
#######################################################
#                                                     #
#                        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   97 (   97),  selected   97 , name T0311TS168_3
# Molecule2: number of CA atoms   87 (  672),  selected   87 , name T0311.pdb
# PARAMETERS: T0311TS168_3.T0311.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    K       2      -       -           -
LGA    M       3      -       -           -
LGA    A       4      -       -           -
LGA    N       5      -       -           -
LGA    H       6      -       -           -
LGA    P       7      -       -           -
LGA    R       8      -       -           -
LGA    P       9      -       -           -
LGA    G      10      -       -           -
LGA    D      11      -       -           -
LGA    I      12      R       8           #
LGA    I      13      P       9          4.928
LGA    Q      14      G      10          2.266
LGA    E      15      D      11          2.710
LGA    S      16      I      12          2.595
LGA    L      17      -       -           -
LGA    D      18      I      13          3.325
LGA    E      19      Q      14           -
LGA    L      20      E      15           #
LGA    N      21      S      16          2.072
LGA    V      22      L      17          2.033
LGA    S      23      D      18          4.434
LGA    L      24      E      19           -
LGA    -       -      L      20           -
LGA    -       -      N      21           -
LGA    -       -      V      22           -
LGA    -       -      S      23           -
LGA    R      25      L      24          3.584
LGA    E      26      R      25           #
LGA    -       -      E      26           -
LGA    F      27      F      27          4.140
LGA    A      28      A      28          2.999
LGA    R      29      R      29          2.961
LGA    A      30      A      30          1.166
LGA    M      31      M      31          0.798
LGA    E      32      E      32          1.863
LGA    I      33      I      33          1.815
LGA    A      34      A      34          2.259
LGA    P      35      P      35          2.748
LGA    S      36      S      36          2.848
LGA    T      37      T      37          1.889
LGA    A      38      A      38          1.150
LGA    S      39      S      39          1.127
LGA    R      40      R      40          2.787
LGA    L      41      L      41          3.246
LGA    L      42      L      42          2.862
LGA    T      43      T      43          3.343
LGA    G      44      G      44           -
LGA    K      45      -       -           -
LGA    A      46      -       -           -
LGA    A      47      K      45          4.139
LGA    L      48      A      46          2.807
LGA    T      49      A      47          3.048
LGA    P      50      -       -           -
LGA    E      51      -       -           -
LGA    M      52      -       -           -
LGA    A      53      L      48          1.978
LGA    I      54      T      49          1.960
LGA    K      55      P      50           -
LGA    -       -      E      51           -
LGA    L      56      M      52          3.979
LGA    S      57      A      53          2.184
LGA    V      58      I      54          4.279
LGA    V      59      K      55          4.194
LGA    I      60      L      56          1.484
LGA    -       -      S      57           -
LGA    G      61      V      58          3.173
LGA    S      62      V      59           #
LGA    S      63      I      60           -
LGA    P      64      G      61           #
LGA    Q      65      S      62          3.832
LGA    M      66      S      63          3.259
LGA    W      67      P      64          2.133
LGA    L      68      Q      65          1.876
LGA    N      69      M      66          0.944
LGA    L      70      W      67          0.409
LGA    Q      71      L      68          0.609
LGA    N      72      N      69          1.345
LGA    A      73      L      70          1.041
LGA    W      74      Q      71          1.088
LGA    S      75      N      72          1.468
LGA    L      76      A      73          1.380
LGA    A      77      W      74          1.315
LGA    E      78      S      75          1.850
LGA    A      79      L      76          2.085
LGA    E      80      A      77          1.439
LGA    K      81      E      78          1.398
LGA    -       -      A      79           -
LGA    -       -      E      80           -
LGA    T      82      K      81          4.544
LGA    V      83      T      82           -
LGA    D      84      V      83           -
LGA    V      85      D      84           -
LGA    S      86      V      85           -
LGA    R      87      S      86           -
LGA    L      88      R      87           -
LGA    R      89      L      88           -
LGA    R      90      R      89           -
LGA    L      91      R      90           -
LGA    V      92      L      91           -
LGA    T      93      V      92           -
LGA    Q      94      T      93           -
LGA    S      95      Q      94           -
LGA    T      96      -       -           -
LGA    P      97      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   97   87    5.0     55    2.67    32.73     41.141     1.987

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.701105 * X  +  -0.654923 * Y  +   0.282007 * Z  +  36.674847
  Y_new =  -0.551139 * X  +   0.748657 * Y  +   0.368455 * Z  +   0.393652
  Z_new =  -0.452436 * X  +   0.102901 * Y  +  -0.885840 * Z  +  13.021783 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.025949   -0.115643  [ DEG:   173.3741     -6.6259 ]
  Theta =   0.469495    2.672098  [ DEG:    26.9001    153.0999 ]
  Phi   =  -2.475385    0.666208  [ DEG:  -141.8291     38.1709 ]
 
# 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: T0311TS168_3                                  
REMARK     2: T0311.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0311TS168_3.T0311.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   97   87   5.0   55   2.67   32.73  41.141
REMARK  ---------------------------------------------------------- 
MOLECULE T0311TS168_3
PFRMAT TS
TARGET T0311
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      49.263  -7.716  29.133  1.00 25.00           C
ATOM      2  CA  LYS     2      47.551  -7.823  32.588  1.00 25.00           C
ATOM      3  CA  MET     3      44.703  -6.672  34.852  1.00 25.00           C
ATOM      4  CA  ALA     4      41.168  -5.926  33.719  1.00 25.00           C
ATOM      5  CA  ASN     5      38.836  -2.951  34.142  1.00 25.00           C
ATOM      6  CA  HIS     6      36.669  -0.932  31.812  1.00 25.00           C
ATOM      7  CA  PRO     7      37.607  -1.450  28.180  1.00 25.00           C
ATOM      8  CA  ARG     8      38.353  -2.906  24.778  1.00 25.00           C
ATOM      9  CA  PRO     9      38.583  -3.704  21.030  1.00 25.00           C
ATOM     10  CA  GLY    10      35.891  -4.414  18.399  1.00 25.00           C
ATOM     11  CA  ASP    11      33.853  -1.419  19.641  1.00 25.00           C
ATOM     12  CA  ILE    12      36.960   0.811  19.440  1.00 25.00           C
ATOM     13  CA  ILE    13      37.628  -0.399  15.868  1.00 25.00           C
ATOM     14  CA  GLN    14      33.997   0.351  14.908  1.00 25.00           C
ATOM     15  CA  GLU    15      34.299   3.860  16.413  1.00 25.00           C
ATOM     16  CA  SER    16      37.533   4.451  14.450  1.00 25.00           C
ATOM     17  CA  LEU    17      35.817   3.296  11.227  1.00 25.00           C
ATOM     18  CA  ASP    18      32.887   5.666  11.909  1.00 25.00           C
ATOM     19  CA  GLU    19      35.330   8.557  12.495  1.00 25.00           C
ATOM     20  CA  LEU    20      32.042  10.519  12.978  1.00 25.00           C
ATOM     21  CA  ASN    21      29.249   8.228  14.290  1.00 25.00           C
ATOM     22  CA  VAL    22      28.039   5.513  16.710  1.00 25.00           C
ATOM     23  CA  SER    23      29.538   2.241  17.872  1.00 25.00           C
ATOM     24  CA  LEU    24      28.708   1.098  14.335  1.00 25.00           C
ATOM     25  CA  ARG    25      25.962  -1.157  15.761  1.00 25.00           C
ATOM     26  CA  GLU    26      23.279   1.044  14.141  1.00 25.00           C
ATOM     27  CA  PHE    27      25.118   0.858  10.787  1.00 25.00           C
ATOM     28  CA  ALA    28      25.322  -2.954  11.081  1.00 25.00           C
ATOM     29  CA  ARG    29      21.572  -3.121  11.843  1.00 25.00           C
ATOM     30  CA  ALA    30      20.830  -0.926   8.794  1.00 25.00           C
ATOM     31  CA  MET    31      22.997  -3.198   6.601  1.00 25.00           C
ATOM     32  CA  GLU    32      23.138  -6.569   4.792  1.00 25.00           C
ATOM     33  CA  ILE    33      26.105  -7.292   7.051  1.00 25.00           C
ATOM     34  CA  ALA    34      23.587  -9.347   9.099  1.00 25.00           C
ATOM     35  CA  PRO    35      24.213  -7.947  12.595  1.00 25.00           C
ATOM     36  CA  SER    36      26.045 -11.083  13.814  1.00 25.00           C
ATOM     37  CA  THR    37      28.198 -11.086  10.646  1.00 25.00           C
ATOM     38  CA  ALA    38      29.032  -7.387  11.179  1.00 25.00           C
ATOM     39  CA  SER    39      30.004  -8.104  14.813  1.00 25.00           C
ATOM     40  CA  ARG    40      32.246 -10.991  13.669  1.00 25.00           C
ATOM     41  CA  LEU    41      33.909  -8.707  11.083  1.00 25.00           C
ATOM     42  CA  LEU    42      34.504  -6.050  13.776  1.00 25.00           C
ATOM     43  CA  THR    43      36.048  -8.693  16.078  1.00 25.00           C
ATOM     44  CA  GLY    44      37.851 -11.916  16.977  1.00 25.00           C
ATOM     45  CA  LYS    45      34.817 -14.127  16.827  1.00 25.00           C
ATOM     46  CA  ALA    46      35.762 -14.492  13.199  1.00 25.00           C
ATOM     47  CA  ALA    47      37.571 -12.244  10.718  1.00 25.00           C
ATOM     48  CA  LEU    48      39.256  -9.886   8.252  1.00 25.00           C
ATOM     49  CA  THR    49      40.568  -7.684   5.508  1.00 25.00           C
ATOM     50  CA  PRO    50      39.076  -7.965   1.974  1.00 25.00           C
ATOM     51  CA  GLU    51      35.511  -9.361   2.075  1.00 25.00           C
ATOM     52  CA  MET    52      35.197  -8.360   5.758  1.00 25.00           C
ATOM     53  CA  ALA    53      36.434  -4.832   4.930  1.00 25.00           C
ATOM     54  CA  ILE    54      33.881  -4.577   2.086  1.00 25.00           C
ATOM     55  CA  LYS    55      31.094  -5.714   4.454  1.00 25.00           C
ATOM     56  CA  LEU    56      32.177  -3.093   7.027  1.00 25.00           C
ATOM     57  CA  SER    57      32.151  -0.386   4.318  1.00 25.00           C
ATOM     58  CA  VAL    58      28.640  -1.466   3.238  1.00 25.00           C
ATOM     59  CA  VAL    59      27.448  -1.318   6.875  1.00 25.00           C
ATOM     60  CA  ILE    60      28.936   2.192   7.245  1.00 25.00           C
ATOM     61  CA  GLY    61      25.575   3.182   5.700  1.00 25.00           C
ATOM     62  CA  SER    62      26.327   2.831   1.943  1.00 25.00           C
ATOM     63  CA  SER    63      28.599   2.941  -1.071  1.00 25.00           C
ATOM     64  CA  PRO    64      28.106   6.669  -0.204  1.00 25.00           C
ATOM     65  CA  GLN    65      29.982   9.538   1.505  1.00 25.00           C
ATOM     66  CA  MET    66      30.237   7.483   4.727  1.00 25.00           C
ATOM     67  CA  TRP    67      31.588   4.498   2.745  1.00 25.00           C
ATOM     68  CA  LEU    68      34.178   6.757   1.058  1.00 25.00           C
ATOM     69  CA  ASN    69      35.244   8.127   4.473  1.00 25.00           C
ATOM     70  CA  LEU    70      35.598   4.561   5.820  1.00 25.00           C
ATOM     71  CA  GLN    71      37.724   3.598   2.785  1.00 25.00           C
ATOM     72  CA  ASN    72      39.946   6.668   3.338  1.00 25.00           C
ATOM     73  CA  ALA    73      40.363   5.733   7.028  1.00 25.00           C
ATOM     74  CA  TRP    74      41.312   2.156   6.040  1.00 25.00           C
ATOM     75  CA  SER    75      43.881   3.502   3.539  1.00 25.00           C
ATOM     76  CA  LEU    76      45.355   5.780   6.242  1.00 25.00           C
ATOM     77  CA  ALA    77      45.589   2.811   8.650  1.00 25.00           C
ATOM     78  CA  GLU    78      47.348   0.733   5.957  1.00 25.00           C
ATOM     79  CA  ALA    79      49.818   3.592   5.331  1.00 25.00           C
ATOM     80  CA  GLU    80      50.516   3.846   9.088  1.00 25.00           C
ATOM     81  CA  LYS    81      51.118   0.068   9.256  1.00 25.00           C
ATOM     82  CA  THR    82      54.115   1.070  11.431  1.00 25.00           C
ATOM     83  CA  VAL    83      52.702   3.649  13.755  1.00 25.00           C
ATOM     84  CA  ASP    84      53.949   5.777  16.706  1.00 25.00           C
ATOM     85  CA  VAL    85      53.324   8.865  14.577  1.00 25.00           C
ATOM     86  CA  SER    86      52.835  12.414  15.929  1.00 25.00           C
ATOM     87  CA  ARG    87      49.088  11.755  16.374  1.00 25.00           C
ATOM     88  CA  LEU    88      49.858   8.498  18.237  1.00 25.00           C
ATOM     89  CA  ARG    89      52.316  10.353  20.514  1.00 25.00           C
ATOM     90  CA  ARG    90      49.672  13.030  21.229  1.00 25.00           C
ATOM     91  CA  LEU    91      47.113  10.309  22.073  1.00 25.00           C
ATOM     92  CA  VAL    92      49.625   8.642  24.434  1.00 25.00           C
ATOM     93  CA  THR    93      50.292  12.006  26.139  1.00 25.00           C
ATOM     94  CA  GLN    94      46.527  12.570  26.555  1.00 25.00           C
ATOM     95  CA  SER    95      44.738  15.406  28.352  1.00 25.00           C
ATOM     96  CA  THR    96      41.156  15.167  27.282  1.00 25.00           C
ATOM     97  CA  PRO    97      38.579  12.981  25.404  1.00 25.00           C
TER
END
