
#######################################################
#                                                     #
#                        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 T0323TS168_2-D2
# Molecule2: number of CA atoms  116 (  868),  selected  116 , name T0323_D2.pdb
# PARAMETERS: T0323TS168_2-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      T      35           -
LGA    K      36      K      36           -
LGA    P      37      P      37           #
LGA    N      38      N      38          3.527
LGA    P      39      P      39          1.405
LGA    F      40      F      40          2.135
LGA    Q      41      Q      41          1.889
LGA    S      42      S      42          1.896
LGA    L      43      L      43          3.145
LGA    V      44      V      44          2.562
LGA    S      45      S      45          0.278
LGA    S      46      S      46          3.336
LGA    I      47      I      47          4.160
LGA    V      48      V      48          2.119
LGA    E      49      E      49          2.306
LGA    Q      50      Q      50          4.739
LGA    Q      51      Q      51          3.000
LGA    L      52      L      52          2.555
LGA    S      53      S      53          3.513
LGA    I      54      I      54          3.959
LGA    K      55      K      55          3.220
LGA    A      56      A      56          3.371
LGA    A      57      A      57          2.121
LGA    S      58      S      58          1.329
LGA    A      59      A      59          1.621
LGA    I      60      I      60          1.886
LGA    Y      61      Y      61          1.411
LGA    G      62      G      62          1.174
LGA    R      63      R      63          1.400
LGA    V      64      V      64          2.129
LGA    E      65      E      65          2.115
LGA    Q      66      Q      66          2.244
LGA    L      67      L      67          2.899
LGA    V      68      V      68          3.177
LGA    G      69      G      69          2.944
LGA    G      70      G      70           #
LGA    A      71      A      71           -
LGA    -       -      L      72           -
LGA    -       -      E      73           -
LGA    -       -      K      74           -
LGA    -       -      P      75           -
LGA    L      72      E      76           #
LGA    E      73      Q      77           #
LGA    K      74      -       -           -
LGA    P      75      L      78          4.789
LGA    E      76      Y      79          4.949
LGA    Q      77      R      80          5.249
LGA    L      78      V      81          2.053
LGA    Y      79      -       -           -
LGA    R      80      S      82          2.664
LGA    V      81      D      83          1.412
LGA    S      82      E      84          2.866
LGA    D      83      -       -           -
LGA    E      84      A      85          5.417
LGA    A      85      L      86          3.848
LGA    L      86      R      87          0.905
LGA    R      87      Q      88          3.301
LGA    Q      88      A      89          2.396
LGA    A      89      G      90          1.352
LGA    G      90      -       -           -
LGA    V      91      -       -           -
LGA    S      92      -       -           -
LGA    K      93      -       -           -
LGA    R      94      -       -           -
LGA    K      95      V      91          3.913
LGA    I      96      S      92          3.691
LGA    E      97      K      93           #
LGA    -       -      R      94           -
LGA    Y      98      K      95          3.869
LGA    I      99      I      96          4.919
LGA    R     100      E      97          3.299
LGA    H     101      Y      98          2.779
LGA    -       -      I      99           -
LGA    -       -      R     100           -
LGA    V     102      H     101           #
LGA    C     103      V     102          1.929
LGA    E     104      -       -           -
LGA    H     105      -       -           -
LGA    V     106      C     103           #
LGA    E     107      -       -           -
LGA    S     108      -       -           -
LGA    G     109      E     104          3.789
LGA    R     110      H     105          2.652
LGA    L     111      V     106          3.468
LGA    -       -      E     107           -
LGA    -       -      S     108           -
LGA    -       -      G     109           -
LGA    D     112      R     110          3.868
LGA    F     113      L     111          3.237
LGA    T     114      D     112          3.696
LGA    E     115      F     113          2.981
LGA    L     116      T     114           #
LGA    E     117      -       -           -
LGA    G     118      E     115          2.035
LGA    A     119      L     116          3.157
LGA    E     120      E     117          4.429
LGA    -       -      G     118           -
LGA    A     121      A     119          3.259
LGA    T     122      E     120          3.378
LGA    -       -      A     121           -
LGA    -       -      T     122           -
LGA    T     123      T     123          2.915
LGA    V     124      V     124          1.446
LGA    I     125      I     125          1.529
LGA    E     126      E     126          1.239
LGA    K     127      K     127          0.772
LGA    L     128      L     128          1.704
LGA    T     129      T     129          2.316
LGA    A     130      A     130          1.023
LGA    I     131      I     131          2.922
LGA    K     132      K     132          3.566
LGA    G     133      -       -           -
LGA    I     134      -       -           -
LGA    G     135      G     133          3.255
LGA    Q     136      -       -           -
LGA    W     137      -       -           -
LGA    T     138      -       -           -
LGA    A     139      I     134          2.126
LGA    E     140      G     135          2.452
LGA    M     141      -       -           -
LGA    F     142      Q     136           #
LGA    M     143      W     137          4.086
LGA    M     144      T     138          3.999
LGA    -       -      A     139           -
LGA    F     145      E     140          2.083
LGA    -       -      M     141           -
LGA    -       -      F     142           -
LGA    S     146      M     143          4.804
LGA    L     147      M     144           #
LGA    G     148      F     145           -
LGA    -       -      S     146           -
LGA    -       -      L     147           -
LGA    -       -      G     148           -
LGA    R     149      R     149           #

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  116  116    5.0     81    3.03    56.79     40.263     2.591

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.701683 * X  +   0.448434 * Y  +   0.553667 * Z  +   9.366488
  Y_new =   0.537294 * X  +  -0.177313 * Y  +   0.824545 * Z  +  37.936726
  Z_new =   0.467927 * X  +   0.876052 * Y  +  -0.116524 * Z  +   1.566022 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.703030   -1.438563  [ DEG:    97.5764    -82.4236 ]
  Theta =  -0.486943   -2.654649  [ DEG:   -27.8998   -152.1002 ]
  Phi   =   2.488105   -0.653487  [ DEG:   142.5579    -37.4421 ]
 
# 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: T0323TS168_2-D2                               
REMARK     2: T0323_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0323TS168_2-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   81   3.03   56.79  40.263
REMARK  ---------------------------------------------------------- 
MOLECULE T0323TS168_2-D2
PFRMAT TS
TARGET T0323
MODEL 2
PARENT N/A
ATOM     34  CA  PRO    34      29.049  27.905  -5.425  1.00 25.00           C
ATOM     35  CA  THR    35      26.057  28.430  -7.805  1.00 25.00           C
ATOM     36  CA  LYS    36      25.892  31.684  -9.843  1.00 25.00           C
ATOM     37  CA  PRO    37      22.574  32.729 -11.454  1.00 25.00           C
ATOM     38  CA  ASN    38      20.050  35.264 -10.224  1.00 25.00           C
ATOM     39  CA  PRO    39      17.526  35.996  -7.465  1.00 25.00           C
ATOM     40  CA  PHE    40      15.600  39.297  -7.229  1.00 25.00           C
ATOM     41  CA  GLN    41      12.433  37.569  -8.514  1.00 25.00           C
ATOM     42  CA  SER    42      12.869  34.786  -5.919  1.00 25.00           C
ATOM     43  CA  LEU    43      13.295  37.400  -3.153  1.00 25.00           C
ATOM     44  CA  VAL    44      10.121  39.194  -4.324  1.00 25.00           C
ATOM     45  CA  SER    45       8.207  35.876  -4.301  1.00 25.00           C
ATOM     46  CA  SER    46       9.456  35.154  -0.753  1.00 25.00           C
ATOM     47  CA  ILE    47       8.346  38.641   0.375  1.00 25.00           C
ATOM     48  CA  VAL    48       4.893  38.071  -1.181  1.00 25.00           C
ATOM     49  CA  GLU    49       4.613  34.701   0.615  1.00 25.00           C
ATOM     50  CA  GLN    50       5.572  36.360   3.931  1.00 25.00           C
ATOM     51  CA  GLN    51       2.930  39.074   3.366  1.00 25.00           C
ATOM     52  CA  LEU    52      -0.864  38.861   3.833  1.00 25.00           C
ATOM     53  CA  SER    53      -2.062  35.380   4.772  1.00 25.00           C
ATOM     54  CA  ILE    54       0.010  33.035   2.545  1.00 25.00           C
ATOM     55  CA  LYS    55      -2.207  30.392   0.882  1.00 25.00           C
ATOM     56  CA  ALA    56      -3.394  32.970  -1.690  1.00 25.00           C
ATOM     57  CA  ALA    57       0.236  33.949  -2.421  1.00 25.00           C
ATOM     58  CA  SER    58       1.163  30.261  -2.881  1.00 25.00           C
ATOM     59  CA  ALA    59      -1.789  29.794  -5.278  1.00 25.00           C
ATOM     60  CA  ILE    60      -0.690  32.874  -7.271  1.00 25.00           C
ATOM     61  CA  TYR    61       2.880  31.502  -7.470  1.00 25.00           C
ATOM     62  CA  GLY    62       1.542  28.128  -8.694  1.00 25.00           C
ATOM     63  CA  ARG    63      -0.563  29.902 -11.357  1.00 25.00           C
ATOM     64  CA  VAL    64       2.506  31.889 -12.495  1.00 25.00           C
ATOM     65  CA  GLU    65       4.547  28.656 -12.723  1.00 25.00           C
ATOM     66  CA  GLN    66       1.769  27.022 -14.793  1.00 25.00           C
ATOM     67  CA  LEU    67       1.695  30.053 -17.132  1.00 25.00           C
ATOM     68  CA  VAL    68       5.499  29.865 -17.538  1.00 25.00           C
ATOM     69  CA  GLY    69       5.076  26.445 -19.181  1.00 25.00           C
ATOM     70  CA  GLY    70       7.528  27.879 -21.707  1.00 25.00           C
ATOM     71  CA  ALA    71       7.368  30.805 -24.057  1.00 25.00           C
ATOM     72  CA  LEU    72       7.645  34.103 -22.258  1.00 25.00           C
ATOM     73  CA  GLU    73       5.705  35.765 -25.079  1.00 25.00           C
ATOM     74  CA  LYS    74       2.258  35.643 -23.470  1.00 25.00           C
ATOM     75  CA  PRO    75       3.709  37.359 -20.461  1.00 25.00           C
ATOM     76  CA  GLU    76       1.768  40.354 -21.851  1.00 25.00           C
ATOM     77  CA  GLN    77      -1.128  39.620 -19.454  1.00 25.00           C
ATOM     78  CA  LEU    78       1.321  39.425 -16.516  1.00 25.00           C
ATOM     79  CA  TYR    79       2.867  42.772 -17.551  1.00 25.00           C
ATOM     80  CA  ARG    80      -0.617  44.350 -17.749  1.00 25.00           C
ATOM     81  CA  VAL    81      -3.452  42.963 -15.551  1.00 25.00           C
ATOM     82  CA  SER    82      -6.884  43.706 -17.080  1.00 25.00           C
ATOM     83  CA  ASP    83      -7.938  43.723 -13.379  1.00 25.00           C
ATOM     84  CA  GLU    84      -9.341  40.169 -13.633  1.00 25.00           C
ATOM     85  CA  ALA    85      -5.788  38.756 -13.857  1.00 25.00           C
ATOM     86  CA  LEU    86      -4.762  40.780 -10.772  1.00 25.00           C
ATOM     87  CA  ARG    87      -7.815  39.469  -8.867  1.00 25.00           C
ATOM     88  CA  GLN    88      -6.924  35.880  -9.861  1.00 25.00           C
ATOM     89  CA  ALA    89      -5.685  35.720  -6.298  1.00 25.00           C
ATOM     90  CA  GLY    90      -8.560  37.014  -4.072  1.00 25.00           C
ATOM     91  CA  VAL    91      -7.358  38.443  -0.722  1.00 25.00           C
ATOM     92  CA  SER    92      -6.363  42.054  -0.574  1.00 25.00           C
ATOM     93  CA  LYS    93      -4.387  41.155  -3.750  1.00 25.00           C
ATOM     94  CA  ARG    94      -1.584  40.658  -1.188  1.00 25.00           C
ATOM     95  CA  LYS    95       0.510  38.801  -3.803  1.00 25.00           C
ATOM     96  CA  ILE    96      -0.055  41.642  -6.309  1.00 25.00           C
ATOM     97  CA  GLU    97       1.010  44.210  -3.676  1.00 25.00           C
ATOM     98  CA  TYR    98       4.171  42.177  -2.936  1.00 25.00           C
ATOM     99  CA  ILE    99       4.970  42.013  -6.679  1.00 25.00           C
ATOM    100  CA  ARG   100       4.496  45.802  -6.970  1.00 25.00           C
ATOM    101  CA  HIS   101       6.825  46.349  -3.980  1.00 25.00           C
ATOM    102  CA  VAL   102       9.454  44.069  -5.579  1.00 25.00           C
ATOM    103  CA  CYS   103       9.176  46.012  -8.866  1.00 25.00           C
ATOM    104  CA  GLU   104       9.607  49.316  -6.978  1.00 25.00           C
ATOM    105  CA  HIS   105      12.699  47.923  -5.198  1.00 25.00           C
ATOM    106  CA  VAL   106      14.159  46.802  -8.557  1.00 25.00           C
ATOM    107  CA  GLU   107      13.524  50.283 -10.022  1.00 25.00           C
ATOM    108  CA  SER   108      11.984  52.839 -12.379  1.00 25.00           C
ATOM    109  CA  GLY   109      14.172  51.061 -14.933  1.00 25.00           C
ATOM    110  CA  ARG   110      15.637  47.766 -13.920  1.00 25.00           C
ATOM    111  CA  LEU   111      17.870  47.542 -10.870  1.00 25.00           C
ATOM    112  CA  ASP   112      20.505  48.534  -8.273  1.00 25.00           C
ATOM    113  CA  PHE   113      20.620  44.753  -7.723  1.00 25.00           C
ATOM    114  CA  THR   114      23.871  42.761  -8.086  1.00 25.00           C
ATOM    115  CA  GLU   115      22.412  40.881 -11.087  1.00 25.00           C
ATOM    116  CA  LEU   116      21.370  44.199 -12.690  1.00 25.00           C
ATOM    117  CA  GLU   117      24.893  45.600 -12.141  1.00 25.00           C
ATOM    118  CA  GLY   118      28.020  46.023  -9.915  1.00 25.00           C
ATOM    119  CA  ALA   119      26.087  47.060  -6.798  1.00 25.00           C
ATOM    120  CA  GLU   120      27.231  45.557  -3.494  1.00 25.00           C
ATOM    121  CA  ALA   121      26.728  45.686   0.254  1.00 25.00           C
ATOM    122  CA  THR   122      26.202  49.460   0.643  1.00 25.00           C
ATOM    123  CA  THR   123      24.887  49.672  -2.947  1.00 25.00           C
ATOM    124  CA  VAL   124      22.482  46.771  -2.264  1.00 25.00           C
ATOM    125  CA  ILE   125      21.245  48.511   0.915  1.00 25.00           C
ATOM    126  CA  GLU   126      20.692  51.753  -1.047  1.00 25.00           C
ATOM    127  CA  LYS   127      18.733  49.832  -3.718  1.00 25.00           C
ATOM    128  CA  LEU   128      16.580  48.202  -1.003  1.00 25.00           C
ATOM    129  CA  THR   129      15.899  51.635   0.552  1.00 25.00           C
ATOM    130  CA  ALA   130      14.902  53.018  -2.878  1.00 25.00           C
ATOM    131  CA  ILE   131      11.155  52.371  -3.223  1.00 25.00           C
ATOM    132  CA  LYS   132       8.415  53.990  -5.282  1.00 25.00           C
ATOM    133  CA  GLY   133       5.323  52.052  -6.410  1.00 25.00           C
ATOM    134  CA  ILE   134       2.988  50.145  -4.013  1.00 25.00           C
ATOM    135  CA  GLY   135       6.013  51.126  -1.864  1.00 25.00           C
ATOM    136  CA  GLN   136       4.241  50.155   1.371  1.00 25.00           C
ATOM    137  CA  TRP   137       4.280  47.038   3.596  1.00 25.00           C
ATOM    138  CA  THR   138       6.223  45.117   0.913  1.00 25.00           C
ATOM    139  CA  ALA   139       8.748  47.985   0.653  1.00 25.00           C
ATOM    140  CA  GLU   140       9.167  47.994   4.460  1.00 25.00           C
ATOM    141  CA  MET   141       9.735  44.206   4.430  1.00 25.00           C
ATOM    142  CA  PHE   142      12.358  44.596   1.667  1.00 25.00           C
ATOM    143  CA  MET   143      14.117  47.332   3.689  1.00 25.00           C
ATOM    144  CA  MET   144      14.123  45.076   6.782  1.00 25.00           C
ATOM    145  CA  PHE   145      15.601  42.208   4.720  1.00 25.00           C
ATOM    146  CA  SER   146      18.321  44.544   3.374  1.00 25.00           C
ATOM    147  CA  LEU   147      19.435  44.505   7.052  1.00 25.00           C
ATOM    148  CA  GLY   148      23.028  45.244   8.058  1.00 25.00           C
ATOM    149  CA  ARG   149      23.608  41.786   6.567  1.00 25.00           C
TER
END
