
#######################################################
#                                                     #
#                        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  116 (  116),  selected  116 , name T0323TS393_1-D2
# Molecule2: number of CA atoms  116 (  868),  selected  116 , name T0323_D2.pdb
# PARAMETERS: T0323TS393_1-D2.T0323_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    P      34      P      34           #
LGA    T      35      -       -           -
LGA    K      36      -       -           -
LGA    P      37      T      35           #
LGA    N      38      K      36           #
LGA    -       -      P      37           -
LGA    P      39      N      38          3.781
LGA    F      40      P      39          2.335
LGA    Q      41      F      40          1.544
LGA    S      42      Q      41          3.313
LGA    L      43      S      42          2.472
LGA    V      44      L      43          0.522
LGA    S      45      V      44          2.706
LGA    S      46      S      45          2.696
LGA    I      47      S      46          0.721
LGA    V      48      I      47          2.192
LGA    E      49      V      48          2.773
LGA    Q      50      E      49          0.856
LGA    Q      51      Q      50          2.170
LGA    L      52      Q      51          3.978
LGA    -       -      L      52           -
LGA    -       -      S      53           -
LGA    -       -      I      54           -
LGA    -       -      K      55           -
LGA    S      53      A      56           #
LGA    I      54      A      57          3.037
LGA    K      55      S      58           #
LGA    -       -      A      59           -
LGA    A      56      I      60          3.482
LGA    A      57      Y      61          2.767
LGA    S      58      G      62          2.480
LGA    A      59      R      63          1.334
LGA    I      60      V      64          1.371
LGA    Y      61      E      65          2.752
LGA    G      62      Q      66          3.366
LGA    R      63      L      67          3.519
LGA    V      64      V      68          4.015
LGA    -       -      G      69           -
LGA    -       -      G      70           -
LGA    E      65      A      71          1.967
LGA    Q      66      L      72           -
LGA    L      67      -       -           -
LGA    V      68      -       -           -
LGA    G      69      -       -           -
LGA    G      70      -       -           -
LGA    A      71      -       -           -
LGA    L      72      E      73           #
LGA    E      73      -       -           -
LGA    K      74      -       -           -
LGA    P      75      -       -           -
LGA    E      76      -       -           -
LGA    Q      77      -       -           -
LGA    L      78      K      74          4.545
LGA    Y      79      P      75          3.290
LGA    R      80      E      76          3.003
LGA    -       -      Q      77           -
LGA    V      81      L      78          4.957
LGA    S      82      Y      79          3.929
LGA    D      83      R      80          1.324
LGA    E      84      V      81          3.481
LGA    A      85      -       -           -
LGA    L      86      S      82          3.549
LGA    R      87      D      83          4.023
LGA    -       -      E      84           -
LGA    Q      88      A      85          1.072
LGA    A      89      L      86          1.478
LGA    G      90      R      87          6.414
LGA    -       -      Q      88           -
LGA    -       -      A      89           -
LGA    -       -      G      90           -
LGA    V      91      V      91          6.250
LGA    S      92      S      92          2.703
LGA    K      93      K      93          2.452
LGA    R      94      R      94          2.653
LGA    K      95      K      95          2.882
LGA    I      96      I      96          2.874
LGA    E      97      E      97          2.837
LGA    Y      98      Y      98          3.004
LGA    I      99      I      99          2.940
LGA    R     100      R     100          2.937
LGA    H     101      H     101          3.153
LGA    V     102      V     102          3.414
LGA    C     103      C     103          3.419
LGA    E     104      E     104          3.357
LGA    H     105      H     105          3.707
LGA    V     106      V     106          3.574
LGA    E     107      E     107          3.778
LGA    S     108      S     108          3.324
LGA    G     109      G     109          1.268
LGA    R     110      R     110          5.231
LGA    L     111      L     111          1.182
LGA    D     112      D     112          2.612
LGA    F     113      F     113          2.463
LGA    T     114      T     114          2.652
LGA    E     115      E     115          0.965
LGA    L     116      L     116          1.207
LGA    E     117      E     117          2.787
LGA    G     118      -       -           -
LGA    A     119      G     118          0.979
LGA    E     120      A     119           #
LGA    A     121      E     120          5.298
LGA    T     122      A     121          2.884
LGA    T     123      T     122           #
LGA    -       -      T     123           -
LGA    V     124      V     124          3.286
LGA    I     125      I     125          2.697
LGA    E     126      E     126          2.793
LGA    K     127      K     127          2.202
LGA    L     128      L     128          1.081
LGA    T     129      T     129          2.168
LGA    A     130      A     130          2.601
LGA    I     131      I     131          2.948
LGA    K     132      -       -           -
LGA    G     133      -       -           -
LGA    I     134      -       -           -
LGA    G     135      -       -           -
LGA    Q     136      K     132          2.128
LGA    W     137      G     133          3.521
LGA    T     138      I     134          3.938
LGA    A     139      G     135           #
LGA    E     140      Q     136          5.285
LGA    M     141      W     137          4.197
LGA    F     142      T     138          2.986
LGA    M     143      A     139          2.356
LGA    M     144      E     140          2.676
LGA    F     145      M     141          1.768
LGA    S     146      F     142          1.778
LGA    L     147      M     143          1.943
LGA    -       -      M     144           -
LGA    -       -      F     145           -
LGA    -       -      S     146           -
LGA    -       -      L     147           -
LGA    -       -      G     148           -
LGA    G     148      R     149          4.371
LGA    R     149      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  116  116    5.0     87    3.09    43.68     42.822     2.726

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.658977 * X  +  -0.198705 * Y  +   0.725441 * Z  +  11.216224
  Y_new =   0.747914 * X  +  -0.275477 * Y  +   0.603935 * Z  +  38.720119
  Z_new =   0.079837 * X  +   0.940547 * Y  +   0.330147 * Z  +   0.584361 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.233217   -1.908376  [ DEG:    70.6581   -109.3419 ]
  Theta =  -0.079922   -3.061670  [ DEG:    -4.5792   -175.4208 ]
  Phi   =   2.293064   -0.848529  [ DEG:   131.3829    -48.6171 ]
 
# 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: T0323TS393_1-D2                               
REMARK     2: T0323_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0323TS393_1-D2.T0323_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  116  116   5.0   87   3.09   43.68  42.822
REMARK  ---------------------------------------------------------- 
MOLECULE T0323TS393_1-D2
PFRMAT TS
TARGET T0323
MODEL 1
PARENT N/A
ATOM     34  CA  PRO    34      24.500  22.591  -1.331  1.00 25.00           C
ATOM     35  CA  THR    35      26.896  25.523  -1.895  1.00 25.00           C
ATOM     36  CA  LYS    36      26.445  26.972  -5.377  1.00 25.00           C
ATOM     37  CA  PRO    37      23.382  29.281  -5.556  1.00 25.00           C
ATOM     38  CA  ASN    38      22.188  32.859  -6.146  1.00 25.00           C
ATOM     39  CA  PRO    39      19.404  35.364  -5.500  1.00 25.00           C
ATOM     40  CA  PHE    40      17.972  38.911  -5.305  1.00 25.00           C
ATOM     41  CA  GLN    41      15.244  37.975  -7.824  1.00 25.00           C
ATOM     42  CA  SER    42      14.382  34.859  -5.772  1.00 25.00           C
ATOM     43  CA  LEU    43      14.170  36.982  -2.592  1.00 25.00           C
ATOM     44  CA  VAL    44      11.864  39.466  -4.376  1.00 25.00           C
ATOM     45  CA  SER    45       9.638  36.585  -5.564  1.00 25.00           C
ATOM     46  CA  SER    46       9.476  35.206  -1.995  1.00 25.00           C
ATOM     47  CA  ILE    47       8.517  38.671  -0.673  1.00 25.00           C
ATOM     48  CA  VAL    48       5.772  38.951  -3.329  1.00 25.00           C
ATOM     49  CA  GLU    49       4.443  35.494  -2.355  1.00 25.00           C
ATOM     50  CA  GLN    50       4.409  36.520   1.335  1.00 25.00           C
ATOM     51  CA  GLN    51       2.510  39.726   0.453  1.00 25.00           C
ATOM     52  CA  LEU    52      -1.185  39.848   1.123  1.00 25.00           C
ATOM     53  CA  SER    53      -2.564  37.901  -1.792  1.00 25.00           C
ATOM     54  CA  ILE    54      -1.083  34.433  -2.302  1.00 25.00           C
ATOM     55  CA  LYS    55      -2.988  32.652  -5.107  1.00 25.00           C
ATOM     56  CA  ALA    56      -1.973  35.399  -7.574  1.00 25.00           C
ATOM     57  CA  ALA    57       1.683  35.062  -6.484  1.00 25.00           C
ATOM     58  CA  SER    58       1.502  31.266  -6.967  1.00 25.00           C
ATOM     59  CA  ALA    59       0.013  31.757 -10.462  1.00 25.00           C
ATOM     60  CA  ILE    60       2.815  34.217 -11.337  1.00 25.00           C
ATOM     61  CA  TYR    61       5.435  31.708 -10.111  1.00 25.00           C
ATOM     62  CA  GLY    62       3.827  28.954 -12.233  1.00 25.00           C
ATOM     63  CA  ARG    63       3.869  31.256 -15.294  1.00 25.00           C
ATOM     64  CA  VAL    64       7.566  32.045 -14.680  1.00 25.00           C
ATOM     65  CA  GLU    65       8.344  28.306 -14.404  1.00 25.00           C
ATOM     66  CA  GLN    66       6.480  27.650 -17.685  1.00 25.00           C
ATOM     67  CA  LEU    67       8.454  30.452 -19.394  1.00 25.00           C
ATOM     68  CA  VAL    68      11.735  28.969 -18.091  1.00 25.00           C
ATOM     69  CA  GLY    69      10.899  25.273 -18.431  1.00 25.00           C
ATOM     70  CA  GLY    70      14.013  24.808 -20.479  1.00 25.00           C
ATOM     71  CA  ALA    71      16.862  27.384 -20.668  1.00 25.00           C
ATOM     72  CA  LEU    72      17.257  31.144 -20.055  1.00 25.00           C
ATOM     73  CA  GLU    73      17.817  31.485 -23.847  1.00 25.00           C
ATOM     74  CA  LYS    74      14.428  32.893 -24.735  1.00 25.00           C
ATOM     75  CA  PRO    75      14.737  35.389 -21.806  1.00 25.00           C
ATOM     76  CA  GLU    76      13.071  38.356 -23.566  1.00 25.00           C
ATOM     77  CA  GLN    77       9.614  36.876 -22.842  1.00 25.00           C
ATOM     78  CA  LEU    78      10.556  36.414 -19.158  1.00 25.00           C
ATOM     79  CA  TYR    79      11.763  40.045 -18.987  1.00 25.00           C
ATOM     80  CA  ARG    80       8.478  41.236 -20.554  1.00 25.00           C
ATOM     81  CA  VAL    81       5.438  43.456 -19.815  1.00 25.00           C
ATOM     82  CA  SER    82       3.332  42.282 -22.684  1.00 25.00           C
ATOM     83  CA  ASP    83       2.591  38.698 -21.501  1.00 25.00           C
ATOM     84  CA  GLU    84      -0.636  36.917 -20.461  1.00 25.00           C
ATOM     85  CA  ALA    85       0.694  36.538 -16.890  1.00 25.00           C
ATOM     86  CA  LEU    86       1.587  40.261 -16.801  1.00 25.00           C
ATOM     87  CA  ARG    87      -1.926  41.159 -18.034  1.00 25.00           C
ATOM     88  CA  GLN    88      -3.471  38.935 -15.326  1.00 25.00           C
ATOM     89  CA  ALA    89      -1.180  39.859 -12.436  1.00 25.00           C
ATOM     90  CA  GLY    90      -0.881  43.460 -13.627  1.00 25.00           C
ATOM     91  CA  VAL    91      -2.248  44.383 -10.263  1.00 25.00           C
ATOM     92  CA  SER    92      -3.888  42.216  -7.628  1.00 25.00           C
ATOM     93  CA  LYS    93      -3.812  44.759  -4.765  1.00 25.00           C
ATOM     94  CA  ARG    94      -1.383  46.293  -2.231  1.00 25.00           C
ATOM     95  CA  LYS    95       0.787  43.140  -2.366  1.00 25.00           C
ATOM     96  CA  ILE    96       0.808  43.289  -6.192  1.00 25.00           C
ATOM     97  CA  GLU    97       1.833  46.977  -6.069  1.00 25.00           C
ATOM     98  CA  TYR    98       4.658  46.135  -3.625  1.00 25.00           C
ATOM     99  CA  ILE    99       5.855  43.326  -5.938  1.00 25.00           C
ATOM    100  CA  ARG   100       5.816  45.730  -8.918  1.00 25.00           C
ATOM    101  CA  HIS   101       7.835  48.291  -6.911  1.00 25.00           C
ATOM    102  CA  VAL   102      10.376  45.585  -5.967  1.00 25.00           C
ATOM    103  CA  CYS   103      10.676  44.551  -9.643  1.00 25.00           C
ATOM    104  CA  GLU   104      11.235  48.204 -10.649  1.00 25.00           C
ATOM    105  CA  HIS   105      13.943  48.556  -7.965  1.00 25.00           C
ATOM    106  CA  VAL   106      15.647  45.368  -9.230  1.00 25.00           C
ATOM    107  CA  GLU   107      15.550  46.710 -12.815  1.00 25.00           C
ATOM    108  CA  SER   108      16.103  50.465 -13.259  1.00 25.00           C
ATOM    109  CA  GLY   109      19.647  49.548 -14.487  1.00 25.00           C
ATOM    110  CA  ARG   110      20.436  45.871 -13.864  1.00 25.00           C
ATOM    111  CA  LEU   111      20.432  46.936 -10.210  1.00 25.00           C
ATOM    112  CA  ASP   112      24.156  46.881 -10.870  1.00 25.00           C
ATOM    113  CA  PHE   113      23.754  43.131 -10.270  1.00 25.00           C
ATOM    114  CA  THR   114      27.497  42.834 -11.028  1.00 25.00           C
ATOM    115  CA  GLU   115      28.279  45.392  -8.287  1.00 25.00           C
ATOM    116  CA  LEU   116      26.109  43.438  -5.809  1.00 25.00           C
ATOM    117  CA  GLU   117      27.924  40.196  -6.739  1.00 25.00           C
ATOM    118  CA  GLY   118      31.499  41.446  -6.607  1.00 25.00           C
ATOM    119  CA  ALA   119      30.449  42.539  -3.099  1.00 25.00           C
ATOM    120  CA  GLU   120      27.524  40.461  -1.698  1.00 25.00           C
ATOM    121  CA  ALA   121      25.896  43.533  -0.073  1.00 25.00           C
ATOM    122  CA  THR   122      25.675  47.313   0.507  1.00 25.00           C
ATOM    123  CA  THR   123      25.375  47.899  -3.265  1.00 25.00           C
ATOM    124  CA  VAL   124      22.593  45.277  -3.477  1.00 25.00           C
ATOM    125  CA  ILE   125      20.751  46.962  -0.573  1.00 25.00           C
ATOM    126  CA  GLU   126      21.066  50.359  -2.312  1.00 25.00           C
ATOM    127  CA  LYS   127      19.690  48.854  -5.555  1.00 25.00           C
ATOM    128  CA  LEU   128      16.745  47.340  -3.632  1.00 25.00           C
ATOM    129  CA  THR   129      16.036  50.731  -2.000  1.00 25.00           C
ATOM    130  CA  ALA   130      16.120  52.428  -5.432  1.00 25.00           C
ATOM    131  CA  ILE   131      12.334  52.875  -5.545  1.00 25.00           C
ATOM    132  CA  LYS   132       9.688  52.989  -8.330  1.00 25.00           C
ATOM    133  CA  GLY   133       6.510  53.460  -6.293  1.00 25.00           C
ATOM    134  CA  ILE   134       3.255  51.816  -5.185  1.00 25.00           C
ATOM    135  CA  GLY   135       3.135  50.703  -1.579  1.00 25.00           C
ATOM    136  CA  GLN   136       6.841  50.538  -2.205  1.00 25.00           C
ATOM    137  CA  TRP   137       7.096  49.738   1.531  1.00 25.00           C
ATOM    138  CA  THR   138       6.867  45.991   0.770  1.00 25.00           C
ATOM    139  CA  ALA   139       9.625  46.333  -1.865  1.00 25.00           C
ATOM    140  CA  GLU   140      11.829  48.202   0.648  1.00 25.00           C
ATOM    141  CA  MET   141      11.240  45.452   3.248  1.00 25.00           C
ATOM    142  CA  PHE   142      12.173  42.779   0.669  1.00 25.00           C
ATOM    143  CA  MET   143      15.372  44.698  -0.199  1.00 25.00           C
ATOM    144  CA  MET   144      16.261  44.946   3.518  1.00 25.00           C
ATOM    145  CA  PHE   145      15.686  41.182   3.931  1.00 25.00           C
ATOM    146  CA  SER   146      17.930  40.483   0.907  1.00 25.00           C
ATOM    147  CA  LEU   147      20.511  39.412   3.468  1.00 25.00           C
ATOM    148  CA  GLY   148      22.978  40.130   6.228  1.00 25.00           C
ATOM    149  CA  ARG   149      22.041  37.618   8.983  1.00 25.00           C
TER
END
