
#######################################################
#                                                     #
#                        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_2-D1
# Molecule2: number of CA atoms  129 ( 2108),  selected  129 , name T0302_D1.pdb
# PARAMETERS: T0302TS168_2-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          4.941
LGA    S       4      S       4          4.881
LGA    P       5      P       5          2.620
LGA    E       6      E       6          2.373
LGA    E       7      E       7          4.185
LGA    A       8      A       8          4.377
LGA    V       9      V       9          3.698
LGA    K      10      K      10          3.756
LGA    W      11      -       -           -
LGA    G      12      -       -           -
LGA    E      13      W      11          2.218
LGA    S      14      G      12           -
LGA    F      15      E      13           -
LGA    -       -      S      14           -
LGA    -       -      F      15           -
LGA    -       -      D      16           -
LGA    -       -      K      17           -
LGA    D      16      L      18          1.482
LGA    K      17      L      19          4.319
LGA    L      18      S      20          1.355
LGA    L      19      H      21           #
LGA    S      20      -       -           -
LGA    H      21      R      22          1.691
LGA    R      22      D      23          2.665
LGA    D      23      -       -           -
LGA    G      24      G      24          3.950
LGA    L      25      L      25          2.753
LGA    E      26      E      26          2.212
LGA    A      27      A      27          3.496
LGA    F      28      F      28          2.653
LGA    T      29      T      29          1.669
LGA    R      30      R      30          2.758
LGA    F      31      F      31          2.906
LGA    L      32      L      32          1.510
LGA    K      33      K      33          1.476
LGA    T      34      T      34          1.826
LGA    E      35      E      35          1.056
LGA    F      36      F      36          4.495
LGA    S      37      S      37          2.941
LGA    E      38      E      38          2.025
LGA    E      39      E      39          3.409
LGA    N      40      N      40          1.604
LGA    I      41      I      41          1.202
LGA    E      42      E      42          2.564
LGA    F      43      F      43          1.303
LGA    W      44      W      44          1.215
LGA    I      45      I      45          1.509
LGA    A      46      A      46          1.749
LGA    C      47      C      47          1.245
LGA    E      48      E      48          0.947
LGA    D      49      D      49          1.625
LGA    F      50      F      50          1.990
LGA    K      51      K      51          0.854
LGA    K      52      K      52          2.356
LGA    S      53      S      53          3.844
LGA    K      54      K      54          4.988
LGA    G      55      G      55          4.354
LGA    P      56      P      56          0.896
LGA    Q      57      Q      57          0.813
LGA    Q      58      Q      58          1.239
LGA    I      59      I      59          1.519
LGA    H      60      H      60          1.645
LGA    L      61      L      61          1.108
LGA    K      62      K      62          1.038
LGA    A      63      A      63          0.734
LGA    K      64      K      64          0.978
LGA    A      65      A      65          0.979
LGA    I      66      I      66          1.034
LGA    Y      67      Y      67          0.736
LGA    E      68      E      68          1.749
LGA    K      69      K      69          1.743
LGA    F      70      F      70          0.611
LGA    -       -      I      71           -
LGA    I      71      Q      72          2.982
LGA    Q      72      T      73           #
LGA    -       -      D      74           -
LGA    T      73      A      75          3.359
LGA    D      74      P      76          2.452
LGA    A      75      K      77          4.316
LGA    P      76      E      78           #
LGA    K      77      V      79           -
LGA    E      78      -       -           -
LGA    V      79      N      80           #
LGA    N      80      L      81           -
LGA    L      81      D      82           #
LGA    D      82      -       -           -
LGA    F      83      F      83          3.782
LGA    H      84      H      84          3.108
LGA    T      85      T      85          3.193
LGA    K      86      K      86          3.327
LGA    E      87      E      87          2.720
LGA    V      88      V      88          1.833
LGA    I      89      I      89          2.117
LGA    T      90      T      90          1.984
LGA    N      91      N      91          1.346
LGA    S      92      S      92          1.811
LGA    I      93      I      93          2.425
LGA    T      94      T      94          1.594
LGA    Q      95      Q      95          2.631
LGA    P      96      P      96          1.584
LGA    T      97      T      97          2.470
LGA    L      98      L      98          3.238
LGA    H      99      H      99          4.562
LGA    S     100      S     100          3.086
LGA    F     101      F     101          1.152
LGA    D     102      D     102          1.230
LGA    A     103      A     103          1.249
LGA    A     104      A     104          1.075
LGA    Q     105      Q     105          0.952
LGA    S     106      S     106          1.207
LGA    R     107      R     107          0.723
LGA    V     108      V     108          0.749
LGA    Y     109      Y     109          1.016
LGA    Q     110      Q     110          1.828
LGA    L     111      L     111          1.966
LGA    M     112      M     112          2.348
LGA    E     113      E     113          2.731
LGA    Q     114      Q     114          2.651
LGA    D     115      D     115          4.308
LGA    S     116      S     116          2.439
LGA    Y     117      Y     117          0.697
LGA    T     118      T     118          2.032
LGA    R     119      R     119          1.916
LGA    F     120      F     120          0.943
LGA    L     121      L     121          0.736
LGA    K     122      K     122          2.841
LGA    S     123      S     123          3.505
LGA    D     124      D     124          2.656
LGA    I     125      I     125          3.254
LGA    Y     126      Y     126          2.464
LGA    L     127      L     127          2.424
LGA    D     128      D     128          4.535
LGA    L     129      L     129          4.590
LGA    -       -      M     130           -
LGA    M     130      E     131          2.816
LGA    E     131      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  129  129    5.0    113    2.57    90.27     57.448     4.232

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.633466 * X  +   0.465733 * Y  +  -0.617911 * Z  + 123.006691
  Y_new =   0.268388 * X  +  -0.616744 * Y  +  -0.739997 * Z  +  -3.846046
  Z_new =  -0.725734 * X  +  -0.634602 * Y  +   0.265689 * Z  +   0.743945 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.174300    1.967293  [ DEG:   -67.2824    112.7176 ]
  Theta =   0.812100    2.329492  [ DEG:    46.5299    133.4701 ]
  Phi   =   2.740839   -0.400754  [ DEG:   157.0385    -22.9615 ]
 
# 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_2-D1                               
REMARK     2: T0302_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0302TS168_2-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  113   2.57   90.27  57.448
REMARK  ---------------------------------------------------------- 
MOLECULE T0302TS168_2-D1
PFRMAT TS
TARGET T0302
MODEL 2
PARENT N/A
ATOM      3  CA  VAL     3     143.412   9.291   5.518  1.00 25.00           C
ATOM      4  CA  SER     4     143.486  12.192   3.041  1.00 25.00           C
ATOM      5  CA  PRO     5     143.135  12.963  -0.649  1.00 25.00           C
ATOM      6  CA  GLU     6     143.104  11.355  -4.126  1.00 25.00           C
ATOM      7  CA  GLU     7     144.451   8.087  -2.652  1.00 25.00           C
ATOM      8  CA  ALA     8     141.738   8.157   0.049  1.00 25.00           C
ATOM      9  CA  VAL     9     139.056   8.727  -2.625  1.00 25.00           C
ATOM     10  CA  LYS    10     140.424   5.786  -4.660  1.00 25.00           C
ATOM     11  CA  TRP    11     140.354   3.564  -1.542  1.00 25.00           C
ATOM     12  CA  GLY    12     136.733   4.604  -0.852  1.00 25.00           C
ATOM     13  CA  GLU    13     135.784   3.792  -4.472  1.00 25.00           C
ATOM     14  CA  SER    14     137.457   0.361  -4.167  1.00 25.00           C
ATOM     15  CA  PHE    15     135.549  -0.308  -0.915  1.00 25.00           C
ATOM     16  CA  ASP    16     132.261   0.682  -2.612  1.00 25.00           C
ATOM     17  CA  LYS    17     133.035  -1.665  -5.537  1.00 25.00           C
ATOM     18  CA  LEU    18     133.777  -4.513  -3.086  1.00 25.00           C
ATOM     19  CA  LEU    19     130.469  -3.849  -1.274  1.00 25.00           C
ATOM     20  CA  SER    20     132.589  -3.293   1.833  1.00 25.00           C
ATOM     21  CA  HIS    21     136.003  -3.631   3.393  1.00 25.00           C
ATOM     22  CA  ARG    22     137.509  -0.480   4.855  1.00 25.00           C
ATOM     23  CA  ASP    23     137.343   2.649   7.058  1.00 25.00           C
ATOM     24  CA  GLY    24     135.478   4.529   4.291  1.00 25.00           C
ATOM     25  CA  LEU    25     133.004   1.626   3.953  1.00 25.00           C
ATOM     26  CA  GLU    26     132.440   1.632   7.740  1.00 25.00           C
ATOM     27  CA  ALA    27     131.823   5.411   7.668  1.00 25.00           C
ATOM     28  CA  PHE    28     129.313   4.970   4.808  1.00 25.00           C
ATOM     29  CA  THR    29     127.515   2.222   6.778  1.00 25.00           C
ATOM     30  CA  ARG    30     127.361   4.495   9.856  1.00 25.00           C
ATOM     31  CA  PHE    31     125.925   7.332   7.721  1.00 25.00           C
ATOM     32  CA  LEU    32     123.289   4.951   6.287  1.00 25.00           C
ATOM     33  CA  LYS    33     122.352   3.820   9.824  1.00 25.00           C
ATOM     34  CA  THR    34     122.025   7.471  10.932  1.00 25.00           C
ATOM     35  CA  GLU    35     119.133   7.782   8.526  1.00 25.00           C
ATOM     36  CA  PHE    36     117.183   7.427   5.238  1.00 25.00           C
ATOM     37  CA  SER    37     118.926   4.543   3.356  1.00 25.00           C
ATOM     38  CA  GLU    38     119.652   1.210   5.124  1.00 25.00           C
ATOM     39  CA  GLU    39     117.133  -1.345   3.785  1.00 25.00           C
ATOM     40  CA  ASN    40     119.443  -2.109   0.828  1.00 25.00           C
ATOM     41  CA  ILE    41     122.393  -2.587   3.224  1.00 25.00           C
ATOM     42  CA  GLU    42     120.292  -4.955   5.378  1.00 25.00           C
ATOM     43  CA  PHE    43     119.305  -6.953   2.263  1.00 25.00           C
ATOM     44  CA  TRP    44     122.982  -7.189   1.220  1.00 25.00           C
ATOM     45  CA  ILE    45     123.925  -8.406   4.726  1.00 25.00           C
ATOM     46  CA  ALA    46     121.154 -11.045   4.581  1.00 25.00           C
ATOM     47  CA  CYS    47     122.407 -12.209   1.154  1.00 25.00           C
ATOM     48  CA  GLU    48     125.977 -12.463   2.518  1.00 25.00           C
ATOM     49  CA  ASP    49     124.716 -14.509   5.501  1.00 25.00           C
ATOM     50  CA  PHE    50     122.818 -16.842   3.130  1.00 25.00           C
ATOM     51  CA  LYS    51     125.970 -17.284   1.001  1.00 25.00           C
ATOM     52  CA  LYS    52     128.969 -19.331   2.230  1.00 25.00           C
ATOM     53  CA  SER    53     126.929 -22.514   2.102  1.00 25.00           C
ATOM     54  CA  LYS    54     126.402 -25.114  -0.631  1.00 25.00           C
ATOM     55  CA  GLY    55     124.930 -27.479   1.994  1.00 25.00           C
ATOM     56  CA  PRO    56     121.472 -27.550   3.565  1.00 25.00           C
ATOM     57  CA  GLN    57     118.736 -27.339   6.238  1.00 25.00           C
ATOM     58  CA  GLN    58     120.724 -24.643   8.094  1.00 25.00           C
ATOM     59  CA  ILE    59     121.139 -22.671   4.838  1.00 25.00           C
ATOM     60  CA  HIS    60     117.376 -22.931   4.172  1.00 25.00           C
ATOM     61  CA  LEU    61     116.638 -21.693   7.720  1.00 25.00           C
ATOM     62  CA  LYS    62     119.026 -18.743   7.213  1.00 25.00           C
ATOM     63  CA  ALA    63     117.304 -17.886   3.901  1.00 25.00           C
ATOM     64  CA  LYS    64     113.883 -18.014   5.618  1.00 25.00           C
ATOM     65  CA  ALA    65     115.162 -15.707   8.395  1.00 25.00           C
ATOM     66  CA  ILE    66     116.508 -13.259   5.774  1.00 25.00           C
ATOM     67  CA  TYR    67     113.130 -13.297   3.968  1.00 25.00           C
ATOM     68  CA  GLU    68     111.327 -12.611   7.276  1.00 25.00           C
ATOM     69  CA  LYS    69     113.700  -9.692   7.993  1.00 25.00           C
ATOM     70  CA  PHE    70     113.049  -8.272   4.496  1.00 25.00           C
ATOM     71  CA  ILE    71     109.271  -8.564   5.054  1.00 25.00           C
ATOM     72  CA  GLN    72     106.635 -10.894   6.596  1.00 25.00           C
ATOM     73  CA  THR    73     104.824  -8.047   8.383  1.00 25.00           C
ATOM     74  CA  ASP    74     106.925  -5.650  10.454  1.00 25.00           C
ATOM     75  CA  ALA    75     107.674  -2.517   8.520  1.00 25.00           C
ATOM     76  CA  PRO    76     103.987  -1.850   8.132  1.00 25.00           C
ATOM     77  CA  LYS    77     103.739  -1.330   4.370  1.00 25.00           C
ATOM     78  CA  GLU    78     102.624   0.948   1.534  1.00 25.00           C
ATOM     79  CA  VAL    79     106.079   0.384   0.173  1.00 25.00           C
ATOM     80  CA  ASN    80     104.816   0.423  -3.460  1.00 25.00           C
ATOM     81  CA  LEU    81     105.620  -3.122  -4.668  1.00 25.00           C
ATOM     82  CA  ASP    82     105.264  -4.676  -8.169  1.00 25.00           C
ATOM     83  CA  PHE    83     105.234  -8.112  -6.606  1.00 25.00           C
ATOM     84  CA  HIS    84     107.187 -10.483  -8.893  1.00 25.00           C
ATOM     85  CA  THR    85     110.121 -10.481  -6.433  1.00 25.00           C
ATOM     86  CA  LYS    86     107.731 -11.263  -3.544  1.00 25.00           C
ATOM     87  CA  GLU    87     106.209 -14.146  -5.552  1.00 25.00           C
ATOM     88  CA  VAL    88     109.709 -15.515  -6.288  1.00 25.00           C
ATOM     89  CA  ILE    89     110.598 -15.309  -2.569  1.00 25.00           C
ATOM     90  CA  THR    90     107.372 -17.165  -1.669  1.00 25.00           C
ATOM     91  CA  ASN    91     108.185 -19.879  -4.246  1.00 25.00           C
ATOM     92  CA  SER    92     111.711 -20.234  -2.795  1.00 25.00           C
ATOM     93  CA  ILE    93     110.254 -20.549   0.733  1.00 25.00           C
ATOM     94  CA  THR    94     110.022 -24.398   0.560  1.00 25.00           C
ATOM     95  CA  GLN    95     113.244 -26.351  -0.157  1.00 25.00           C
ATOM     96  CA  PRO    96     115.396 -23.317  -0.617  1.00 25.00           C
ATOM     97  CA  THR    97     118.031 -23.169  -3.416  1.00 25.00           C
ATOM     98  CA  LEU    98     120.444 -20.331  -2.654  1.00 25.00           C
ATOM     99  CA  HIS    99     119.022 -17.909  -5.220  1.00 25.00           C
ATOM    100  CA  SER   100     116.153 -15.487  -4.465  1.00 25.00           C
ATOM    101  CA  PHE   101     118.248 -13.821  -1.726  1.00 25.00           C
ATOM    102  CA  ASP   102     121.188 -13.469  -4.154  1.00 25.00           C
ATOM    103  CA  ALA   103     118.871 -11.905  -6.772  1.00 25.00           C
ATOM    104  CA  ALA   104     117.534  -9.447  -4.157  1.00 25.00           C
ATOM    105  CA  GLN   105     121.114  -8.513  -3.169  1.00 25.00           C
ATOM    106  CA  SER   106     122.007  -7.943  -6.850  1.00 25.00           C
ATOM    107  CA  ARG   107     118.916  -5.724  -7.282  1.00 25.00           C
ATOM    108  CA  VAL   108     119.896  -3.712  -4.173  1.00 25.00           C
ATOM    109  CA  TYR   109     123.446  -3.278  -5.543  1.00 25.00           C
ATOM    110  CA  GLN   110     122.033  -2.087  -8.897  1.00 25.00           C
ATOM    111  CA  LEU   111     119.773   0.417  -7.085  1.00 25.00           C
ATOM    112  CA  MET   112     122.770   1.709  -5.082  1.00 25.00           C
ATOM    113  CA  GLU   113     124.788   2.108  -8.313  1.00 25.00           C
ATOM    114  CA  GLN   114     121.889   4.029  -9.916  1.00 25.00           C
ATOM    115  CA  ASP   115     121.260   7.376  -8.354  1.00 25.00           C
ATOM    116  CA  SER   116     121.671   6.603  -4.671  1.00 25.00           C
ATOM    117  CA  TYR   117     125.502   6.583  -4.718  1.00 25.00           C
ATOM    118  CA  THR   118     126.092   9.470  -7.163  1.00 25.00           C
ATOM    119  CA  ARG   119     124.189  11.853  -4.847  1.00 25.00           C
ATOM    120  CA  PHE   120     126.295  10.681  -1.870  1.00 25.00           C
ATOM    121  CA  LEU   121     129.502  11.249  -3.886  1.00 25.00           C
ATOM    122  CA  LYS   122     128.419  14.609  -5.350  1.00 25.00           C
ATOM    123  CA  SER   123     126.918  15.672  -1.954  1.00 25.00           C
ATOM    124  CA  ASP   124     128.829  16.450   1.251  1.00 25.00           C
ATOM    125  CA  ILE   125     131.511  15.240   3.702  1.00 25.00           C
ATOM    126  CA  TYR   126     133.465  13.648   0.819  1.00 25.00           C
ATOM    127  CA  LEU   127     133.243  16.915  -1.167  1.00 25.00           C
ATOM    128  CA  ASP   128     134.504  18.877   1.870  1.00 25.00           C
ATOM    129  CA  LEU   129     137.427  16.432   2.265  1.00 25.00           C
ATOM    130  CA  MET   130     138.287  16.824  -1.446  1.00 25.00           C
ATOM    131  CA  GLU   131     139.404  20.422  -0.897  1.00 25.00           C
TER
END
