
#######################################################
#                                                     #
#                        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 T0311TS393_1
# Molecule2: number of CA atoms   87 (  672),  selected   87 , name T0311.pdb
# PARAMETERS: T0311TS393_1.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      R       8          3.261
LGA    P       9      P       9          3.478
LGA    G      10      G      10          2.464
LGA    D      11      D      11          1.843
LGA    I      12      I      12          2.018
LGA    I      13      I      13          2.181
LGA    Q      14      Q      14          1.503
LGA    E      15      E      15          1.193
LGA    S      16      S      16          1.974
LGA    L      17      L      17          3.115
LGA    D      18      D      18          3.173
LGA    E      19      E      19          3.197
LGA    L      20      L      20          2.228
LGA    N      21      N      21          1.743
LGA    V      22      V      22          0.567
LGA    S      23      S      23          1.175
LGA    L      24      L      24          2.544
LGA    R      25      R      25          2.415
LGA    E      26      E      26          2.657
LGA    F      27      F      27          2.199
LGA    A      28      A      28          1.292
LGA    R      29      R      29          1.598
LGA    A      30      A      30          1.710
LGA    M      31      M      31          1.891
LGA    E      32      E      32          1.519
LGA    I      33      I      33          0.708
LGA    A      34      A      34          1.951
LGA    P      35      P      35          1.398
LGA    S      36      S      36          2.877
LGA    T      37      T      37          3.518
LGA    A      38      A      38          2.081
LGA    S      39      S      39          0.481
LGA    R      40      R      40          2.117
LGA    L      41      L      41          2.554
LGA    L      42      L      42          1.894
LGA    T      43      T      43          1.111
LGA    G      44      G      44          3.151
LGA    K      45      K      45          2.757
LGA    A      46      A      46          1.958
LGA    A      47      A      47          2.036
LGA    L      48      L      48          2.244
LGA    -       -      T      49           -
LGA    T      49      P      50          4.503
LGA    P      50      E      51           #
LGA    E      51      M      52          5.159
LGA    M      52      A      53          2.793
LGA    A      53      I      54          5.199
LGA    I      54      K      55          5.706
LGA    K      55      L      56          2.871
LGA    L      56      S      57          2.541
LGA    -       -      V      58           -
LGA    S      57      V      59          1.727
LGA    V      58      I      60          1.829
LGA    V      59      G      61          1.929
LGA    I      60      S      62           #
LGA    G      61      -       -           -
LGA    S      62      -       -           -
LGA    S      63      S      63           #
LGA    P      64      P      64          1.217
LGA    Q      65      Q      65          1.823
LGA    M      66      M      66          5.342
LGA    W      67      W      67          4.939
LGA    L      68      L      68          5.723
LGA    N      69      N      69           #
LGA    L      70      -       -           -
LGA    Q      71      -       -           -
LGA    N      72      L      70           #
LGA    A      73      Q      71           -
LGA    W      74      N      72           -
LGA    S      75      A      73           -
LGA    L      76      W      74           -
LGA    A      77      S      75           -
LGA    E      78      L      76           -
LGA    A      79      A      77           -
LGA    E      80      E      78           -
LGA    K      81      A      79           -
LGA    T      82      E      80           -
LGA    V      83      K      81           -
LGA    D      84      T      82           -
LGA    V      85      V      83           -
LGA    S      86      D      84           -
LGA    R      87      V      85           -
LGA    L      88      S      86           -
LGA    R      89      R      87           -
LGA    R      90      L      88           -
LGA    L      91      R      89           -
LGA    V      92      R      90           -
LGA    T      93      L      91           -
LGA    Q      94      V      92           -
LGA    S      95      T      93           -
LGA    T      96      Q      94           -
LGA    P      97      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   97   87    5.0     56    2.78    82.14     45.726     1.944

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.098602 * X  +   0.904462 * Y  +  -0.415001 * Z  +  33.296989
  Y_new =   0.802071 * X  +   0.174617 * Y  +   0.571132 * Z  +   2.174418
  Z_new =   0.589033 * X  +  -0.389175 * Y  +  -0.708225 * Z  +  14.425101 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.639128    0.502465  [ DEG:  -151.2109     28.7891 ]
  Theta =  -0.629862   -2.511731  [ DEG:   -36.0884   -143.9116 ]
  Phi   =   1.448475   -1.693117  [ DEG:    82.9915    -97.0085 ]
 
# 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: T0311TS393_1                                  
REMARK     2: T0311.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0311TS393_1.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   56   2.78   82.14  45.726
REMARK  ---------------------------------------------------------- 
MOLECULE T0311TS393_1
PFRMAT TS
TARGET T0311
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1      50.797   7.909   4.441  1.00 25.00           C
ATOM      2  CA  LYS     2      53.671   5.641   5.569  1.00 25.00           C
ATOM      3  CA  MET     3      53.684   6.751   9.189  1.00 25.00           C
ATOM      4  CA  ALA     4      52.506   4.829  12.253  1.00 25.00           C
ATOM      5  CA  ASN     5      52.247   3.651  15.823  1.00 25.00           C
ATOM      6  CA  HIS     6      50.784   0.475  17.278  1.00 25.00           C
ATOM      7  CA  PRO     7      47.679   0.636  15.136  1.00 25.00           C
ATOM      8  CA  ARG     8      44.018   1.159  14.112  1.00 25.00           C
ATOM      9  CA  PRO     9      40.293   2.161  13.960  1.00 25.00           C
ATOM     10  CA  GLY    10      37.941  -0.672  15.015  1.00 25.00           C
ATOM     11  CA  ASP    11      36.921   1.303  18.134  1.00 25.00           C
ATOM     12  CA  ILE    12      36.236   4.396  15.980  1.00 25.00           C
ATOM     13  CA  ILE    13      34.102   2.293  13.596  1.00 25.00           C
ATOM     14  CA  GLN    14      32.137   0.878  16.561  1.00 25.00           C
ATOM     15  CA  GLU    15      31.562   4.418  17.902  1.00 25.00           C
ATOM     16  CA  SER    16      30.335   5.550  14.455  1.00 25.00           C
ATOM     17  CA  LEU    17      27.945   2.563  14.297  1.00 25.00           C
ATOM     18  CA  ASP    18      26.610   3.414  17.783  1.00 25.00           C
ATOM     19  CA  GLU    19      26.072   7.053  16.716  1.00 25.00           C
ATOM     20  CA  LEU    20      22.334   6.903  15.840  1.00 25.00           C
ATOM     21  CA  ASN    21      22.082   5.789  19.499  1.00 25.00           C
ATOM     22  CA  VAL    22      21.729   2.173  18.445  1.00 25.00           C
ATOM     23  CA  SER    23      23.946  -0.806  19.299  1.00 25.00           C
ATOM     24  CA  LEU    24      24.985  -2.176  15.879  1.00 25.00           C
ATOM     25  CA  ARG    25      21.579  -3.883  15.482  1.00 25.00           C
ATOM     26  CA  GLU    26      20.312  -0.923  13.407  1.00 25.00           C
ATOM     27  CA  PHE    27      23.429  -1.109  11.190  1.00 25.00           C
ATOM     28  CA  ALA    28      22.885  -4.868  10.700  1.00 25.00           C
ATOM     29  CA  ARG    29      19.228  -4.241   9.753  1.00 25.00           C
ATOM     30  CA  ALA    30      20.312  -1.564   7.239  1.00 25.00           C
ATOM     31  CA  MET    31      22.864  -3.986   5.725  1.00 25.00           C
ATOM     32  CA  GLU    32      21.804  -7.634   5.734  1.00 25.00           C
ATOM     33  CA  ILE    33      25.179  -8.667   7.248  1.00 25.00           C
ATOM     34  CA  ALA    34      23.186  -9.920  10.253  1.00 25.00           C
ATOM     35  CA  PRO    35      25.315  -8.858  13.218  1.00 25.00           C
ATOM     36  CA  SER    36      28.410 -10.242  11.437  1.00 25.00           C
ATOM     37  CA  THR    37      29.126  -6.787   9.945  1.00 25.00           C
ATOM     38  CA  ALA    38      28.789  -5.193  13.411  1.00 25.00           C
ATOM     39  CA  SER    39      31.198  -7.791  14.866  1.00 25.00           C
ATOM     40  CA  ARG    40      33.706  -7.072  12.062  1.00 25.00           C
ATOM     41  CA  LEU    41      33.434  -3.315  12.748  1.00 25.00           C
ATOM     42  CA  LEU    42      34.029  -3.928  16.481  1.00 25.00           C
ATOM     43  CA  THR    43      37.102  -6.063  15.666  1.00 25.00           C
ATOM     44  CA  GLY    44      39.245  -8.174  13.416  1.00 25.00           C
ATOM     45  CA  LYS    45      38.190 -10.171  10.401  1.00 25.00           C
ATOM     46  CA  ALA    46      38.429  -6.899   8.472  1.00 25.00           C
ATOM     47  CA  ALA    47      38.281  -5.860   4.815  1.00 25.00           C
ATOM     48  CA  LEU    48      36.591  -2.852   3.335  1.00 25.00           C
ATOM     49  CA  THR    49      33.182  -4.406   2.467  1.00 25.00           C
ATOM     50  CA  PRO    50      31.622  -5.497   5.791  1.00 25.00           C
ATOM     51  CA  GLU    51      33.037  -2.712   8.008  1.00 25.00           C
ATOM     52  CA  MET    52      32.604  -0.191   5.158  1.00 25.00           C
ATOM     53  CA  ALA    53      28.985  -1.337   4.660  1.00 25.00           C
ATOM     54  CA  ILE    54      28.319  -0.947   8.411  1.00 25.00           C
ATOM     55  CA  LYS    55      29.815   2.577   8.336  1.00 25.00           C
ATOM     56  CA  LEU    56      27.606   3.477   5.339  1.00 25.00           C
ATOM     57  CA  SER    57      24.521   2.154   7.184  1.00 25.00           C
ATOM     58  CA  VAL    58      25.446   4.227  10.269  1.00 25.00           C
ATOM     59  CA  VAL    59      25.854   7.345   8.081  1.00 25.00           C
ATOM     60  CA  ILE    60      22.432   6.702   6.485  1.00 25.00           C
ATOM     61  CA  GLY    61      22.860   5.431   2.879  1.00 25.00           C
ATOM     62  CA  SER    62      26.082   5.404   0.912  1.00 25.00           C
ATOM     63  CA  SER    63      28.875   2.780   0.457  1.00 25.00           C
ATOM     64  CA  PRO    64      32.413   4.259   0.576  1.00 25.00           C
ATOM     65  CA  GLN    65      34.345   7.564   0.493  1.00 25.00           C
ATOM     66  CA  MET    66      31.315   9.400   1.948  1.00 25.00           C
ATOM     67  CA  TRP    67      31.034   6.784   4.731  1.00 25.00           C
ATOM     68  CA  LEU    68      34.761   7.184   5.516  1.00 25.00           C
ATOM     69  CA  ASN    69      34.348  10.988   5.666  1.00 25.00           C
ATOM     70  CA  LEU    70      31.364  10.595   8.035  1.00 25.00           C
ATOM     71  CA  GLN    71      33.414   8.254  10.268  1.00 25.00           C
ATOM     72  CA  ASN    72      36.284  10.787  10.329  1.00 25.00           C
ATOM     73  CA  ALA    73      33.837  13.575  11.281  1.00 25.00           C
ATOM     74  CA  TRP    74      32.416  11.401  14.094  1.00 25.00           C
ATOM     75  CA  SER    75      35.956  10.696  15.371  1.00 25.00           C
ATOM     76  CA  LEU    76      36.748  14.442  15.320  1.00 25.00           C
ATOM     77  CA  ALA    77      33.532  15.173  17.267  1.00 25.00           C
ATOM     78  CA  GLU    78      34.457  12.500  19.848  1.00 25.00           C
ATOM     79  CA  ALA    79      37.951  14.024  20.210  1.00 25.00           C
ATOM     80  CA  GLU    80      36.413  17.495  20.709  1.00 25.00           C
ATOM     81  CA  LYS    81      34.052  16.093  23.378  1.00 25.00           C
ATOM     82  CA  THR    82      37.202  15.584  25.346  1.00 25.00           C
ATOM     83  CA  VAL    83      37.404  11.753  25.638  1.00 25.00           C
ATOM     84  CA  ASP    84      39.792  12.568  28.482  1.00 25.00           C
ATOM     85  CA  VAL    85      37.522  10.264  30.484  1.00 25.00           C
ATOM     86  CA  SER    86      36.402   8.436  33.659  1.00 25.00           C
ATOM     87  CA  ARG    87      34.560   5.832  31.539  1.00 25.00           C
ATOM     88  CA  LEU    88      37.689   5.333  29.388  1.00 25.00           C
ATOM     89  CA  ARG    89      39.815   4.880  32.541  1.00 25.00           C
ATOM     90  CA  ARG    90      37.318   2.306  33.884  1.00 25.00           C
ATOM     91  CA  LEU    91      37.429   0.422  30.552  1.00 25.00           C
ATOM     92  CA  VAL    92      41.257   0.421  30.653  1.00 25.00           C
ATOM     93  CA  THR    93      41.187  -0.927  34.238  1.00 25.00           C
ATOM     94  CA  GLN    94      38.753  -3.687  33.179  1.00 25.00           C
ATOM     95  CA  SER    95      40.984  -6.134  34.930  1.00 25.00           C
ATOM     96  CA  THR    96      42.287  -7.813  31.797  1.00 25.00           C
ATOM     97  CA  PRO    97      39.241  -8.088  29.516  1.00 25.00           C
TER
END
