
#######################################################
#                                                     #
#                        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  101 (  101),  selected  101 , name T0304TS168_4-D1
# Molecule2: number of CA atoms  101 (  799),  selected  101 , name T0304_D1.pdb
# PARAMETERS: T0304TS168_4-D1.T0304_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    R      17      R      17           -
LGA    P      18      P      18           -
LGA    W      19      W      19           -
LGA    W      20      W      20           -
LGA    G      21      G      21           -
LGA    L      22      L      22           -
LGA    P      23      P      23           -
LGA    C      24      C      24           -
LGA    T      25      T      25           -
LGA    V      26      V      26           -
LGA    -       -      T      27           -
LGA    -       -      P      28           -
LGA    -       -      C      29           -
LGA    -       -      F      30           -
LGA    -       -      G      31           -
LGA    -       -      A      32           -
LGA    T      27      R      33           #
LGA    P      28      L      34           #
LGA    -       -      V      35           -
LGA    -       -      Q      36           -
LGA    C      29      E      37          1.628
LGA    -       -      G      38           -
LGA    -       -      N      39           -
LGA    F      30      R      40          1.085
LGA    G      31      L      41          4.103
LGA    A      32      H      42          2.235
LGA    R      33      -       -           -
LGA    L      34      -       -           -
LGA    V      35      Y      43          1.848
LGA    Q      36      L      44          3.672
LGA    E      37      -       -           -
LGA    G      38      -       -           -
LGA    N      39      -       -           -
LGA    R      40      A      45           #
LGA    L      41      D      46           -
LGA    H      42      R      47           -
LGA    Y      43      A      48          4.945
LGA    L      44      G      49          5.108
LGA    A      45      I      50           #
LGA    D      46      -       -           -
LGA    R      47      R      51          4.869
LGA    A      48      G      52          4.026
LGA    G      49      L      53          4.446
LGA    I      50      F      54          4.475
LGA    R      51      -       -           -
LGA    G      52      -       -           -
LGA    L      53      S      55          1.397
LGA    F      54      D      56          3.742
LGA    S      55      -       -           -
LGA    D      56      -       -           -
LGA    A      57      A      57          4.953
LGA    D      58      D      58          3.905
LGA    A      59      A      59          2.243
LGA    Y      60      Y      60          2.083
LGA    H      61      H      61          1.282
LGA    L      62      L      62          1.489
LGA    D      63      D      63          0.874
LGA    Q      64      Q      64          1.837
LGA    A      65      A      65          2.873
LGA    F      66      F      66          2.804
LGA    P      67      P      67          2.683
LGA    L      68      L      68          2.534
LGA    L      69      L      69          2.089
LGA    M      70      M      70          1.648
LGA    K      71      K      71          1.664
LGA    Q      72      Q      72          1.279
LGA    L      73      L      73          0.704
LGA    E      74      E      74          0.846
LGA    L      75      L      75          0.739
LGA    M      76      M      76          0.302
LGA    L      77      L      77          0.639
LGA    T      78      T      78          1.130
LGA    S      79      S      79          1.160
LGA    G      80      -       -           -
LGA    E      81      G      80           #
LGA    L      82      E      81          3.856
LGA    N      83      -       -           -
LGA    P      84      -       -           -
LGA    R      85      -       -           -
LGA    H      86      L      82           #
LGA    Q      87      N      83           #
LGA    -       -      P      84           -
LGA    -       -      R      85           -
LGA    -       -      H      86           -
LGA    -       -      Q      87           -
LGA    -       -      H      88           -
LGA    -       -      T      89           -
LGA    -       -      V      90           -
LGA    -       -      T      91           -
LGA    -       -      L      92           -
LGA    -       -      Y      93           -
LGA    -       -      A      94           -
LGA    -       -      K      95           -
LGA    -       -      G      96           -
LGA    -       -      L      97           -
LGA    -       -      T      98           -
LGA    -       -      C      99           -
LGA    -       -      K     100           -
LGA    -       -      A     101           -
LGA    H      88      D     102          4.856
LGA    T      89      T     103          2.990
LGA    -       -      L     104           -
LGA    V      90      S     105           #
LGA    -       -      S     106           -
LGA    -       -      C     107           -
LGA    -       -      D     108           -
LGA    T      91      Y     109          3.625
LGA    L      92      V     110          4.883
LGA    Y      93      -       -           -
LGA    A      94      -       -           -
LGA    K      95      -       -           -
LGA    G      96      -       -           -
LGA    L      97      -       -           -
LGA    T      98      -       -           -
LGA    C      99      -       -           -
LGA    K     100      -       -           -
LGA    A     101      -       -           -
LGA    D     102      -       -           -
LGA    T     103      -       -           -
LGA    L     104      -       -           -
LGA    S     105      -       -           -
LGA    S     106      -       -           -
LGA    C     107      -       -           -
LGA    D     108      -       -           -
LGA    Y     109      -       -           -
LGA    V     110      -       -           -
LGA    Y     111      Y     111          4.981
LGA    L     112      L     112          3.123
LGA    A     113      -       -           -
LGA    V     114      A     113          4.108
LGA    Y     115      V     114           -
LGA    P     116      Y     115           -
LGA    T     117      P     116           -
LGA    -       -      T     117           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  101  101    5.0     45    3.08    60.00     28.511     1.414

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.373430 * X  +  -0.659834 * Y  +   0.652050 * Z  +  43.729950
  Y_new =  -0.253982 * X  +   0.748764 * Y  +   0.612246 * Z  +  27.022738
  Z_new =  -0.892212 * X  +   0.063023 * Y  +  -0.447197 * Z  +  46.503288 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.001586   -0.140006  [ DEG:   171.9782     -8.0218 ]
  Theta =   1.102221    2.039372  [ DEG:    63.1526    116.8474 ]
  Phi   =  -2.544326    0.597266  [ DEG:  -145.7791     34.2209 ]
 
# 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: T0304TS168_4-D1                               
REMARK     2: T0304_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304TS168_4-D1.T0304_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  101  101   5.0   45   3.08   60.00  28.511
REMARK  ---------------------------------------------------------- 
MOLECULE T0304TS168_4-D1
PFRMAT TS
TARGET T0304
MODEL 4
PARENT N/A
ATOM     17  CA  ARG    17      29.776  46.509  60.145  1.00 25.00           C
ATOM     18  CA  PRO    18      33.017  45.349  58.569  1.00 25.00           C
ATOM     19  CA  TRP    19      36.619  44.157  58.299  1.00 25.00           C
ATOM     20  CA  TRP    20      38.410  41.303  59.988  1.00 25.00           C
ATOM     21  CA  GLY    21      41.947  41.835  61.229  1.00 25.00           C
ATOM     22  CA  LEU    22      44.339  38.919  61.413  1.00 25.00           C
ATOM     23  CA  PRO    23      43.055  38.089  57.891  1.00 25.00           C
ATOM     24  CA  CYS    24      44.394  35.508  55.353  1.00 25.00           C
ATOM     25  CA  THR    25      45.794  33.285  58.158  1.00 25.00           C
ATOM     26  CA  VAL    26      45.709  30.525  55.498  1.00 25.00           C
ATOM     27  CA  THR    27      47.859  28.167  57.528  1.00 25.00           C
ATOM     28  CA  PRO    28      49.132  24.968  55.898  1.00 25.00           C
ATOM     29  CA  CYS    29      52.617  25.295  54.347  1.00 25.00           C
ATOM     30  CA  PHE    30      55.541  24.549  52.040  1.00 25.00           C
ATOM     31  CA  GLY    31      55.812  20.809  51.260  1.00 25.00           C
ATOM     32  CA  ALA    32      52.155  20.307  52.279  1.00 25.00           C
ATOM     33  CA  ARG    33      51.102  23.218  50.026  1.00 25.00           C
ATOM     34  CA  LEU    34      53.073  21.707  47.110  1.00 25.00           C
ATOM     35  CA  VAL    35      51.389  18.317  47.697  1.00 25.00           C
ATOM     36  CA  GLN    36      47.951  20.003  47.729  1.00 25.00           C
ATOM     37  CA  GLU    37      48.775  21.804  44.452  1.00 25.00           C
ATOM     38  CA  GLY    38      49.875  18.490  42.879  1.00 25.00           C
ATOM     39  CA  ASN    39      46.616  16.837  44.022  1.00 25.00           C
ATOM     40  CA  ARG    40      44.596  19.722  42.519  1.00 25.00           C
ATOM     41  CA  LEU    41      46.505  19.370  39.218  1.00 25.00           C
ATOM     42  CA  HIS    42      45.809  15.604  39.188  1.00 25.00           C
ATOM     43  CA  TYR    43      42.090  16.261  39.821  1.00 25.00           C
ATOM     44  CA  LEU    44      42.024  18.796  36.951  1.00 25.00           C
ATOM     45  CA  ALA    45      43.714  16.256  34.636  1.00 25.00           C
ATOM     46  CA  ASP    46      41.141  13.600  35.630  1.00 25.00           C
ATOM     47  CA  ARG    47      38.292  16.060  34.921  1.00 25.00           C
ATOM     48  CA  ALA    48      37.107  19.541  36.032  1.00 25.00           C
ATOM     49  CA  GLY    49      37.989  20.700  32.504  1.00 25.00           C
ATOM     50  CA  ILE    50      41.461  21.846  31.464  1.00 25.00           C
ATOM     51  CA  ARG    51      43.887  23.804  29.367  1.00 25.00           C
ATOM     52  CA  GLY    52      42.975  21.760  26.337  1.00 25.00           C
ATOM     53  CA  LEU    53      41.855  18.160  26.855  1.00 25.00           C
ATOM     54  CA  PHE    54      42.117  14.943  28.870  1.00 25.00           C
ATOM     55  CA  SER    55      43.604  11.651  27.841  1.00 25.00           C
ATOM     56  CA  ASP    56      47.229  10.397  27.567  1.00 25.00           C
ATOM     57  CA  ALA    57      49.743  12.921  26.161  1.00 25.00           C
ATOM     58  CA  ASP    58      47.308  15.787  26.883  1.00 25.00           C
ATOM     59  CA  ALA    59      46.840  14.518  30.467  1.00 25.00           C
ATOM     60  CA  TYR    60      50.638  14.343  30.927  1.00 25.00           C
ATOM     61  CA  HIS    61      50.986  17.923  29.612  1.00 25.00           C
ATOM     62  CA  LEU    62      48.268  19.105  32.036  1.00 25.00           C
ATOM     63  CA  ASP    63      50.063  17.365  34.937  1.00 25.00           C
ATOM     64  CA  GLN    64      53.359  19.037  33.933  1.00 25.00           C
ATOM     65  CA  ALA    65      51.619  22.446  33.808  1.00 25.00           C
ATOM     66  CA  PHE    66      50.128  21.840  37.283  1.00 25.00           C
ATOM     67  CA  PRO    67      53.585  20.892  38.628  1.00 25.00           C
ATOM     68  CA  LEU    68      55.076  24.078  37.114  1.00 25.00           C
ATOM     69  CA  LEU    69      52.301  26.170  38.723  1.00 25.00           C
ATOM     70  CA  MET    70      52.974  24.507  42.106  1.00 25.00           C
ATOM     71  CA  LYS    71      56.716  25.242  41.750  1.00 25.00           C
ATOM     72  CA  GLN    72      55.943  28.900  40.918  1.00 25.00           C
ATOM     73  CA  LEU    73      53.670  29.145  43.991  1.00 25.00           C
ATOM     74  CA  GLU    74      56.432  27.652  46.184  1.00 25.00           C
ATOM     75  CA  LEU    75      58.946  30.176  44.777  1.00 25.00           C
ATOM     76  CA  MET    76      56.510  33.042  45.500  1.00 25.00           C
ATOM     77  CA  LEU    77      56.043  31.773  49.083  1.00 25.00           C
ATOM     78  CA  THR    78      59.841  31.598  49.544  1.00 25.00           C
ATOM     79  CA  SER    79      59.782  35.376  48.916  1.00 25.00           C
ATOM     80  CA  GLY    80      62.052  36.098  45.896  1.00 25.00           C
ATOM     81  CA  GLU    81      60.018  38.876  44.346  1.00 25.00           C
ATOM     82  CA  LEU    82      57.493  40.167  46.964  1.00 25.00           C
ATOM     83  CA  ASN    83      57.779  43.394  44.912  1.00 25.00           C
ATOM     84  CA  PRO    84      55.363  45.346  47.009  1.00 25.00           C
ATOM     85  CA  ARG    85      53.007  44.845  44.010  1.00 25.00           C
ATOM     86  CA  HIS    86      52.937  41.209  42.900  1.00 25.00           C
ATOM     87  CA  GLN    87      51.093  39.097  45.472  1.00 25.00           C
ATOM     88  CA  HIS    88      47.915  37.126  45.246  1.00 25.00           C
ATOM     89  CA  THR    89      46.626  34.229  47.315  1.00 25.00           C
ATOM     90  CA  VAL    90      44.358  31.160  47.653  1.00 25.00           C
ATOM     91  CA  THR    91      43.672  28.048  49.762  1.00 25.00           C
ATOM     92  CA  LEU    92      45.094  24.648  50.914  1.00 25.00           C
ATOM     93  CA  TYR    93      42.919  23.016  53.586  1.00 25.00           C
ATOM     94  CA  ALA    94      40.126  23.582  51.064  1.00 25.00           C
ATOM     95  CA  LYS    95      37.818  26.307  49.818  1.00 25.00           C
ATOM     96  CA  GLY    96      36.525  25.697  46.277  1.00 25.00           C
ATOM     97  CA  LEU    97      39.152  25.635  43.548  1.00 25.00           C
ATOM     98  CA  THR    98      39.451  23.127  40.680  1.00 25.00           C
ATOM     99  CA  CYS    99      38.758  19.878  42.629  1.00 25.00           C
ATOM    100  CA  LYS   100      37.763  16.381  43.859  1.00 25.00           C
ATOM    101  CA  ALA   101      38.088  17.591  47.462  1.00 25.00           C
ATOM    102  CA  ASP   102      35.639  20.550  47.350  1.00 25.00           C
ATOM    103  CA  THR   103      35.727  20.443  51.151  1.00 25.00           C
ATOM    104  CA  LEU   104      38.397  18.189  52.671  1.00 25.00           C
ATOM    105  CA  SER   105      36.430  14.972  52.842  1.00 25.00           C
ATOM    106  CA  SER   106      39.029  13.308  50.689  1.00 25.00           C
ATOM    107  CA  CYS   107      39.255  12.738  46.949  1.00 25.00           C
ATOM    108  CA  ASP   108      42.542  14.547  47.333  1.00 25.00           C
ATOM    109  CA  TYR   109      44.285  16.783  49.928  1.00 25.00           C
ATOM    110  CA  VAL   110      42.961  19.532  47.600  1.00 25.00           C
ATOM    111  CA  TYR   111      42.781  22.942  45.925  1.00 25.00           C
ATOM    112  CA  LEU   112      45.312  25.764  45.360  1.00 25.00           C
ATOM    113  CA  ALA   113      46.596  26.144  41.792  1.00 25.00           C
ATOM    114  CA  VAL   114      44.791  29.461  41.765  1.00 25.00           C
ATOM    115  CA  TYR   115      43.200  32.926  41.217  1.00 25.00           C
ATOM    116  CA  PRO   116      39.834  33.484  42.884  1.00 25.00           C
ATOM    117  CA  THR   117      37.065  35.074  40.809  1.00 25.00           C
TER
END
