
#######################################################
#                                                     #
#                        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 T0329TS393_2-D2
# Molecule2: number of CA atoms   92 (  716),  selected   92 , name T0329_D2.pdb
# PARAMETERS: T0329TS393_2-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      -       -           -
LGA    A      19      T      17          2.803
LGA    D      20      S      18          1.762
LGA    L      21      A      19          1.067
LGA    T      22      D      20          1.571
LGA    S      23      L      21          1.756
LGA    A      24      T      22          1.170
LGA    L      25      S      23          1.258
LGA    N      26      A      24          1.562
LGA    Y      27      L      25          1.730
LGA    A      28      N      26          1.880
LGA    F      29      Y      27          1.841
LGA    E      30      A      28          1.859
LGA    Q      31      F      29          2.362
LGA    T      32      E      30          2.373
LGA    G      33      Q      31          2.722
LGA    H      34      T      32          3.440
LGA    R      35      G      33          2.950
LGA    H      36      H      34          4.177
LGA    D      37      R      35          0.944
LGA    F      38      H      36          4.499
LGA    T      39      -       -           -
LGA    V      40      D      37          3.741
LGA    E      41      F      38          3.002
LGA    D      42      T      39           -
LGA    -       -      V      40           -
LGA    -       -      E      41           -
LGA    I      43      D      42          4.693
LGA    K      44      I      43           #
LGA    N      45      -       -           -
LGA    F      46      K      44           #
LGA    F      47      N      45          3.501
LGA    G      48      -       -           -
LGA    S      49      -       -           -
LGA    G      50      -       -           -
LGA    V      51      F      46          2.884
LGA    V      52      F      47           #
LGA    V      53      -       -           -
LGA    A      54      -       -           -
LGA    V      55      G      48          2.843
LGA    T      56      S      49          2.550
LGA    R      57      G      50          4.572
LGA    A      58      V      51          4.380
LGA    L      59      V      52           -
LGA    A      60      V      53           -
LGA    Y      61      A      54           -
LGA    E      62      V      55           -
LGA    A      63      T      56           -
LGA    G      64      R      57           -
LGA    S      65      A      58           -
LGA    -       -      L      59           -
LGA    -       -      A      60           -
LGA    -       -      Y      61           -
LGA    -       -      E      62           -
LGA    -       -      A      63           -
LGA    -       -      G      64           -
LGA    -       -      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    S      66      G      74           #
LGA    R      67      T      75           -
LGA    E      68      K      76           -
LGA    S      69      D      77           -
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    E      82      -       -           -
LGA    A      83      E      78           #
LGA    V      84      Q      79          4.112
LGA    T      85      I      80          2.006
LGA    Q      86      P      81          1.027
LGA    T      87      E      82          3.846
LGA    E      88      A      83          4.718
LGA    V      89      -       -           -
LGA    N      90      -       -           -
LGA    R      91      V      84          4.657
LGA    V      92      T      85           -
LGA    L      93      Q      86           -
LGA    -       -      T      87           -
LGA    -       -      E      88           -
LGA    E      94      V      89          3.014
LGA    V      95      N      90           -
LGA    F      96      R      91           -
LGA    K      97      V      92           -
LGA    P      98      L      93          3.364
LGA    Y      99      E      94           -
LGA    Y     100      V      95           -
LGA    -       -      F      96           -
LGA    A     101      K      97          2.859
LGA    D     102      P      98          4.684
LGA    -       -      Y      99           -
LGA    H     103      Y     100          4.241
LGA    C     104      -       -           -
LGA    Q     105      A     101          2.116
LGA    I     106      D     102          1.840
LGA    K     107      H     103           #
LGA    T     108      C     104           #
LGA    -       -      Q     105           -
LGA    -       -      I     106           -
LGA    -       -      K     107           -
LGA    -       -      T     108           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   92   92    5.0     42    3.05     2.38     28.837     1.332

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.823539 * X  +  -0.563865 * Y  +  -0.061958 * Z  +  -3.187629
  Y_new =   0.566196 * X  +  -0.810396 * Y  +  -0.150600 * Z  +   8.210746
  Z_new =   0.034708 * X  +  -0.159106 * Y  +   0.986651 * Z  +  43.768810 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.159882    2.981711  [ DEG:    -9.1606    170.8394 ]
  Theta =  -0.034715   -3.106878  [ DEG:    -1.9890   -178.0110 ]
  Phi   =   2.539294   -0.602298  [ DEG:   145.4909    -34.5091 ]
 
# 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: T0329TS393_2-D2                               
REMARK     2: T0329_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0329TS393_2-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   42   3.05    2.38  28.837
REMARK  ---------------------------------------------------------- 
MOLECULE T0329TS393_2-D2
PFRMAT TS
TARGET T0329
MODEL 2
PARENT N/A
ATOM     17  CA  THR    17      -4.677  13.266  53.137  1.00 25.00           C
ATOM     18  CA  SER    18      -5.696  10.466  50.732  1.00 25.00           C
ATOM     19  CA  ALA    19      -4.712  12.790  47.851  1.00 25.00           C
ATOM     20  CA  ASP    20      -7.701  11.554  45.801  1.00 25.00           C
ATOM     21  CA  LEU    21     -10.031  12.175  48.776  1.00 25.00           C
ATOM     22  CA  THR    22      -8.617  15.712  49.176  1.00 25.00           C
ATOM     23  CA  SER    23      -9.161  16.378  45.444  1.00 25.00           C
ATOM     24  CA  ALA    24     -12.770  15.126  45.723  1.00 25.00           C
ATOM     25  CA  LEU    25     -13.356  17.411  48.741  1.00 25.00           C
ATOM     26  CA  ASN    26     -11.928  20.386  46.796  1.00 25.00           C
ATOM     27  CA  TYR    27     -14.223  19.584  43.836  1.00 25.00           C
ATOM     28  CA  ALA    28     -17.237  19.404  46.190  1.00 25.00           C
ATOM     29  CA  PHE    29     -16.280  22.785  47.715  1.00 25.00           C
ATOM     30  CA  GLU    30     -15.981  24.307  44.214  1.00 25.00           C
ATOM     31  CA  GLN    31     -19.427  22.914  43.288  1.00 25.00           C
ATOM     32  CA  THR    32     -22.130  25.290  44.504  1.00 25.00           C
ATOM     33  CA  GLY    33     -20.692  27.824  42.001  1.00 25.00           C
ATOM     34  CA  HIS    34     -23.211  26.569  39.421  1.00 25.00           C
ATOM     35  CA  ARG    35     -25.841  24.237  40.868  1.00 25.00           C
ATOM     36  CA  HIS    36     -27.104  21.102  39.228  1.00 25.00           C
ATOM     37  CA  ASP    37     -24.663  18.624  40.673  1.00 25.00           C
ATOM     38  CA  PHE    38     -21.230  19.749  39.476  1.00 25.00           C
ATOM     39  CA  THR    39     -18.277  17.681  40.696  1.00 25.00           C
ATOM     40  CA  VAL    40     -18.567  14.650  42.895  1.00 25.00           C
ATOM     41  CA  GLU    41     -21.731  12.894  41.641  1.00 25.00           C
ATOM     42  CA  ASP    42     -21.228  14.419  38.164  1.00 25.00           C
ATOM     43  CA  ILE    43     -17.586  13.234  38.144  1.00 25.00           C
ATOM     44  CA  LYS    44     -18.702   9.710  39.146  1.00 25.00           C
ATOM     45  CA  ASN    45     -21.304   9.709  36.336  1.00 25.00           C
ATOM     46  CA  PHE    46     -18.633  10.823  33.828  1.00 25.00           C
ATOM     47  CA  PHE    47     -16.306   8.027  35.027  1.00 25.00           C
ATOM     48  CA  GLY    48     -16.889   6.335  31.622  1.00 25.00           C
ATOM     49  CA  SER    49     -14.340   8.497  29.751  1.00 25.00           C
ATOM     50  CA  GLY    50     -14.115  11.646  31.949  1.00 25.00           C
ATOM     51  CA  VAL    51     -10.964  10.061  33.295  1.00 25.00           C
ATOM     52  CA  VAL    52      -8.256   9.045  30.783  1.00 25.00           C
ATOM     53  CA  VAL    53      -9.437  11.774  28.370  1.00 25.00           C
ATOM     54  CA  ALA    54      -9.326  14.356  31.196  1.00 25.00           C
ATOM     55  CA  VAL    55      -5.775  13.245  32.105  1.00 25.00           C
ATOM     56  CA  THR    56      -4.711  13.563  28.440  1.00 25.00           C
ATOM     57  CA  ARG    57      -6.223  17.079  28.282  1.00 25.00           C
ATOM     58  CA  ALA    58      -4.353  18.053  31.479  1.00 25.00           C
ATOM     59  CA  LEU    59      -1.082  16.714  30.004  1.00 25.00           C
ATOM     60  CA  ALA    60      -1.679  18.719  26.795  1.00 25.00           C
ATOM     61  CA  TYR    61       1.782  18.713  25.088  1.00 25.00           C
ATOM     62  CA  GLU    62       0.719  16.705  21.999  1.00 25.00           C
ATOM     63  CA  ALA    63      -2.389  18.799  21.879  1.00 25.00           C
ATOM     64  CA  GLY    64      -3.075  22.200  20.258  1.00 25.00           C
ATOM     65  CA  SER    65      -6.812  21.831  21.011  1.00 25.00           C
ATOM     66  CA  SER    66      -6.018  20.958  24.654  1.00 25.00           C
ATOM     67  CA  ARG    67      -3.747  24.031  24.920  1.00 25.00           C
ATOM     68  CA  GLU    68      -6.521  26.237  23.469  1.00 25.00           C
ATOM     69  CA  SER    69      -9.019  24.798  25.990  1.00 25.00           C
ATOM     70  CA  LEU    70      -6.568  25.492  28.851  1.00 25.00           C
ATOM     71  CA  VAL    71      -6.112  29.089  27.620  1.00 25.00           C
ATOM     72  CA  ALA    72      -9.912  29.546  27.472  1.00 25.00           C
ATOM     73  CA  PHE    73     -10.238  28.190  31.038  1.00 25.00           C
ATOM     74  CA  GLY    74     -11.262  31.675  32.306  1.00 25.00           C
ATOM     75  CA  THR    75     -13.679  32.302  29.439  1.00 25.00           C
ATOM     76  CA  LYS    76     -15.317  30.188  26.733  1.00 25.00           C
ATOM     77  CA  ASP    77     -17.705  27.592  25.470  1.00 25.00           C
ATOM     78  CA  GLU    78     -19.026  26.453  22.060  1.00 25.00           C
ATOM     79  CA  GLN    79     -15.488  25.444  20.999  1.00 25.00           C
ATOM     80  CA  ILE    80     -15.049  23.469  24.250  1.00 25.00           C
ATOM     81  CA  PRO    81     -18.393  21.700  23.657  1.00 25.00           C
ATOM     82  CA  GLU    82     -17.324  20.825  20.084  1.00 25.00           C
ATOM     83  CA  ALA    83     -14.004  19.434  21.393  1.00 25.00           C
ATOM     84  CA  VAL    84     -15.963  16.301  22.218  1.00 25.00           C
ATOM     85  CA  THR    85     -19.422  14.678  22.497  1.00 25.00           C
ATOM     86  CA  GLN    86     -21.446  17.270  24.443  1.00 25.00           C
ATOM     87  CA  THR    87     -22.092  20.117  26.921  1.00 25.00           C
ATOM     88  CA  GLU    88     -22.035  17.630  29.832  1.00 25.00           C
ATOM     89  CA  VAL    89     -18.727  16.179  28.560  1.00 25.00           C
ATOM     90  CA  ASN    90     -17.250  19.704  28.309  1.00 25.00           C
ATOM     91  CA  ARG    91     -18.389  20.463  31.886  1.00 25.00           C
ATOM     92  CA  VAL    92     -16.787  17.208  33.112  1.00 25.00           C
ATOM     93  CA  LEU    93     -13.523  18.112  31.327  1.00 25.00           C
ATOM     94  CA  GLU    94     -13.575  21.586  32.938  1.00 25.00           C
ATOM     95  CA  VAL    95     -14.140  20.008  36.381  1.00 25.00           C
ATOM     96  CA  PHE    96     -11.208  17.615  35.793  1.00 25.00           C
ATOM     97  CA  LYS    97      -8.980  20.558  34.771  1.00 25.00           C
ATOM     98  CA  PRO    98     -10.003  22.461  37.933  1.00 25.00           C
ATOM     99  CA  TYR    99      -9.193  19.391  40.073  1.00 25.00           C
ATOM    100  CA  TYR   100      -5.770  19.086  38.386  1.00 25.00           C
ATOM    101  CA  ALA   101      -5.086  22.795  39.049  1.00 25.00           C
ATOM    102  CA  ASP   102      -6.065  22.344  42.724  1.00 25.00           C
ATOM    103  CA  HIS   103      -3.727  19.325  43.002  1.00 25.00           C
ATOM    104  CA  CYS   104      -0.877  21.357  41.449  1.00 25.00           C
ATOM    105  CA  GLN   105      -1.523  24.204  43.928  1.00 25.00           C
ATOM    106  CA  ILE   106      -2.216  24.536  47.711  1.00 25.00           C
ATOM    107  CA  LYS   107       1.114  22.909  48.603  1.00 25.00           C
ATOM    108  CA  THR   108      -0.140  21.644  51.967  1.00 25.00           C
TER
END
