
#######################################################
#                                                     #
#                        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   92 (   92),  selected   92 , name T0329TS168_1-D2
# Molecule2: number of CA atoms   92 (  716),  selected   92 , name T0329_D2.pdb
# PARAMETERS: T0329TS168_1-D2.T0329_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    T      17      -       -           -
LGA    S      18      T      17          1.856
LGA    A      19      S      18          1.254
LGA    D      20      A      19          0.975
LGA    L      21      D      20          0.924
LGA    T      22      L      21          0.965
LGA    S      23      T      22          1.078
LGA    A      24      S      23          1.156
LGA    L      25      A      24          0.872
LGA    N      26      L      25          1.618
LGA    Y      27      N      26          2.175
LGA    A      28      Y      27          1.597
LGA    F      29      A      28          1.675
LGA    E      30      F      29          2.839
LGA    Q      31      E      30          2.834
LGA    T      32      Q      31          3.663
LGA    G      33      -       -           -
LGA    H      34      T      32          2.648
LGA    R      35      G      33           -
LGA    H      36      H      34           -
LGA    D      37      R      35           -
LGA    F      38      H      36           -
LGA    T      39      D      37           -
LGA    V      40      F      38           -
LGA    E      41      T      39           -
LGA    D      42      V      40           -
LGA    I      43      E      41           -
LGA    K      44      D      42           -
LGA    N      45      I      43           -
LGA    F      46      K      44           -
LGA    F      47      N      45           -
LGA    G      48      F      46           -
LGA    S      49      F      47           -
LGA    G      50      -       -           -
LGA    V      51      -       -           -
LGA    V      52      -       -           -
LGA    V      53      G      48           #
LGA    A      54      S      49          3.105
LGA    -       -      G      50           -
LGA    V      55      V      51          4.161
LGA    T      56      V      52           #
LGA    R      57      V      53          4.952
LGA    A      58      A      54          4.447
LGA    L      59      V      55           -
LGA    A      60      T      56           -
LGA    Y      61      -       -           -
LGA    E      62      -       -           -
LGA    A      63      -       -           -
LGA    G      64      -       -           -
LGA    S      65      -       -           -
LGA    S      66      -       -           -
LGA    R      67      -       -           -
LGA    E      68      R      57           #
LGA    S      69      A      58          5.597
LGA    L      70      L      59          4.005
LGA    V      71      A      60          3.255
LGA    A      72      Y      61          1.538
LGA    F      73      E      62          2.192
LGA    G      74      A      63          3.268
LGA    T      75      G      64           -
LGA    K      76      S      65           -
LGA    -       -      S      66           -
LGA    -       -      R      67           -
LGA    -       -      E      68           -
LGA    -       -      S      69           -
LGA    -       -      L      70           -
LGA    -       -      V      71           -
LGA    -       -      A      72           -
LGA    -       -      F      73           -
LGA    -       -      G      74           -
LGA    -       -      T      75           -
LGA    -       -      K      76           -
LGA    -       -      D      77           -
LGA    -       -      E      78           -
LGA    -       -      Q      79           -
LGA    -       -      I      80           -
LGA    -       -      P      81           -
LGA    D      77      E      82           #
LGA    E      78      A      83          2.955
LGA    Q      79      V      84          5.160
LGA    I      80      T      85          1.680
LGA    P      81      -       -           -
LGA    E      82      -       -           -
LGA    A      83      Q      86          1.726
LGA    V      84      T      87          3.653
LGA    T      85      -       -           -
LGA    Q      86      -       -           -
LGA    T      87      -       -           -
LGA    E      88      E      88          4.216
LGA    V      89      V      89          4.217
LGA    N      90      N      90          1.780
LGA    R      91      R      91          2.314
LGA    V      92      V      92          3.094
LGA    L      93      -       -           -
LGA    E      94      -       -           -
LGA    V      95      L      93          3.867
LGA    F      96      E      94           -
LGA    K      97      V      95           -
LGA    P      98      F      96           #
LGA    Y      99      K      97           -
LGA    Y     100      P      98           -
LGA    A     101      Y      99           -
LGA    D     102      Y     100           -
LGA    H     103      A     101           -
LGA    C     104      D     102           -
LGA    Q     105      H     103           -
LGA    I     106      C     104           -
LGA    K     107      Q     105           -
LGA    -       -      I     106           -
LGA    -       -      K     107           -
LGA    T     108      T     108           #

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   92   92    5.0     37    2.99    21.62     26.604     1.198

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.037871 * X  +  -0.992126 * Y  +   0.119381 * Z  + -11.889229
  Y_new =   0.474580 * X  +  -0.087277 * Y  +  -0.875875 * Z  +   7.484106
  Z_new =   0.879397 * X  +   0.089826 * Y  +   0.467538 * Z  +  48.516846 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.189813   -2.951780  [ DEG:    10.8755   -169.1245 ]
  Theta =  -1.074594   -2.066998  [ DEG:   -61.5697   -118.4303 ]
  Phi   =   1.491166   -1.650427  [ DEG:    85.4375    -94.5625 ]
 
# 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: T0329TS168_1-D2                               
REMARK     2: T0329_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0329TS168_1-D2.T0329_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   92   92   5.0   37   2.99   21.62  26.604
REMARK  ---------------------------------------------------------- 
MOLECULE T0329TS168_1-D2
PFRMAT TS
TARGET T0329
MODEL 1
PARENT N/A
ATOM     17  CA  THR    17      -3.211  12.127  50.532  1.00 25.00           C
ATOM     18  CA  SER    18      -4.375  12.342  46.975  1.00 25.00           C
ATOM     19  CA  ALA    19      -7.632  10.928  45.542  1.00 25.00           C
ATOM     20  CA  ASP    20      -9.483  11.862  48.763  1.00 25.00           C
ATOM     21  CA  LEU    21      -8.054  15.410  48.584  1.00 25.00           C
ATOM     22  CA  THR    22      -9.171  15.703  44.932  1.00 25.00           C
ATOM     23  CA  SER    23     -12.684  14.511  45.886  1.00 25.00           C
ATOM     24  CA  ALA    24     -12.817  17.092  48.713  1.00 25.00           C
ATOM     25  CA  LEU    25     -11.730  19.846  46.284  1.00 25.00           C
ATOM     26  CA  ASN    26     -14.445  18.768  43.808  1.00 25.00           C
ATOM     27  CA  TYR    27     -17.062  18.847  46.603  1.00 25.00           C
ATOM     28  CA  ALA    28     -15.909  22.356  47.616  1.00 25.00           C
ATOM     29  CA  PHE    29     -16.164  23.517  43.974  1.00 25.00           C
ATOM     30  CA  GLU    30     -19.700  22.063  43.734  1.00 25.00           C
ATOM     31  CA  GLN    31     -20.688  23.866  46.964  1.00 25.00           C
ATOM     32  CA  THR    32     -19.459  27.467  47.536  1.00 25.00           C
ATOM     33  CA  GLY    33     -22.466  28.438  45.421  1.00 25.00           C
ATOM     34  CA  HIS    34     -20.262  28.906  42.356  1.00 25.00           C
ATOM     35  CA  ARG    35     -20.086  32.526  43.304  1.00 25.00           C
ATOM     36  CA  HIS    36     -16.644  31.926  44.765  1.00 25.00           C
ATOM     37  CA  ASP    37     -12.837  31.510  44.788  1.00 25.00           C
ATOM     38  CA  PHE    38     -12.378  27.743  44.332  1.00 25.00           C
ATOM     39  CA  THR    39     -12.778  27.384  48.156  1.00 25.00           C
ATOM     40  CA  VAL    40      -9.098  26.483  48.570  1.00 25.00           C
ATOM     41  CA  GLU    41      -5.492  27.360  47.623  1.00 25.00           C
ATOM     42  CA  ASP    42      -4.681  23.645  47.171  1.00 25.00           C
ATOM     43  CA  ILE    43      -7.771  23.215  44.950  1.00 25.00           C
ATOM     44  CA  LYS    44      -6.712  26.237  42.849  1.00 25.00           C
ATOM     45  CA  ASN    45      -3.193  24.775  42.475  1.00 25.00           C
ATOM     46  CA  PHE    46      -4.677  21.418  41.382  1.00 25.00           C
ATOM     47  CA  PHE    47      -6.886  23.204  38.811  1.00 25.00           C
ATOM     48  CA  GLY    48      -5.486  26.518  37.571  1.00 25.00           C
ATOM     49  CA  SER    49      -2.862  26.127  34.875  1.00 25.00           C
ATOM     50  CA  GLY    50      -4.646  22.809  34.252  1.00 25.00           C
ATOM     51  CA  VAL    51      -2.565  19.665  34.639  1.00 25.00           C
ATOM     52  CA  VAL    52      -2.042  19.893  30.852  1.00 25.00           C
ATOM     53  CA  VAL    53      -1.957  16.071  30.610  1.00 25.00           C
ATOM     54  CA  ALA    54      -5.199  15.846  32.636  1.00 25.00           C
ATOM     55  CA  VAL    55      -6.849  18.420  30.330  1.00 25.00           C
ATOM     56  CA  THR    56      -5.724  16.427  27.258  1.00 25.00           C
ATOM     57  CA  ARG    57      -7.155  13.219  28.786  1.00 25.00           C
ATOM     58  CA  ALA    58     -10.473  15.002  29.482  1.00 25.00           C
ATOM     59  CA  LEU    59     -10.580  16.265  25.867  1.00 25.00           C
ATOM     60  CA  ALA    60      -9.914  12.718  24.582  1.00 25.00           C
ATOM     61  CA  TYR    61      -8.811  13.883  21.115  1.00 25.00           C
ATOM     62  CA  GLU    62     -11.826  11.994  19.641  1.00 25.00           C
ATOM     63  CA  ALA    63     -14.585  14.155  21.209  1.00 25.00           C
ATOM     64  CA  GLY    64     -17.115  11.346  21.820  1.00 25.00           C
ATOM     65  CA  SER    65     -15.369  10.455  25.111  1.00 25.00           C
ATOM     66  CA  SER    66     -15.466  14.130  26.185  1.00 25.00           C
ATOM     67  CA  ARG    67     -19.200  14.301  25.350  1.00 25.00           C
ATOM     68  CA  GLU    68     -19.828  11.123  27.394  1.00 25.00           C
ATOM     69  CA  SER    69     -17.898  12.613  30.348  1.00 25.00           C
ATOM     70  CA  LEU    70     -19.962  15.830  30.107  1.00 25.00           C
ATOM     71  CA  VAL    71     -23.197  13.781  30.065  1.00 25.00           C
ATOM     72  CA  ALA    72     -22.031  11.832  33.149  1.00 25.00           C
ATOM     73  CA  PHE    73     -21.223  15.115  34.947  1.00 25.00           C
ATOM     74  CA  GLY    74     -24.747  16.545  35.238  1.00 25.00           C
ATOM     75  CA  THR    75     -23.181  19.840  34.031  1.00 25.00           C
ATOM     76  CA  LYS    76     -25.938  21.068  31.715  1.00 25.00           C
ATOM     77  CA  ASP    77     -24.110  22.533  28.708  1.00 25.00           C
ATOM     78  CA  GLU    78     -23.370  22.604  24.951  1.00 25.00           C
ATOM     79  CA  GLN    79     -20.984  25.557  25.452  1.00 25.00           C
ATOM     80  CA  ILE    80     -19.206  23.674  28.274  1.00 25.00           C
ATOM     81  CA  PRO    81     -18.864  20.588  26.031  1.00 25.00           C
ATOM     82  CA  GLU    82     -17.413  22.757  23.228  1.00 25.00           C
ATOM     83  CA  ALA    83     -14.914  24.303  25.683  1.00 25.00           C
ATOM     84  CA  VAL    84     -13.798  27.909  25.691  1.00 25.00           C
ATOM     85  CA  THR    85     -16.843  29.837  24.606  1.00 25.00           C
ATOM     86  CA  GLN    86     -16.442  31.829  27.805  1.00 25.00           C
ATOM     87  CA  THR    87     -14.377  32.361  30.985  1.00 25.00           C
ATOM     88  CA  GLU    88     -16.937  30.361  33.012  1.00 25.00           C
ATOM     89  CA  VAL    89     -16.801  27.530  30.437  1.00 25.00           C
ATOM     90  CA  ASN    90     -12.976  27.520  30.613  1.00 25.00           C
ATOM     91  CA  ARG    91     -13.127  27.360  34.437  1.00 25.00           C
ATOM     92  CA  VAL    92     -15.588  24.432  34.242  1.00 25.00           C
ATOM     93  CA  LEU    93     -13.269  22.615  31.796  1.00 25.00           C
ATOM     94  CA  GLU    94     -10.301  23.182  34.149  1.00 25.00           C
ATOM     95  CA  VAL    95     -12.339  21.809  37.087  1.00 25.00           C
ATOM     96  CA  PHE    96     -13.286  18.726  35.022  1.00 25.00           C
ATOM     97  CA  LYS    97      -9.607  18.175  34.111  1.00 25.00           C
ATOM     98  CA  PRO    98      -8.625  18.456  37.802  1.00 25.00           C
ATOM     99  CA  TYR    99     -11.332  15.916  38.741  1.00 25.00           C
ATOM    100  CA  TYR   100     -10.062  13.524  36.033  1.00 25.00           C
ATOM    101  CA  ALA   101      -6.483  13.902  37.344  1.00 25.00           C
ATOM    102  CA  ASP   102      -7.684  13.169  40.906  1.00 25.00           C
ATOM    103  CA  HIS   103      -9.533  10.053  39.667  1.00 25.00           C
ATOM    104  CA  CYS   104      -6.378   8.874  37.844  1.00 25.00           C
ATOM    105  CA  GLN   105      -4.312   9.407  41.025  1.00 25.00           C
ATOM    106  CA  ILE   106      -1.725   7.381  39.174  1.00 25.00           C
ATOM    107  CA  LYS   107       1.779   6.267  40.294  1.00 25.00           C
ATOM    108  CA  THR   108       1.480   7.563  43.895  1.00 25.00           C
TER
END
