
#######################################################
#                                                     #
#                        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  129 (  129),  selected  129 , name T0302TS168_3-D1
# Molecule2: number of CA atoms  129 ( 2108),  selected  129 , name T0302_D1.pdb
# PARAMETERS: T0302TS168_3-D1.T0302_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    V       3      V       3           #
LGA    S       4      S       4           #
LGA    P       5      -       -           -
LGA    E       6      P       5           #
LGA    E       7      E       6          2.667
LGA    A       8      E       7          4.257
LGA    V       9      A       8          3.343
LGA    K      10      V       9          2.593
LGA    W      11      K      10          3.369
LGA    G      12      W      11          3.586
LGA    E      13      G      12          3.516
LGA    S      14      E      13           #
LGA    -       -      S      14           -
LGA    -       -      F      15           -
LGA    F      15      D      16           #
LGA    D      16      K      17          3.398
LGA    K      17      L      18          4.486
LGA    L      18      -       -           -
LGA    L      19      L      19          2.754
LGA    S      20      S      20          2.304
LGA    H      21      H      21          1.851
LGA    R      22      R      22          2.885
LGA    D      23      D      23          2.337
LGA    G      24      G      24          2.076
LGA    L      25      L      25          2.327
LGA    E      26      E      26          1.685
LGA    A      27      A      27          1.107
LGA    F      28      F      28          1.298
LGA    T      29      T      29          1.549
LGA    R      30      R      30          0.919
LGA    F      31      F      31          0.970
LGA    L      32      L      32          1.088
LGA    K      33      K      33          0.438
LGA    T      34      T      34          0.882
LGA    E      35      E      35          1.159
LGA    F      36      F      36          4.213
LGA    S      37      S      37          2.920
LGA    E      38      E      38          1.909
LGA    E      39      E      39          2.709
LGA    N      40      N      40          1.336
LGA    I      41      I      41          1.346
LGA    E      42      E      42          2.050
LGA    F      43      F      43          0.799
LGA    W      44      W      44          1.338
LGA    I      45      I      45          1.012
LGA    A      46      A      46          0.652
LGA    C      47      C      47          1.015
LGA    E      48      E      48          1.265
LGA    D      49      D      49          0.477
LGA    F      50      F      50          1.287
LGA    K      51      K      51          1.392
LGA    K      52      K      52          4.218
LGA    S      53      S      53          2.233
LGA    K      54      K      54          3.231
LGA    G      55      G      55          3.708
LGA    P      56      P      56          1.858
LGA    Q      57      Q      57          1.294
LGA    Q      58      Q      58          1.526
LGA    I      59      I      59          1.734
LGA    H      60      H      60          1.004
LGA    L      61      L      61          0.365
LGA    K      62      K      62          0.542
LGA    A      63      A      63          0.639
LGA    K      64      K      64          0.627
LGA    A      65      A      65          0.310
LGA    I      66      I      66          0.858
LGA    Y      67      Y      67          0.307
LGA    E      68      E      68          0.969
LGA    K      69      K      69          1.522
LGA    F      70      F      70          1.225
LGA    I      71      I      71          3.728
LGA    -       -      Q      72           -
LGA    -       -      T      73           -
LGA    Q      72      D      74          3.972
LGA    T      73      A      75          2.893
LGA    D      74      P      76           #
LGA    -       -      K      77           -
LGA    A      75      E      78          5.307
LGA    P      76      V      79           -
LGA    K      77      -       -           -
LGA    E      78      -       -           -
LGA    V      79      N      80           #
LGA    N      80      L      81           -
LGA    L      81      D      82          5.938
LGA    D      82      -       -           -
LGA    F      83      F      83          3.551
LGA    H      84      H      84          3.595
LGA    T      85      T      85          2.798
LGA    K      86      K      86          2.527
LGA    E      87      E      87          2.889
LGA    V      88      V      88          1.783
LGA    I      89      I      89          1.168
LGA    T      90      T      90          1.822
LGA    N      91      N      91          1.814
LGA    S      92      S      92          1.312
LGA    I      93      I      93          1.874
LGA    T      94      T      94          2.758
LGA    Q      95      Q      95          2.319
LGA    P      96      P      96          2.684
LGA    T      97      T      97          1.407
LGA    L      98      L      98          4.549
LGA    H      99      H      99          5.901
LGA    S     100      S     100          3.756
LGA    F     101      F     101          0.971
LGA    D     102      D     102          0.424
LGA    A     103      A     103          0.632
LGA    A     104      A     104          0.732
LGA    Q     105      Q     105          0.718
LGA    S     106      S     106          1.221
LGA    R     107      R     107          0.823
LGA    V     108      V     108          0.962
LGA    Y     109      Y     109          1.242
LGA    Q     110      Q     110          1.676
LGA    L     111      L     111          1.679
LGA    M     112      M     112          2.134
LGA    E     113      E     113          2.399
LGA    Q     114      Q     114          2.121
LGA    D     115      D     115          2.651
LGA    S     116      S     116          1.334
LGA    Y     117      Y     117          1.223
LGA    T     118      T     118          1.382
LGA    R     119      R     119          1.645
LGA    F     120      F     120          1.561
LGA    L     121      L     121          1.073
LGA    K     122      K     122          2.348
LGA    S     123      S     123          2.976
LGA    D     124      D     124          2.300
LGA    I     125      I     125          3.685
LGA    Y     126      Y     126          2.893
LGA    L     127      L     127          2.018
LGA    D     128      D     128          3.620
LGA    L     129      L     129          4.145
LGA    M     130      M     130          2.384
LGA    E     131      E     131          2.384

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  129  129    5.0    115    2.43    89.57     61.180     4.553

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.188538 * X  +   0.275435 * Y  +  -0.942650 * Z  + 123.109291
  Y_new =   0.339235 * X  +   0.919045 * Y  +   0.200688 * Z  +  -3.666165
  Z_new =   0.921614 * X  +  -0.281943 * Y  +  -0.266712 * Z  +   0.169718 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.328442    0.813151  [ DEG:  -133.4099     46.5901 ]
  Theta =  -1.172220   -1.969373  [ DEG:   -67.1632   -112.8368 ]
  Phi   =   2.078062   -1.063531  [ DEG:   119.0642    -60.9358 ]
 
# 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: T0302TS168_3-D1                               
REMARK     2: T0302_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0302TS168_3-D1.T0302_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  129  129   5.0  115   2.43   89.57  61.180
REMARK  ---------------------------------------------------------- 
MOLECULE T0302TS168_3-D1
PFRMAT TS
TARGET T0302
MODEL 3
PARENT N/A
ATOM      3  CA  VAL     3     145.349  11.912   2.412  1.00 25.00           C
ATOM      4  CA  SER     4     145.260  13.598  -0.956  1.00 25.00           C
ATOM      5  CA  PRO     5     142.615  14.967  -3.327  1.00 25.00           C
ATOM      6  CA  GLU     6     141.312  14.031  -6.805  1.00 25.00           C
ATOM      7  CA  GLU     7     143.360  10.795  -6.728  1.00 25.00           C
ATOM      8  CA  ALA     8     141.950   9.958  -3.266  1.00 25.00           C
ATOM      9  CA  VAL     9     138.392  10.587  -4.535  1.00 25.00           C
ATOM     10  CA  LYS    10     139.036   8.308  -7.546  1.00 25.00           C
ATOM     11  CA  TRP    11     140.370   5.573  -5.221  1.00 25.00           C
ATOM     12  CA  GLY    12     137.262   5.904  -3.007  1.00 25.00           C
ATOM     13  CA  GLU    13     135.006   5.627  -6.091  1.00 25.00           C
ATOM     14  CA  SER    14     136.897   2.496  -7.223  1.00 25.00           C
ATOM     15  CA  PHE    15     136.496   0.962  -3.736  1.00 25.00           C
ATOM     16  CA  ASP    16     132.743   1.730  -3.804  1.00 25.00           C
ATOM     17  CA  LYS    17     132.447   0.099  -7.257  1.00 25.00           C
ATOM     18  CA  LEU    18     134.301  -2.999  -5.979  1.00 25.00           C
ATOM     19  CA  LEU    19     131.953  -3.190  -2.960  1.00 25.00           C
ATOM     20  CA  SER    20     134.245  -3.559   0.054  1.00 25.00           C
ATOM     21  CA  HIS    21     137.505  -1.808   0.697  1.00 25.00           C
ATOM     22  CA  ARG    22     138.099  -0.391   4.223  1.00 25.00           C
ATOM     23  CA  ASP    23     137.794   3.355   4.955  1.00 25.00           C
ATOM     24  CA  GLY    24     135.477   3.781   1.935  1.00 25.00           C
ATOM     25  CA  LEU    25     133.322   0.856   3.145  1.00 25.00           C
ATOM     26  CA  GLU    26     133.123   2.416   6.638  1.00 25.00           C
ATOM     27  CA  ALA    27     132.083   5.769   5.107  1.00 25.00           C
ATOM     28  CA  PHE    28     129.379   4.014   3.040  1.00 25.00           C
ATOM     29  CA  THR    29     128.093   2.240   6.181  1.00 25.00           C
ATOM     30  CA  ARG    30     127.979   5.581   8.051  1.00 25.00           C
ATOM     31  CA  PHE    31     126.039   7.164   5.153  1.00 25.00           C
ATOM     32  CA  LEU    32     123.562   4.243   5.183  1.00 25.00           C
ATOM     33  CA  LYS    33     123.098   4.644   8.964  1.00 25.00           C
ATOM     34  CA  THR    34     122.471   8.396   8.514  1.00 25.00           C
ATOM     35  CA  GLU    35     118.720   7.628   8.603  1.00 25.00           C
ATOM     36  CA  PHE    36     117.477   6.698   5.082  1.00 25.00           C
ATOM     37  CA  SER    37     117.922   3.710   2.818  1.00 25.00           C
ATOM     38  CA  GLU    38     119.665   1.404   5.376  1.00 25.00           C
ATOM     39  CA  GLU    39     117.130  -1.428   4.905  1.00 25.00           C
ATOM     40  CA  ASN    40     118.641  -2.245   1.483  1.00 25.00           C
ATOM     41  CA  ILE    41     122.148  -2.315   3.022  1.00 25.00           C
ATOM     42  CA  GLU    42     120.914  -4.658   5.788  1.00 25.00           C
ATOM     43  CA  PHE    43     119.332  -6.959   3.168  1.00 25.00           C
ATOM     44  CA  TRP    44     122.611  -7.003   1.190  1.00 25.00           C
ATOM     45  CA  ILE    45     124.550  -7.871   4.375  1.00 25.00           C
ATOM     46  CA  ALA    46     122.094 -10.712   5.126  1.00 25.00           C
ATOM     47  CA  CYS    47     122.504 -12.041   1.557  1.00 25.00           C
ATOM     48  CA  GLU    48     126.314 -11.924   1.926  1.00 25.00           C
ATOM     49  CA  ASP    49     126.077 -13.820   5.245  1.00 25.00           C
ATOM     50  CA  PHE    50     123.844 -16.464   3.603  1.00 25.00           C
ATOM     51  CA  LYS    51     126.353 -16.835   0.733  1.00 25.00           C
ATOM     52  CA  LYS    52     127.499 -20.491   0.908  1.00 25.00           C
ATOM     53  CA  SER    53     125.927 -22.232   3.831  1.00 25.00           C
ATOM     54  CA  LYS    54     124.593 -25.479   2.258  1.00 25.00           C
ATOM     55  CA  GLY    55     123.913 -28.998   3.530  1.00 25.00           C
ATOM     56  CA  PRO    56     120.890 -27.731   5.462  1.00 25.00           C
ATOM     57  CA  GLN    57     118.091 -27.020   7.977  1.00 25.00           C
ATOM     58  CA  GLN    58     120.090 -24.084   9.408  1.00 25.00           C
ATOM     59  CA  ILE    59     120.633 -22.702   5.878  1.00 25.00           C
ATOM     60  CA  HIS    60     116.884 -23.006   5.155  1.00 25.00           C
ATOM     61  CA  LEU    61     116.082 -21.169   8.419  1.00 25.00           C
ATOM     62  CA  LYS    62     118.547 -18.390   7.490  1.00 25.00           C
ATOM     63  CA  ALA    63     116.932 -18.079   4.032  1.00 25.00           C
ATOM     64  CA  LYS    64     113.465 -17.852   5.643  1.00 25.00           C
ATOM     65  CA  ALA    65     114.723 -15.129   8.025  1.00 25.00           C
ATOM     66  CA  ILE    66     116.191 -13.188   5.067  1.00 25.00           C
ATOM     67  CA  TYR    67     112.863 -13.473   3.196  1.00 25.00           C
ATOM     68  CA  GLU    68     110.989 -12.202   6.285  1.00 25.00           C
ATOM     69  CA  LYS    69     113.407  -9.246   6.567  1.00 25.00           C
ATOM     70  CA  PHE    70     112.879  -8.430   2.862  1.00 25.00           C
ATOM     71  CA  ILE    71     109.083  -8.556   3.349  1.00 25.00           C
ATOM     72  CA  GLN    72     106.195 -10.718   4.360  1.00 25.00           C
ATOM     73  CA  THR    73     105.028  -8.274   7.004  1.00 25.00           C
ATOM     74  CA  ASP    74     102.742  -5.206   7.197  1.00 25.00           C
ATOM     75  CA  ALA    75     105.826  -3.198   6.165  1.00 25.00           C
ATOM     76  CA  PRO    76     104.765   0.439   5.420  1.00 25.00           C
ATOM     77  CA  LYS    77     102.881  -0.720   2.315  1.00 25.00           C
ATOM     78  CA  GLU    78     103.854   1.438  -0.665  1.00 25.00           C
ATOM     79  CA  VAL    79     105.936  -1.094  -2.551  1.00 25.00           C
ATOM     80  CA  ASN    80     104.105  -0.414  -5.832  1.00 25.00           C
ATOM     81  CA  LEU    81     106.669  -2.793  -7.291  1.00 25.00           C
ATOM     82  CA  ASP    82     104.668  -5.449  -9.170  1.00 25.00           C
ATOM     83  CA  PHE    83     105.569  -8.845  -7.590  1.00 25.00           C
ATOM     84  CA  HIS    84     106.826 -11.668  -9.850  1.00 25.00           C
ATOM     85  CA  THR    85     110.186 -11.675  -8.013  1.00 25.00           C
ATOM     86  CA  LYS    86     108.373 -11.845  -4.645  1.00 25.00           C
ATOM     87  CA  GLU    87     106.253 -14.774  -5.905  1.00 25.00           C
ATOM     88  CA  VAL    88     109.414 -16.584  -7.090  1.00 25.00           C
ATOM     89  CA  ILE    89     111.046 -16.022  -3.671  1.00 25.00           C
ATOM     90  CA  THR    90     107.929 -17.403  -1.928  1.00 25.00           C
ATOM     91  CA  ASN    91     107.989 -20.482  -4.206  1.00 25.00           C
ATOM     92  CA  SER    92     111.697 -21.026  -3.412  1.00 25.00           C
ATOM     93  CA  ILE    93     110.960 -20.755   0.336  1.00 25.00           C
ATOM     94  CA  THR    94     111.815 -24.156   1.899  1.00 25.00           C
ATOM     95  CA  GLN    95     113.603 -26.334  -0.671  1.00 25.00           C
ATOM     96  CA  PRO    96     116.929 -24.509  -1.278  1.00 25.00           C
ATOM     97  CA  THR    97     120.436 -23.049  -1.485  1.00 25.00           C
ATOM     98  CA  LEU    98     119.507 -19.969  -3.528  1.00 25.00           C
ATOM     99  CA  HIS    99     118.920 -18.082  -6.745  1.00 25.00           C
ATOM    100  CA  SER   100     116.093 -15.715  -5.707  1.00 25.00           C
ATOM    101  CA  PHE   101     118.209 -14.429  -2.786  1.00 25.00           C
ATOM    102  CA  ASP   102     121.164 -13.842  -5.151  1.00 25.00           C
ATOM    103  CA  ALA   103     118.884 -11.933  -7.565  1.00 25.00           C
ATOM    104  CA  ALA   104     117.583  -9.783  -4.675  1.00 25.00           C
ATOM    105  CA  GLN   105     121.177  -9.039  -3.578  1.00 25.00           C
ATOM    106  CA  SER   106     122.091  -8.049  -7.162  1.00 25.00           C
ATOM    107  CA  ARG   107     119.042  -5.737  -7.327  1.00 25.00           C
ATOM    108  CA  VAL   108     120.048  -4.132  -3.998  1.00 25.00           C
ATOM    109  CA  TYR   109     123.610  -3.602  -5.303  1.00 25.00           C
ATOM    110  CA  GLN   110     122.229  -1.991  -8.491  1.00 25.00           C
ATOM    111  CA  LEU   111     120.009   0.319  -6.393  1.00 25.00           C
ATOM    112  CA  MET   112     123.023   1.306  -4.246  1.00 25.00           C
ATOM    113  CA  GLU   113     125.058   2.053  -7.404  1.00 25.00           C
ATOM    114  CA  GLN   114     122.199   4.205  -8.767  1.00 25.00           C
ATOM    115  CA  ASP   115     120.334   6.975  -7.032  1.00 25.00           C
ATOM    116  CA  SER   116     121.206   7.386  -3.366  1.00 25.00           C
ATOM    117  CA  TYR   117     124.963   7.714  -3.412  1.00 25.00           C
ATOM    118  CA  THR   118     125.317  10.838  -5.598  1.00 25.00           C
ATOM    119  CA  ARG   119     124.809  13.073  -2.530  1.00 25.00           C
ATOM    120  CA  PHE   120     127.473  11.094  -0.617  1.00 25.00           C
ATOM    121  CA  LEU   121     129.897  11.468  -3.558  1.00 25.00           C
ATOM    122  CA  LYS   122     129.638  15.303  -3.638  1.00 25.00           C
ATOM    123  CA  SER   123     128.270  16.491  -0.255  1.00 25.00           C
ATOM    124  CA  ASP   124     129.079  17.724   3.251  1.00 25.00           C
ATOM    125  CA  ILE   125     131.158  15.594   5.661  1.00 25.00           C
ATOM    126  CA  TYR   126     132.723  13.733   2.701  1.00 25.00           C
ATOM    127  CA  LEU   127     133.563  17.068   1.016  1.00 25.00           C
ATOM    128  CA  ASP   128     135.169  18.329   4.256  1.00 25.00           C
ATOM    129  CA  LEU   129     137.235  15.114   4.513  1.00 25.00           C
ATOM    130  CA  MET   130     138.375  15.528   0.879  1.00 25.00           C
ATOM    131  CA  GLU   131     140.661  18.335   2.131  1.00 25.00           C
TER
END
