00           C
ATOM     13  CA  ALA    13      19.465  29.487   2.939  1.00 25.00           C
ATOM     14  CA  GLN    14      20.267  26.011   1.501  1.00 25.00           C
ATOM     15  CA  ASN    15      23.742  26.897   2.683  1.00 25.00           C
ATOM     16  CA  LEU    16      23.494  23.871   5.065  1.00 25.00           C
ATOM     17  CA  ILE    17      24.548  24.904   8.607  1.00 25.00           C
ATOM     18  CA  GLY    18      28.071  25.613   7.545  1.00 25.00           C
ATOM     19  CA  ILE    19      29.147  22.112   8.721  1.00 25.00           C
ATOM     20  CA  SER    20      31.980  20.677   6.628  1.00 25.00           C
ATOM     21  CA  ILE    21      32.218  16.991   7.537  1.00 25.00           C
ATOM     22  CA  GLY    22      35.081  14.632   8.068  1.00 25.00           C
ATOM     23  CA  GLY    23      37.998  13.011   9.855  1.00 25.00           C
ATOM     24  CA  GLY    24      39.001  10.640   7.018  1.00 25.00           C
ATOM     25  CA  ALA    25      38.009   6.951   6.928  1.00 25.00           C
ATOM     26  CA  GLN    26      40.930   5.728   9.137  1.00 25.00           C
ATOM     27  CA  TYR    27      39.134   7.170  12.174  1.00 25.00           C
ATOM     28  CA  CYS    28      37.321   4.309  13.909  1.00 25.00           C
ATOM     29  CA  PRO    29      33.635   5.057  13.509  1.00 25.00           C
ATOM     30  CA  CYS    30      32.263   8.603  13.857  1.00 25.00           C
ATOM     31  CA  LEU    31      32.645  11.966  12.153  1.00 25.00           C
ATOM     32  CA  TYR    32      33.168  15.715  12.677  1.00 25.00           C
ATOM     33  CA  ILE    33      32.434  19.463  13.180  1.00 25.00           C
ATOM     34  CA  VAL    34      35.539  20.669  11.272  1.00 25.00           C
ATOM     35  CA  GLN    35      34.932  24.218  12.528  1.00 25.00           C
ATOM     36  CA  VAL    36      32.234  25.937  10.398  1.00 25.00           C
ATOM     37  CA  PHE    37      31.688  29.376  11.930  1.00 25.00           C
ATOM     38  CA  ASP    38      30.055  32.360  10.212  1.00 25.00           C
ATOM     39  CA  ASN    39      26.484  33.577  10.359  1.00 25.00           C
ATOM     40  CA  THR    40      25.482  30.140   9.201  1.00 25.00           C
ATOM     41  CA  PRO    41      23.013  28.689  11.683  1.00 25.00           C
ATOM     42  CA  ALA    42      25.109  26.212  13.604  1.00 25.00           C
ATOM     43  CA  ALA    43      27.711  28.596  15.091  1.00 25.00           C
ATOM     44  CA  LEU    44      25.054  31.335  15.410  1.00 25.00           C
ATOM     45  CA  ASP    45      23.474  28.968  17.993  1.00 25.00           C
ATOM     46  CA  GLY    46      26.259  27.305  20.046  1.00 25.00           C
ATOM     47  CA  THR    47      25.986  23.527  19.698  1.00 25.00           C
ATOM     48  CA  VAL    48      27.979  22.286  16.668  1.00 25.00           C
ATOM     49  CA  ALA    49      31.058  22.935  18.818  1.00 25.00           C
ATOM     50  CA  ALA    50      34.532  22.882  17.337  1.00 25.00           C
ATOM     51  CA  GLY    51      36.130  19.517  18.321  1.00 25.00           C
ATOM     52  CA  ASP    52      32.753  17.811  18.012  1.00 25.00           C
ATOM     53  CA  GLU    53      32.327  14.066  17.476  1.00 25.00           C
ATOM     54  CA  ILE    54      29.077  13.231  15.579  1.00 25.00           C
ATOM     55  CA  THR    55      26.212  10.874  16.450  1.00 25.00           C
ATOM     56  CA  GLY    56      23.394  11.127  13.933  1.00 25.00           C
ATOM     57  CA  VAL    57      21.502  11.577  10.680  1.00 25.00           C
ATOM     58  CA  ASN    58      18.167  13.128  11.599  1.00 25.00           C
ATOM     59  CA  GLY    59      16.210  10.717  13.757  1.00 25.00           C
ATOM     60  CA  ARG    60      18.140   8.025  11.868  1.00 25.00           C
ATOM     61  CA  SER    61      21.590   6.627  12.508  1.00 25.00           C
ATOM     62  CA  ILE    62      24.621   7.482  10.289  1.00 25.00           C
ATOM     63  CA  LYS    63      27.610   5.972  12.064  1.00 25.00           C
ATOM     64  CA  GLY    64      29.699   3.012  10.782  1.00 25.00           C
ATOM     65  CA  LYS    65      29.160   4.533   7.291  1.00 25.00           C
ATOM     66  CA  THR    66      31.906   7.075   7.748  1.00 25.00           C
ATOM     67  CA  LYS    67      32.108  10.717   6.573  1.00 25.00           C
ATOM     68  CA  VAL    68      31.099  11.328   2.930  1.00 25.00           C
ATOM     69  CA  GLU    69      27.672   9.750   3.587  1.00 25.00           C
ATOM     70  CA  VAL    70      27.213  11.973   6.672  1.00 25.00           C
ATOM     71  CA  ALA    71      28.143  15.066   4.612  1.00 25.00           C
ATOM     72  CA  LYS    72      25.621  14.055   1.912  1.00 25.00           C
ATOM     73  CA  MET    73      22.910  13.600   4.579  1.00 25.00           C
ATOM     74  CA  ILE    74      23.716  17.055   6.022  1.00 25.00           C
ATOM     75  CA  GLN    75      23.489  18.596   2.523  1.00 25.00           C
ATOM     76  CA  GLU    76      20.106  16.892   1.965  1.00 25.00           C
ATOM     77  CA  VAL    77      17.706  18.437   4.429  1.00 25.00           C
ATOM     78  CA  LYS    78      16.194  21.904   4.607  1.00 25.00           C
ATOM     79  CA  GLY    79      13.920  20.733   7.444  1.00 25.00           C
ATOM     80  CA  GLU    80      15.474  20.322  10.927  1.00 25.00           C
ATOM     81  CA  VAL    81      19.236  19.677  10.615  1.00 25.00           C
ATOM     82  CA  THR    82      19.450  17.963  14.009  1.00 25.00           C
ATOM     83  CA  ILE    83      23.216  17.333  13.905  1.00 25.00           C
ATOM     84  CA  HIS    84      24.644  15.734  17.117  1.00 25.00           C
ATOM     85  CA  TYR    85      27.337  16.212  19.782  1.00 25.00           C
ATOM     86  CA  ASN    86      29.289  13.455  21.572  1.00 25.00           C
ATOM     87  CA  LYS    87      31.472  16.299  22.842  1.00 25.00           C
ATOM     88  CA  LEU    88      34.844  15.693  24.494  1.00 25.00           C
TER
END
