
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms   86 (  617),  selected   86 , name T0288_D1.pdb
# PARAMETERS: T0288TS168_4-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          5.959
LGA    P       4      P       4          2.329
LGA    G       5      G       5          1.535
LGA    K       6      K       6          2.685
LGA    V       7      V       7          2.180
LGA    T       8      T       8          1.182
LGA    L       9      L       9          0.691
LGA    Q      10      Q      10          1.289
LGA    K      11      K      11          1.317
LGA    D      12      D      12          1.172
LGA    A      13      A      13          2.161
LGA    Q      14      Q      14          1.831
LGA    N      15      N      15          2.710
LGA    L      16      L      16          1.906
LGA    I      17      I      17          2.388
LGA    G      18      G      18          1.025
LGA    I      19      I      19          1.484
LGA    S      20      S      20          0.831
LGA    I      21      I      21          2.094
LGA    G      22      G      22          1.414
LGA    G      23      G      23          1.335
LGA    G      24      G      24          1.916
LGA    A      25      A      25          3.307
LGA    Q      26      Q      26          2.874
LGA    Y      27      P      29          2.911
LGA    C      28      -       -           -
LGA    P      29      -       -           -
LGA    C      30      C      30          2.101
LGA    L      31      L      31          1.634
LGA    Y      32      Y      32          2.546
LGA    I      33      I      33          1.244
LGA    V      34      V      34          0.852
LGA    Q      35      Q      35          0.622
LGA    V      36      V      36          1.080
LGA    F      37      F      37          0.870
LGA    D      38      D      38          0.917
LGA    N      39      N      39          0.851
LGA    T      40      T      40          0.902
LGA    P      41      P      41          1.792
LGA    A      42      A      42          1.017
LGA    A      43      A      43          0.732
LGA    L      44      L      44          1.938
LGA    D      45      D      45          0.442
LGA    G      46      G      46          0.685
LGA    T      47      T      47          0.194
LGA    V      48      V      48          0.725
LGA    A      49      A      49          2.400
LGA    A      50      A      50          2.058
LGA    G      51      G      51          1.062
LGA    D      52      D      52          1.076
LGA    E      53      E      53          0.926
LGA    I      54      I      54          0.755
LGA    T      55      T      55          1.829
LGA    G      56      G      56          2.060
LGA    V      57      V      57          2.076
LGA    N      58      N      58          0.968
LGA    G      59      G      59          2.231
LGA    R      60      R      60          2.085
LGA    S      61      S      61          1.821
LGA    I      62      I      62          1.444
LGA    K      63      K      63          2.417
LGA    G      64      G      64          2.684
LGA    K      65      K      65          2.750
LGA    T      66      T      66          1.898
LGA    K      67      K      67          1.053
LGA    V      68      V      68          0.690
LGA    E      69      E      69          0.377
LGA    V      70      V      70          1.122
LGA    A      71      A      71          0.625
LGA    K      72      K      72          0.651
LGA    M      73      M      73          1.385
LGA    I      74      I      74          1.594
LGA    Q      75      Q      75          0.967
LGA    E      76      E      76          2.364
LGA    V      77      V      77          2.052
LGA    K      78      K      78          1.483
LGA    G      79      G      79          3.375
LGA    E      80      E      80          0.962
LGA    V      81      V      81          1.053
LGA    T      82      T      82          0.659
LGA    I      83      I      83          1.347
LGA    H      84      H      84          1.550
LGA    Y      85      Y      85          0.992
LGA    N      86      N      86          0.812
LGA    K      87      K      87          0.660
LGA    L      88      L      88          2.403

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   88   86    5.0     84    1.80    98.81     87.179     4.415

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.512999 * X  +  -0.829395 * Y  +   0.221215 * Z  +  27.571880
  Y_new =  -0.811470 * X  +  -0.552613 * Y  +  -0.190093 * Z  +  17.481384
  Z_new =   0.279908 * X  +  -0.081992 * Y  +  -0.956519 * Z  +  13.300929 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.056082    0.085510  [ DEG:  -175.1006      4.8994 ]
  Theta =  -0.283698   -2.857894  [ DEG:   -16.2547   -163.7453 ]
  Phi   =  -1.007048    2.134545  [ DEG:   -57.6996    122.3004 ]
 
# 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_4-D1                               
REMARK     2: T0288_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0288TS168_4-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   1.80   98.81  87.179
REMARK  ---------------------------------------------------------- 
MOLECULE T0288TS168_4-D1
PFRMAT TS
TARGET T0288
MODEL 4
PARENT N/A
ATOM      1  CA  SER     1      26.472  12.365  34.082  1.00 25.00           C
ATOM      2  CA  MET     2      26.557  10.851  30.619  1.00 25.00           C
ATOM      3  CA  VAL     3      26.461  11.751  26.929  1.00 25.00           C
ATOM      4  CA  PRO     4      24.122  14.405  25.435  1.00 25.00           C
ATOM      5  CA  GLY     5      22.981  17.148  23.038  1.00 25.00           C
ATOM      6  CA  LYS     6      20.806  19.357  20.837  1.00 25.00           C
ATOM      7  CA  VAL     7      21.479  21.968  18.222  1.00 25.00           C
ATOM      8  CA  THR     8      18.304  21.666  16.218  1.00 25.00           C
ATOM      9  CA  LEU     9      19.494  24.169  13.609  1.00 25.00           C
ATOM     10  CA  GLN    10      17.247  26.445  11.549  1.00 25.00           C
ATOM     11  CA  LYS    11      18.855  26.378   8.156  1.00 25.00           C
ATOM     12  CA  ASP    12      19.355  29.813   6.500  1.00 25.00           C
ATOM     13  CA  ALA    13      17.348  29.599   3.245  1.00 25.00           C
ATOM     14  CA  GLN    14      20.721  28.343   1.888  1.00 25.00           C
ATOM     15  CA  ASN    15      23.584  26.038   2.750  1.00 25.00           C
ATOM     16  CA  LEU    16      23.884  23.395   5.546  1.00 25.00           C
ATOM     17  CA  ILE    17      25.355  22.980   9.064  1.00 25.00           C
ATOM     18  CA  GLY    18      27.611  25.786   8.027  1.00 25.00           C
ATOM     19  CA  ILE    19      30.684  23.693   9.014  1.00 25.00           C
ATOM     20  CA  SER    20      32.480  20.411   8.339  1.00 25.00           C
ATOM     21  CA  ILE    21      33.500  17.019   6.948  1.00 25.00           C
ATOM     22  CA  GLY    22      36.880  16.295   8.394  1.00 25.00           C
ATOM     23  CA  GLY    23      36.597  12.583   9.083  1.00 25.00           C
ATOM     24  CA  GLY    24      36.423   8.977  10.362  1.00 25.00           C
ATOM     25  CA  ALA    25      37.982   7.111   7.414  1.00 25.00           C
ATOM     26  CA  GLN    26      39.845   4.960  10.025  1.00 25.00           C
ATOM     27  CA  TYR    27      36.545   3.066  10.263  1.00 25.00           C
ATOM     28  CA  CYS    28      36.426   3.265  14.062  1.00 25.00           C
ATOM     29  CA  PRO    29      35.548   6.845  14.915  1.00 25.00           C
ATOM     30  CA  CYS    30      32.412   9.000  14.603  1.00 25.00           C
ATOM     31  CA  LEU    31      31.620  11.147  11.582  1.00 25.00           C
ATOM     32  CA  TYR    32      32.678  14.814  11.390  1.00 25.00           C
ATOM     33  CA  ILE    33      33.857  18.242  12.691  1.00 25.00           C
ATOM     34  CA  VAL    34      36.796  20.483  11.653  1.00 25.00           C
ATOM     35  CA  GLN    35      34.903  23.730  12.298  1.00 25.00           C
ATOM     36  CA  VAL    36      32.549  26.723  12.818  1.00 25.00           C
ATOM     37  CA  PHE    37      32.008  29.421  10.193  1.00 25.00           C
ATOM     38  CA  ASP    38      30.981  33.047  10.764  1.00 25.00           C
ATOM     39  CA  ASN    39      27.431  33.900   9.805  1.00 25.00           C
ATOM     40  CA  THR    40      25.925  30.471   9.432  1.00 25.00           C
ATOM     41  CA  PRO    41      23.552  27.837  10.772  1.00 25.00           C
ATOM     42  CA  ALA    42      25.840  26.042  13.172  1.00 25.00           C
ATOM     43  CA  ALA    43      26.605  29.492  14.686  1.00 25.00           C
ATOM     44  CA  LEU    44      22.881  30.247  15.219  1.00 25.00           C
ATOM     45  CA  ASP    45      23.170  28.256  18.446  1.00 25.00           C
ATOM     46  CA  GLY    46      26.810  27.921  19.598  1.00 25.00           C
ATOM     47  CA  THR    47      26.000  24.394  20.794  1.00 25.00           C
ATOM     48  CA  VAL    48      28.065  22.998  17.958  1.00 25.00           C
ATOM     49  CA  ALA    49      30.947  22.742  20.502  1.00 25.00           C
ATOM     50  CA  ALA    50      33.683  22.695  17.867  1.00 25.00           C
ATOM     51  CA  GLY    51      35.282  19.266  17.447  1.00 25.00           C
ATOM     52  CA  ASP    52      31.733  17.936  18.152  1.00 25.00           C
ATOM     53  CA  GLU    53      31.942  14.406  16.733  1.00 25.00           C
ATOM     54  CA  ILE    54      28.702  14.075  14.802  1.00 25.00           C
ATOM     55  CA  THR    55      26.084  11.336  14.829  1.00 25.00           C
ATOM     56  CA  GLY    56      22.896  12.012  12.889  1.00 25.00           C
ATOM     57  CA  VAL    57      19.878  12.329  10.633  1.00 25.00           C
ATOM     58  CA  ASN    58      16.603  13.183  12.388  1.00 25.00           C
ATOM     59  CA  GLY    59      16.797   9.465  13.021  1.00 25.00           C
ATOM     60  CA  ARG    60      19.245   7.275  11.008  1.00 25.00           C
ATOM     61  CA  SER    61      22.849   6.750  12.061  1.00 25.00           C
ATOM     62  CA  ILE    62      26.103   8.059  10.492  1.00 25.00           C
ATOM     63  CA  LYS    63      27.878   6.264  13.391  1.00 25.00           C
ATOM     64  CA  GLY    64      29.580   3.360  11.692  1.00 25.00           C
ATOM     65  CA  LYS    65      30.584   5.221   8.496  1.00 25.00           C
ATOM     66  CA  THR    66      32.834   7.123   6.143  1.00 25.00           C
ATOM     67  CA  LYS    67      32.669  10.748   5.059  1.00 25.00           C
ATOM     68  CA  VAL    68      30.916  11.631   1.770  1.00 25.00           C
ATOM     69  CA  GLU    69      27.791   9.725   2.896  1.00 25.00           C
ATOM     70  CA  VAL    70      27.829  11.589   6.242  1.00 25.00           C
ATOM     71  CA  ALA    71      28.139  14.934   4.402  1.00 25.00           C
ATOM     72  CA  LYS    72      25.192  13.994   2.144  1.00 25.00           C
ATOM     73  CA  MET    73      23.104  13.062   5.216  1.00 25.00           C
ATOM     74  CA  ILE    74      23.975  16.411   6.855  1.00 25.00           C
ATOM     75  CA  GLN    75      22.960  18.266   3.662  1.00 25.00           C
ATOM     76  CA  GLU    76      19.640  16.359   3.580  1.00 25.00           C
ATOM     77  CA  VAL    77      16.954  17.223   6.154  1.00 25.00           C
ATOM     78  CA  LYS    78      15.918  20.679   4.849  1.00 25.00           C
ATOM     79  CA  GLY    79      12.988  20.301   7.285  1.00 25.00           C
ATOM     80  CA  GLU    80      15.324  21.623   9.985  1.00 25.00           C
ATOM     81  CA  VAL    81      18.701  19.911  10.495  1.00 25.00           C
ATOM     82  CA  THR    82      19.453  17.460  13.381  1.00 25.00           C
ATOM     83  CA  ILE    83      22.225  16.629  15.875  1.00 25.00           C
ATOM     84  CA  HIS    84      22.744  14.306  18.866  1.00 25.00           C
ATOM     85  CA  TYR    85      26.194  15.906  18.886  1.00 25.00           C
ATOM     86  CA  ASN    86      28.433  14.097  21.373  1.00 25.00           C
ATOM     87  CA  LYS    87      31.020  16.138  23.212  1.00 25.00           C
ATOM     88  CA  LEU    88      34.651  16.397  22.269  1.00 25.00           C
TER
END
