
#######################################################
#                                                     #
#                        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_4
# Molecule2: number of CA atoms   87 (  672),  selected   87 , name T0311.pdb
# PARAMETERS: T0311TS393_4.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          4.755
LGA    Q      14      G      10          1.139
LGA    E      15      D      11          1.006
LGA    S      16      I      12          3.880
LGA    L      17      I      13          4.499
LGA    D      18      Q      14          4.859
LGA    E      19      -       -           -
LGA    L      20      -       -           -
LGA    N      21      E      15          1.626
LGA    V      22      -       -           -
LGA    S      23      -       -           -
LGA    L      24      -       -           -
LGA    R      25      S      16           #
LGA    E      26      L      17          1.168
LGA    F      27      D      18           -
LGA    -       -      E      19           -
LGA    -       -      L      20           -
LGA    -       -      N      21           -
LGA    -       -      V      22           -
LGA    -       -      S      23           -
LGA    -       -      L      24           -
LGA    -       -      R      25           -
LGA    -       -      E      26           -
LGA    A      28      F      27          2.888
LGA    R      29      A      28           -
LGA    A      30      R      29           -
LGA    M      31      -       -           -
LGA    E      32      A      30          2.920
LGA    I      33      M      31          1.512
LGA    A      34      E      32          4.561
LGA    P      35      -       -           -
LGA    S      36      -       -           -
LGA    T      37      I      33          2.583
LGA    A      38      A      34           #
LGA    S      39      P      35          3.559
LGA    R      40      S      36          2.222
LGA    L      41      T      37          2.634
LGA    -       -      A      38           -
LGA    L      42      S      39          2.839
LGA    T      43      R      40          3.436
LGA    G      44      L      41           -
LGA    K      45      L      42           -
LGA    A      46      T      43           -
LGA    -       -      G      44           -
LGA    A      47      K      45           #
LGA    L      48      A      46          4.129
LGA    T      49      A      47          4.056
LGA    P      50      -       -           -
LGA    E      51      -       -           -
LGA    M      52      -       -           -
LGA    A      53      L      48          0.875
LGA    I      54      T      49          4.584
LGA    K      55      P      50           -
LGA    L      56      E      51           #
LGA    S      57      M      52          1.082
LGA    V      58      -       -           -
LGA    V      59      -       -           -
LGA    I      60      A      53           #
LGA    G      61      I      54          2.459
LGA    S      62      K      55          5.092
LGA    S      63      L      56           #
LGA    P      64      S      57          2.694
LGA    -       -      V      58           -
LGA    -       -      V      59           -
LGA    -       -      I      60           -
LGA    -       -      G      61           -
LGA    -       -      S      62           -
LGA    -       -      S      63           -
LGA    Q      65      P      64          2.040
LGA    -       -      Q      65           -
LGA    M      66      M      66          2.483
LGA    W      67      W      67          1.574
LGA    L      68      L      68          1.747
LGA    N      69      N      69          2.145
LGA    L      70      L      70          1.526
LGA    Q      71      Q      71          1.671
LGA    N      72      N      72          1.843
LGA    A      73      A      73          1.622
LGA    W      74      W      74          1.992
LGA    S      75      S      75          1.860
LGA    L      76      L      76          1.539
LGA    A      77      A      77          1.941
LGA    E      78      E      78          2.251
LGA    A      79      A      79          1.555
LGA    E      80      E      80          2.549
LGA    K      81      K      81          4.379
LGA    T      82      T      82          4.111
LGA    V      83      V      83           -
LGA    D      84      D      84           -
LGA    V      85      V      85           -
LGA    S      86      S      86           -
LGA    R      87      R      87           -
LGA    L      88      L      88           -
LGA    R      89      R      89           -
LGA    R      90      R      90           -
LGA    L      91      L      91           -
LGA    V      92      V      92           -
LGA    T      93      T      93           -
LGA    Q      94      Q      94           -
LGA    S      95      -       -           -
LGA    T      96      -       -           -
LGA    P      97      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   97   87    5.0     44    2.90    38.64     32.949     1.467

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.465862 * X  +   0.681755 * Y  +   0.564076 * Z  +  37.628487
  Y_new =   0.140146 * X  +  -0.686279 * Y  +   0.713708 * Z  +  -2.019388
  Z_new =   0.873688 * X  +  -0.253437 * Y  +  -0.415257 * Z  +  13.561261 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.593624    0.547969  [ DEG:  -148.6037     31.3963 ]
  Theta =  -1.062733   -2.078860  [ DEG:   -60.8901   -119.1099 ]
  Phi   =   0.292219   -2.849374  [ DEG:    16.7429   -163.2571 ]
 
# 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_4                                  
REMARK     2: T0311.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0311TS393_4.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   44   2.90   38.64  32.949
REMARK  ---------------------------------------------------------- 
MOLECULE T0311TS393_4
PFRMAT TS
TARGET T0311
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1      31.522 -10.477  32.940  1.00 25.00           C
ATOM      2  CA  LYS     2      31.797 -14.073  34.045  1.00 25.00           C
ATOM      3  CA  MET     3      35.528 -14.226  33.150  1.00 25.00           C
ATOM      4  CA  ALA     4      37.908 -15.465  30.434  1.00 25.00           C
ATOM      5  CA  ASN     5      40.134 -12.497  29.608  1.00 25.00           C
ATOM      6  CA  HIS     6      42.784 -12.635  26.948  1.00 25.00           C
ATOM      7  CA  PRO     7      42.268 -10.744  23.732  1.00 25.00           C
ATOM      8  CA  ARG     8      40.878  -9.156  20.564  1.00 25.00           C
ATOM      9  CA  PRO     9      40.994  -6.417  17.927  1.00 25.00           C
ATOM     10  CA  GLY    10      37.886  -6.381  15.688  1.00 25.00           C
ATOM     11  CA  ASP    11      36.018  -4.262  18.274  1.00 25.00           C
ATOM     12  CA  ILE    12      38.962  -1.817  18.434  1.00 25.00           C
ATOM     13  CA  ILE    13      38.994  -1.569  14.613  1.00 25.00           C
ATOM     14  CA  GLN    14      35.227  -0.885  14.599  1.00 25.00           C
ATOM     15  CA  GLU    15      35.690   1.846  17.245  1.00 25.00           C
ATOM     16  CA  SER    16      38.484   3.428  15.159  1.00 25.00           C
ATOM     17  CA  LEU    17      36.238   3.365  12.057  1.00 25.00           C
ATOM     18  CA  ASP    18      33.411   5.020  14.040  1.00 25.00           C
ATOM     19  CA  GLU    19      35.826   7.725  15.273  1.00 25.00           C
ATOM     20  CA  LEU    20      34.501   6.795  18.662  1.00 25.00           C
ATOM     21  CA  ASN    21      30.852   5.952  19.537  1.00 25.00           C
ATOM     22  CA  VAL    22      31.749   2.418  20.710  1.00 25.00           C
ATOM     23  CA  SER    23      32.211  -1.226  19.565  1.00 25.00           C
ATOM     24  CA  LEU    24      30.385  -1.451  16.269  1.00 25.00           C
ATOM     25  CA  ARG    25      26.815  -0.597  17.365  1.00 25.00           C
ATOM     26  CA  GLU    26      27.343   3.051  16.329  1.00 25.00           C
ATOM     27  CA  PHE    27      28.663   1.917  12.917  1.00 25.00           C
ATOM     28  CA  ALA    28      25.612  -0.351  12.463  1.00 25.00           C
ATOM     29  CA  ARG    29      23.286   2.557  13.357  1.00 25.00           C
ATOM     30  CA  ALA    30      25.080   4.802  10.826  1.00 25.00           C
ATOM     31  CA  MET    31      24.717   2.100   8.136  1.00 25.00           C
ATOM     32  CA  GLU    32      21.181   0.593   7.773  1.00 25.00           C
ATOM     33  CA  ILE    33      22.423  -2.653   6.151  1.00 25.00           C
ATOM     34  CA  ALA    34      22.994  -3.731   9.695  1.00 25.00           C
ATOM     35  CA  PRO    35      23.484  -4.826  13.349  1.00 25.00           C
ATOM     36  CA  SER    36      23.681  -8.591  12.674  1.00 25.00           C
ATOM     37  CA  THR    37      25.920  -7.953   9.633  1.00 25.00           C
ATOM     38  CA  ALA    38      28.194  -5.711  11.748  1.00 25.00           C
ATOM     39  CA  SER    39      28.415  -8.428  14.436  1.00 25.00           C
ATOM     40  CA  ARG    40      29.314 -11.027  11.771  1.00 25.00           C
ATOM     41  CA  LEU    41      32.030  -8.707  10.390  1.00 25.00           C
ATOM     42  CA  LEU    42      33.437  -8.215  13.918  1.00 25.00           C
ATOM     43  CA  THR    43      33.481 -12.007  14.456  1.00 25.00           C
ATOM     44  CA  GLY    44      35.816 -14.261  12.475  1.00 25.00           C
ATOM     45  CA  LYS    45      33.844 -16.138   9.817  1.00 25.00           C
ATOM     46  CA  ALA    46      33.895 -13.178   7.519  1.00 25.00           C
ATOM     47  CA  ALA    47      37.398 -13.354   6.094  1.00 25.00           C
ATOM     48  CA  LEU    48      38.898  -9.836   5.870  1.00 25.00           C
ATOM     49  CA  THR    49      39.668  -7.223   3.190  1.00 25.00           C
ATOM     50  CA  PRO    50      41.252  -5.369   6.183  1.00 25.00           C
ATOM     51  CA  GLU    51      38.994  -6.077   9.194  1.00 25.00           C
ATOM     52  CA  MET    52      37.885  -2.411   9.256  1.00 25.00           C
ATOM     53  CA  ALA    53      37.106  -2.559   5.509  1.00 25.00           C
ATOM     54  CA  ILE    54      35.063  -5.755   6.034  1.00 25.00           C
ATOM     55  CA  LYS    55      33.129  -4.080   8.884  1.00 25.00           C
ATOM     56  CA  LEU    56      32.422  -1.048   6.654  1.00 25.00           C
ATOM     57  CA  SER    57      31.179  -3.358   3.865  1.00 25.00           C
ATOM     58  CA  VAL    58      28.895  -5.171   6.348  1.00 25.00           C
ATOM     59  CA  VAL    59      27.509  -1.813   7.562  1.00 25.00           C
ATOM     60  CA  ILE    60      26.851  -0.749   3.942  1.00 25.00           C
ATOM     61  CA  GLY    61      26.867   0.919   0.514  1.00 25.00           C
ATOM     62  CA  SER    62      30.017  -0.841  -0.697  1.00 25.00           C
ATOM     63  CA  SER    63      31.984   2.181   0.446  1.00 25.00           C
ATOM     64  CA  PRO    64      30.225   4.836   2.553  1.00 25.00           C
ATOM     65  CA  GLN    65      32.975   7.297   1.529  1.00 25.00           C
ATOM     66  CA  MET    66      33.922   7.807   5.204  1.00 25.00           C
ATOM     67  CA  TRP    67      34.081   4.015   5.715  1.00 25.00           C
ATOM     68  CA  LEU    68      36.316   3.668   2.625  1.00 25.00           C
ATOM     69  CA  ASN    69      38.619   6.427   3.950  1.00 25.00           C
ATOM     70  CA  LEU    70      38.821   4.662   7.344  1.00 25.00           C
ATOM     71  CA  GLN    71      39.687   1.362   5.602  1.00 25.00           C
ATOM     72  CA  ASN    72      42.422   3.119   3.577  1.00 25.00           C
ATOM     73  CA  ALA    73      43.844   4.654   6.784  1.00 25.00           C
ATOM     74  CA  TRP    74      43.854   1.210   8.459  1.00 25.00           C
ATOM     75  CA  SER    75      45.666  -0.283   5.433  1.00 25.00           C
ATOM     76  CA  LEU    76      48.265   2.526   5.573  1.00 25.00           C
ATOM     77  CA  ALA    77      48.788   1.889   9.313  1.00 25.00           C
ATOM     78  CA  GLU    78      49.245  -1.853   8.637  1.00 25.00           C
ATOM     79  CA  ALA    79      51.801  -1.071   5.895  1.00 25.00           C
ATOM     80  CA  GLU    80      53.694   1.246   8.286  1.00 25.00           C
ATOM     81  CA  LYS    81      53.718  -1.495  10.961  1.00 25.00           C
ATOM     82  CA  THR    82      55.488  -4.842  10.824  1.00 25.00           C
ATOM     83  CA  VAL    83      52.506  -5.959  12.936  1.00 25.00           C
ATOM     84  CA  ASP    84      53.344  -5.439  16.659  1.00 25.00           C
ATOM     85  CA  VAL    85      55.162  -2.160  17.487  1.00 25.00           C
ATOM     86  CA  SER    86      57.119   0.678  19.155  1.00 25.00           C
ATOM     87  CA  ARG    87      54.106   3.012  18.773  1.00 25.00           C
ATOM     88  CA  LEU    88      51.822   0.357  20.323  1.00 25.00           C
ATOM     89  CA  ARG    89      54.253  -0.061  23.252  1.00 25.00           C
ATOM     90  CA  ARG    90      54.319   3.732  23.771  1.00 25.00           C
ATOM     91  CA  LEU    91      50.491   3.827  23.748  1.00 25.00           C
ATOM     92  CA  VAL    92      50.380   0.995  26.322  1.00 25.00           C
ATOM     93  CA  THR    93      52.873   2.877  28.538  1.00 25.00           C
ATOM     94  CA  GLN    94      50.743   6.051  28.278  1.00 25.00           C
ATOM     95  CA  SER    95      49.040   5.436  31.635  1.00 25.00           C
ATOM     96  CA  THR    96      45.220   5.166  31.949  1.00 25.00           C
ATOM     97  CA  PRO    97      41.965   6.367  30.333  1.00 25.00           C
TER
END
