
#######################################################
#                                                     #
#                        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_5
# Molecule2: number of CA atoms   87 (  672),  selected   87 , name T0311.pdb
# PARAMETERS: T0311TS393_5.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          4.578
LGA    I      13      P       9          3.289
LGA    Q      14      G      10          2.046
LGA    E      15      D      11          2.311
LGA    S      16      I      12          0.805
LGA    L      17      I      13          1.721
LGA    D      18      Q      14          3.307
LGA    E      19      E      15          3.731
LGA    L      20      S      16          3.284
LGA    N      21      -       -           -
LGA    V      22      L      17          0.995
LGA    S      23      D      18          4.041
LGA    L      24      E      19           -
LGA    -       -      L      20           -
LGA    -       -      N      21           -
LGA    -       -      V      22           -
LGA    -       -      S      23           -
LGA    R      25      L      24          1.276
LGA    -       -      R      25           -
LGA    E      26      E      26          4.278
LGA    F      27      F      27          2.813
LGA    A      28      A      28          2.266
LGA    R      29      R      29          3.102
LGA    A      30      A      30          2.063
LGA    M      31      M      31          0.807
LGA    E      32      E      32          0.227
LGA    I      33      I      33          1.360
LGA    A      34      A      34          2.154
LGA    P      35      P      35          2.007
LGA    S      36      S      36          2.324
LGA    T      37      T      37          1.294
LGA    A      38      A      38          0.808
LGA    S      39      S      39          1.748
LGA    R      40      R      40          2.727
LGA    L      41      L      41          2.648
LGA    L      42      L      42          3.174
LGA    T      43      T      43          4.296
LGA    -       -      G      44           -
LGA    G      44      K      45          4.775
LGA    K      45      -       -           -
LGA    A      46      -       -           -
LGA    A      47      -       -           -
LGA    L      48      -       -           -
LGA    T      49      A      46          1.810
LGA    P      50      A      47          1.881
LGA    E      51      L      48          3.013
LGA    M      52      T      49           #
LGA    -       -      P      50           -
LGA    A      53      E      51           #
LGA    I      54      M      52          3.613
LGA    K      55      A      53          4.922
LGA    L      56      I      54           -
LGA    S      57      K      55           #
LGA    V      58      L      56          0.630
LGA    V      59      S      57           #
LGA    -       -      V      58           -
LGA    -       -      V      59           -
LGA    I      60      I      60          1.981
LGA    G      61      G      61          2.758
LGA    S      62      S      62           #
LGA    S      63      -       -           -
LGA    P      64      -       -           -
LGA    Q      65      -       -           -
LGA    M      66      S      63          4.861
LGA    W      67      P      64          2.022
LGA    L      68      -       -           -
LGA    N      69      -       -           -
LGA    L      70      Q      65          1.197
LGA    -       -      M      66           -
LGA    Q      71      W      67          0.787
LGA    N      72      L      68          1.254
LGA    A      73      N      69          2.110
LGA    W      74      L      70          2.456
LGA    S      75      Q      71          1.551
LGA    L      76      N      72          0.472
LGA    A      77      A      73          1.953
LGA    E      78      W      74          3.006
LGA    A      79      S      75          2.688
LGA    E      80      L      76          1.968
LGA    K      81      A      77          3.257
LGA    T      82      E      78           -
LGA    V      83      A      79           -
LGA    D      84      E      80           -
LGA    V      85      K      81           -
LGA    S      86      T      82           -
LGA    R      87      V      83           -
LGA    L      88      D      84           -
LGA    R      89      V      85           -
LGA    R      90      S      86           -
LGA    L      91      R      87           -
LGA    V      92      L      88           -
LGA    T      93      R      89           -
LGA    Q      94      R      90           -
LGA    S      95      L      91           -
LGA    T      96      V      92           -
LGA    P      97      T      93           -
LGA    -       -      Q      94           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   97   87    5.0     53    2.67    41.51     39.298     1.916

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.346189 * X  +   0.922784 * Y  +   0.169184 * Z  +  36.096195
  Y_new =   0.889193 * X  +  -0.265237 * Y  +  -0.372807 * Z  +   1.016523
  Z_new =  -0.299146 * X  +   0.279499 * Y  +  -0.912355 * Z  +  12.520878 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.844321   -0.297271  [ DEG:   162.9676    -17.0324 ]
  Theta =   0.303798    2.837795  [ DEG:    17.4063    162.5937 ]
  Phi   =   1.199522   -1.942070  [ DEG:    68.7276   -111.2724 ]
 
# 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_5                                  
REMARK     2: T0311.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0311TS393_5.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   53   2.67   41.51  39.298
REMARK  ---------------------------------------------------------- 
MOLECULE T0311TS393_5
PFRMAT TS
TARGET T0311
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1      54.021  -9.053  19.010  1.00 25.00           C
ATOM      2  CA  LYS     2      55.614  -9.447  22.488  1.00 25.00           C
ATOM      3  CA  MET     3      52.387  -8.612  24.324  1.00 25.00           C
ATOM      4  CA  ALA     4      49.489  -6.149  24.208  1.00 25.00           C
ATOM      5  CA  ASN     5      48.870  -4.734  27.632  1.00 25.00           C
ATOM      6  CA  HIS     6      45.431  -3.083  28.125  1.00 25.00           C
ATOM      7  CA  PRO     7      43.539  -3.474  24.819  1.00 25.00           C
ATOM      8  CA  ARG     8      42.523  -3.071  21.130  1.00 25.00           C
ATOM      9  CA  PRO     9      42.461  -2.945  17.357  1.00 25.00           C
ATOM     10  CA  GLY    10      39.201  -4.430  16.003  1.00 25.00           C
ATOM     11  CA  ASP    11      37.233  -2.747  18.824  1.00 25.00           C
ATOM     12  CA  ILE    12      38.923   0.599  18.039  1.00 25.00           C
ATOM     13  CA  ILE    13      38.052   0.198  14.331  1.00 25.00           C
ATOM     14  CA  GLN    14      34.411  -0.562  15.245  1.00 25.00           C
ATOM     15  CA  GLU    15      34.295   2.547  17.477  1.00 25.00           C
ATOM     16  CA  SER    16      35.723   4.674  14.630  1.00 25.00           C
ATOM     17  CA  LEU    17      33.091   3.270  12.229  1.00 25.00           C
ATOM     18  CA  ASP    18      30.324   4.077  14.751  1.00 25.00           C
ATOM     19  CA  GLU    19      31.665   7.646  15.117  1.00 25.00           C
ATOM     20  CA  LEU    20      28.497   8.826  13.254  1.00 25.00           C
ATOM     21  CA  ASN    21      26.751   7.476  16.391  1.00 25.00           C
ATOM     22  CA  VAL    22      25.932   3.954  17.376  1.00 25.00           C
ATOM     23  CA  SER    23      28.610   1.578  18.783  1.00 25.00           C
ATOM     24  CA  LEU    24      29.071  -1.258  16.292  1.00 25.00           C
ATOM     25  CA  ARG    25      26.091  -3.503  17.154  1.00 25.00           C
ATOM     26  CA  GLU    26      23.668  -0.701  16.181  1.00 25.00           C
ATOM     27  CA  PHE    27      25.510  -0.228  12.857  1.00 25.00           C
ATOM     28  CA  ALA    28      25.313  -3.993  12.185  1.00 25.00           C
ATOM     29  CA  ARG    29      21.560  -3.957  12.943  1.00 25.00           C
ATOM     30  CA  ALA    30      21.080  -1.004  10.553  1.00 25.00           C
ATOM     31  CA  MET    31      23.020  -2.863   7.824  1.00 25.00           C
ATOM     32  CA  GLU    32      21.676  -6.002   6.146  1.00 25.00           C
ATOM     33  CA  ILE    33      25.156  -7.306   6.626  1.00 25.00           C
ATOM     34  CA  ALA    34      23.420  -9.877   8.795  1.00 25.00           C
ATOM     35  CA  PRO    35      24.492  -8.972  12.358  1.00 25.00           C
ATOM     36  CA  SER    36      26.666 -12.119  12.541  1.00 25.00           C
ATOM     37  CA  THR    37      28.946 -10.734   9.794  1.00 25.00           C
ATOM     38  CA  ALA    38      29.255  -7.419  11.686  1.00 25.00           C
ATOM     39  CA  SER    39      30.142  -9.308  14.898  1.00 25.00           C
ATOM     40  CA  ARG    40      32.799 -11.318  13.011  1.00 25.00           C
ATOM     41  CA  LEU    41      34.263  -8.083  11.576  1.00 25.00           C
ATOM     42  CA  LEU    42      34.372  -6.548  15.083  1.00 25.00           C
ATOM     43  CA  THR    43      36.144  -9.668  16.421  1.00 25.00           C
ATOM     44  CA  GLY    44      37.372 -12.912  14.816  1.00 25.00           C
ATOM     45  CA  LYS    45      39.865 -12.602  11.885  1.00 25.00           C
ATOM     46  CA  ALA    46      36.721 -13.357   9.867  1.00 25.00           C
ATOM     47  CA  ALA    47      38.416 -12.524   6.562  1.00 25.00           C
ATOM     48  CA  LEU    48      36.068  -9.611   5.999  1.00 25.00           C
ATOM     49  CA  THR    49      38.046  -7.117   8.107  1.00 25.00           C
ATOM     50  CA  PRO    50      38.380  -4.236   5.670  1.00 25.00           C
ATOM     51  CA  GLU    51      35.123  -5.143   3.872  1.00 25.00           C
ATOM     52  CA  MET    52      33.355  -5.578   7.241  1.00 25.00           C
ATOM     53  CA  ALA    53      34.660  -2.166   8.394  1.00 25.00           C
ATOM     54  CA  ILE    54      33.408  -0.564   5.149  1.00 25.00           C
ATOM     55  CA  LYS    55      29.972  -2.179   5.648  1.00 25.00           C
ATOM     56  CA  LEU    56      29.850  -0.868   9.244  1.00 25.00           C
ATOM     57  CA  SER    57      30.763   2.644   8.021  1.00 25.00           C
ATOM     58  CA  VAL    58      28.000   2.467   5.374  1.00 25.00           C
ATOM     59  CA  VAL    59      25.481   1.368   8.041  1.00 25.00           C
ATOM     60  CA  ILE    60      26.551   4.280  10.287  1.00 25.00           C
ATOM     61  CA  GLY    61      25.449   7.769   9.184  1.00 25.00           C
ATOM     62  CA  SER    62      24.747   6.770   5.530  1.00 25.00           C
ATOM     63  CA  SER    63      23.485   4.054   3.129  1.00 25.00           C
ATOM     64  CA  PRO    64      26.406   4.381   0.697  1.00 25.00           C
ATOM     65  CA  GLN    65      28.952   2.706  -1.623  1.00 25.00           C
ATOM     66  CA  MET    66      30.916   5.984  -1.874  1.00 25.00           C
ATOM     67  CA  TRP    67      30.907   6.310   1.942  1.00 25.00           C
ATOM     68  CA  LEU    68      32.166   2.708   2.276  1.00 25.00           C
ATOM     69  CA  ASN    69      34.957   3.423  -0.246  1.00 25.00           C
ATOM     70  CA  LEU    70      35.949   6.566   1.704  1.00 25.00           C
ATOM     71  CA  GLN    71      36.033   4.549   4.959  1.00 25.00           C
ATOM     72  CA  ASN    72      38.232   1.895   3.287  1.00 25.00           C
ATOM     73  CA  ALA    73      40.604   4.623   2.023  1.00 25.00           C
ATOM     74  CA  TRP    74      40.801   6.119   5.543  1.00 25.00           C
ATOM     75  CA  SER    75      41.580   2.661   6.994  1.00 25.00           C
ATOM     76  CA  LEU    76      44.332   2.156   4.379  1.00 25.00           C
ATOM     77  CA  ALA    77      45.817   5.578   5.245  1.00 25.00           C
ATOM     78  CA  GLU    78      45.770   4.684   8.969  1.00 25.00           C
ATOM     79  CA  ALA    79      47.520   1.362   8.219  1.00 25.00           C
ATOM     80  CA  GLU    80      50.180   3.199   6.165  1.00 25.00           C
ATOM     81  CA  LYS    81      50.725   5.673   9.037  1.00 25.00           C
ATOM     82  CA  THR    82      52.952   8.738   9.681  1.00 25.00           C
ATOM     83  CA  VAL    83      49.737  10.205  11.092  1.00 25.00           C
ATOM     84  CA  ASP    84      51.182  13.255  12.862  1.00 25.00           C
ATOM     85  CA  VAL    85      47.669  14.630  13.020  1.00 25.00           C
ATOM     86  CA  SER    86      45.660  17.561  14.450  1.00 25.00           C
ATOM     87  CA  ARG    87      42.773  15.195  15.308  1.00 25.00           C
ATOM     88  CA  LEU    88      45.213  12.807  17.043  1.00 25.00           C
ATOM     89  CA  ARG    89      46.680  15.723  19.046  1.00 25.00           C
ATOM     90  CA  ARG    90      43.159  16.819  20.078  1.00 25.00           C
ATOM     91  CA  LEU    91      42.342  13.243  21.179  1.00 25.00           C
ATOM     92  CA  VAL    92      45.576  13.110  23.228  1.00 25.00           C
ATOM     93  CA  THR    93      44.698  16.453  24.877  1.00 25.00           C
ATOM     94  CA  GLN    94      41.198  15.145  25.719  1.00 25.00           C
ATOM     95  CA  SER    95      40.333  16.323  29.187  1.00 25.00           C
ATOM     96  CA  THR    96      38.019  13.806  30.823  1.00 25.00           C
ATOM     97  CA  PRO    97      37.086  11.015  28.427  1.00 25.00           C
TER
END
