
#######################################################
#                                                     #
#                        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_3-D2
# Molecule2: number of CA atoms  116 (  868),  selected  116 , name T0323_D2.pdb
# PARAMETERS: T0323TS168_3-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      -       -           -
LGA    N      38      T      35          4.556
LGA    P      39      K      36           #
LGA    -       -      P      37           -
LGA    -       -      N      38           -
LGA    -       -      P      39           -
LGA    -       -      F      40           -
LGA    F      40      Q      41           #
LGA    Q      41      S      42          1.105
LGA    S      42      -       -           -
LGA    L      43      L      43          4.886
LGA    V      44      V      44          4.019
LGA    S      45      S      45          2.873
LGA    S      46      S      46          3.504
LGA    I      47      I      47          3.232
LGA    V      48      V      48          1.969
LGA    E      49      E      49          1.662
LGA    Q      50      Q      50          1.694
LGA    Q      51      Q      51          3.686
LGA    L      52      L      52          2.570
LGA    S      53      S      53          3.432
LGA    I      54      I      54          2.456
LGA    K      55      K      55          2.217
LGA    A      56      A      56          2.796
LGA    A      57      A      57          1.717
LGA    S      58      S      58          1.526
LGA    A      59      A      59          2.349
LGA    I      60      I      60          2.424
LGA    Y      61      Y      61          2.062
LGA    G      62      G      62          2.207
LGA    R      63      R      63          2.356
LGA    V      64      V      64          2.401
LGA    E      65      E      65          2.325
LGA    Q      66      Q      66          2.579
LGA    L      67      L      67          2.708
LGA    V      68      V      68          2.537
LGA    G      69      G      69          4.634
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      L      78           #
LGA    P      75      Y      79          1.444
LGA    E      76      R      80          3.810
LGA    Q      77      V      81          2.848
LGA    L      78      S      82          4.305
LGA    Y      79      -       -           -
LGA    R      80      -       -           -
LGA    V      81      D      83          1.540
LGA    S      82      -       -           -
LGA    D      83      -       -           -
LGA    E      84      E      84          3.364
LGA    A      85      A      85          3.345
LGA    L      86      L      86          4.630
LGA    R      87      R      87          3.404
LGA    Q      88      Q      88          1.605
LGA    A      89      A      89          3.799
LGA    G      90      G      90          2.818
LGA    V      91      V      91          4.246
LGA    S      92      -       -           -
LGA    K      93      -       -           -
LGA    R      94      -       -           -
LGA    K      95      -       -           -
LGA    I      96      S      92          4.841
LGA    E      97      K      93          2.903
LGA    Y      98      R      94          1.584
LGA    I      99      K      95          3.267
LGA    R     100      I      96          4.375
LGA    H     101      E      97          3.074
LGA    V     102      Y      98          1.522
LGA    C     103      I      99          3.886
LGA    E     104      R     100          5.012
LGA    H     105      H     101          3.626
LGA    V     106      V     102          2.987
LGA    E     107      C     103           #
LGA    -       -      E     104           -
LGA    -       -      H     105           -
LGA    S     108      V     106          4.261
LGA    G     109      E     107          2.956
LGA    R     110      S     108           -
LGA    L     111      G     109           -
LGA    -       -      R     110           -
LGA    -       -      L     111           -
LGA    D     112      D     112           #
LGA    F     113      F     113          2.649
LGA    T     114      T     114          1.026
LGA    E     115      E     115          3.816
LGA    L     116      L     116          2.866
LGA    E     117      E     117          1.117
LGA    G     118      G     118          3.486
LGA    A     119      A     119          2.628
LGA    -       -      E     120           -
LGA    E     120      A     121          3.961
LGA    A     121      T     122          4.098
LGA    T     122      T     123          1.741
LGA    T     123      V     124          2.869
LGA    V     124      I     125          4.014
LGA    I     125      E     126          2.553
LGA    E     126      K     127          1.791
LGA    K     127      L     128          3.610
LGA    L     128      T     129          3.645
LGA    T     129      A     130          1.895
LGA    A     130      I     131          4.636
LGA    I     131      K     132          4.595
LGA    K     132      -       -           -
LGA    G     133      -       -           -
LGA    I     134      -       -           -
LGA    G     135      G     133          3.636
LGA    Q     136      -       -           -
LGA    W     137      -       -           -
LGA    T     138      I     134          2.030
LGA    A     139      G     135          2.346
LGA    E     140      Q     136          4.241
LGA    M     141      W     137          4.811
LGA    F     142      T     138          2.338
LGA    M     143      A     139          3.371
LGA    M     144      E     140          4.423
LGA    F     145      M     141          0.692
LGA    -       -      F     142           -
LGA    S     146      M     143          4.432
LGA    L     147      M     144           -
LGA    G     148      F     145           -
LGA    R     149      S     146           -
LGA    -       -      L     147           -
LGA    -       -      G     148           -
LGA    -       -      R     149           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  116  116    5.0     84    3.20    54.76     40.521     2.545

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.010985 * X  +  -0.913768 * Y  +   0.406088 * Z  +   8.075233
  Y_new =  -0.136926 * X  +   0.403661 * Y  +   0.904604 * Z  +  40.918598
  Z_new =  -0.990520 * X  +  -0.045667 * Y  +  -0.129553 * Z  +   1.803730 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.802697    0.338895  [ DEG:  -160.5827     19.4173 ]
  Theta =   1.432995    1.708598  [ DEG:    82.1046     97.8954 ]
  Phi   =  -1.650852    1.490740  [ DEG:   -94.5869     85.4131 ]
 
# 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_3-D2                               
REMARK     2: T0323_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0323TS168_3-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   84   3.20   54.76  40.521
REMARK  ---------------------------------------------------------- 
MOLECULE T0323TS168_3-D2
PFRMAT TS
TARGET T0323
MODEL 3
PARENT N/A
ATOM     34  CA  PRO    34      29.630  32.810  10.123  1.00 25.00           C
ATOM     35  CA  THR    35      28.946  32.073   6.453  1.00 25.00           C
ATOM     36  CA  LYS    36      27.873  33.433   3.065  1.00 25.00           C
ATOM     37  CA  PRO    37      24.939  33.495   0.721  1.00 25.00           C
ATOM     38  CA  ASN    38      21.974  34.605  -1.463  1.00 25.00           C
ATOM     39  CA  PRO    39      18.590  36.398  -1.432  1.00 25.00           C
ATOM     40  CA  PHE    40      16.547  38.729  -3.681  1.00 25.00           C
ATOM     41  CA  GLN    41      14.135  35.868  -4.497  1.00 25.00           C
ATOM     42  CA  SER    42      13.753  35.093  -0.765  1.00 25.00           C
ATOM     43  CA  LEU    43      13.036  38.786  -0.047  1.00 25.00           C
ATOM     44  CA  VAL    44      10.404  38.841  -2.829  1.00 25.00           C
ATOM     45  CA  SER    45       8.773  35.693  -1.383  1.00 25.00           C
ATOM     46  CA  SER    46       8.709  37.295   2.096  1.00 25.00           C
ATOM     47  CA  ILE    47       7.100  40.449   0.640  1.00 25.00           C
ATOM     48  CA  VAL    48       4.461  38.315  -1.134  1.00 25.00           C
ATOM     49  CA  GLU    49       3.724  36.464   2.137  1.00 25.00           C
ATOM     50  CA  GLN    50       3.357  39.805   3.974  1.00 25.00           C
ATOM     51  CA  GLN    51       0.958  41.058   1.264  1.00 25.00           C
ATOM     52  CA  LEU    52      -1.115  37.886   1.925  1.00 25.00           C
ATOM     53  CA  SER    53      -1.755  34.333   3.031  1.00 25.00           C
ATOM     54  CA  ILE    54       1.336  32.081   2.506  1.00 25.00           C
ATOM     55  CA  LYS    55      -0.435  29.373   0.457  1.00 25.00           C
ATOM     56  CA  ALA    56      -2.080  32.059  -1.719  1.00 25.00           C
ATOM     57  CA  ALA    57       1.321  33.731  -2.270  1.00 25.00           C
ATOM     58  CA  SER    58       2.846  30.359  -3.258  1.00 25.00           C
ATOM     59  CA  ALA    59      -0.025  29.754  -5.720  1.00 25.00           C
ATOM     60  CA  ILE    60       0.507  33.232  -7.233  1.00 25.00           C
ATOM     61  CA  TYR    61       4.254  32.524  -7.602  1.00 25.00           C
ATOM     62  CA  GLY    62       3.480  29.188  -9.316  1.00 25.00           C
ATOM     63  CA  ARG    63       1.063  30.950 -11.708  1.00 25.00           C
ATOM     64  CA  VAL    64       3.736  33.570 -12.519  1.00 25.00           C
ATOM     65  CA  GLU    65       6.285  30.794 -13.201  1.00 25.00           C
ATOM     66  CA  GLN    66       3.786  29.033 -15.510  1.00 25.00           C
ATOM     67  CA  LEU    67       3.166  32.316 -17.381  1.00 25.00           C
ATOM     68  CA  VAL    68       6.939  32.832 -17.779  1.00 25.00           C
ATOM     69  CA  GLY    69       8.915  29.950 -19.362  1.00 25.00           C
ATOM     70  CA  GLY    70       7.193  29.672 -22.680  1.00 25.00           C
ATOM     71  CA  ALA    71       7.423  32.669 -25.080  1.00 25.00           C
ATOM     72  CA  LEU    72       6.546  35.430 -22.617  1.00 25.00           C
ATOM     73  CA  GLU    73       6.449  37.964 -25.454  1.00 25.00           C
ATOM     74  CA  LYS    74       8.264  40.778 -23.774  1.00 25.00           C
ATOM     75  CA  PRO    75       6.737  40.898 -20.311  1.00 25.00           C
ATOM     76  CA  GLU    76       4.107  43.222 -21.842  1.00 25.00           C
ATOM     77  CA  GLN    77       1.336  40.762 -20.878  1.00 25.00           C
ATOM     78  CA  LEU    78       2.691  40.601 -17.300  1.00 25.00           C
ATOM     79  CA  TYR    79       2.754  44.426 -17.125  1.00 25.00           C
ATOM     80  CA  ARG    80      -0.862  44.567 -18.381  1.00 25.00           C
ATOM     81  CA  VAL    81      -2.209  44.899 -14.811  1.00 25.00           C
ATOM     82  CA  SER    82      -5.291  46.888 -15.883  1.00 25.00           C
ATOM     83  CA  ASP    83      -6.577  46.214 -12.306  1.00 25.00           C
ATOM     84  CA  GLU    84      -8.635  43.117 -13.224  1.00 25.00           C
ATOM     85  CA  ALA    85      -5.452  40.989 -13.283  1.00 25.00           C
ATOM     86  CA  LEU    86      -4.452  42.346  -9.845  1.00 25.00           C
ATOM     87  CA  ARG    87      -7.934  41.524  -8.480  1.00 25.00           C
ATOM     88  CA  GLN    88      -7.677  37.974  -9.893  1.00 25.00           C
ATOM     89  CA  ALA    89      -4.822  37.937  -7.367  1.00 25.00           C
ATOM     90  CA  GLY    90      -6.089  36.858  -3.945  1.00 25.00           C
ATOM     91  CA  VAL    91      -3.504  39.255  -2.573  1.00 25.00           C
ATOM     92  CA  SER    92      -6.261  41.811  -1.908  1.00 25.00           C
ATOM     93  CA  LYS    93      -6.786  45.274  -0.461  1.00 25.00           C
ATOM     94  CA  ARG    94      -5.107  48.314  -2.075  1.00 25.00           C
ATOM     95  CA  LYS    95      -2.074  47.892   0.224  1.00 25.00           C
ATOM     96  CA  ILE    96      -1.857  44.182  -0.702  1.00 25.00           C
ATOM     97  CA  GLU    97      -2.017  45.076  -4.422  1.00 25.00           C
ATOM     98  CA  TYR    98       0.771  47.659  -3.945  1.00 25.00           C
ATOM     99  CA  ILE    99       2.911  45.051  -2.133  1.00 25.00           C
ATOM    100  CA  ARG   100       2.329  42.557  -4.981  1.00 25.00           C
ATOM    101  CA  HIS   101       3.340  45.215  -7.546  1.00 25.00           C
ATOM    102  CA  VAL   102       6.519  45.969  -5.549  1.00 25.00           C
ATOM    103  CA  CYS   103       7.354  42.233  -5.419  1.00 25.00           C
ATOM    104  CA  GLU   104       6.833  41.960  -9.204  1.00 25.00           C
ATOM    105  CA  HIS   105       9.129  44.974  -9.761  1.00 25.00           C
ATOM    106  CA  VAL   106      11.801  43.384  -7.525  1.00 25.00           C
ATOM    107  CA  GLU   107      11.526  40.105  -9.486  1.00 25.00           C
ATOM    108  CA  SER   108      13.661  41.804 -12.161  1.00 25.00           C
ATOM    109  CA  GLY   109      15.720  44.532 -13.936  1.00 25.00           C
ATOM    110  CA  ARG   110      18.721  43.615 -11.726  1.00 25.00           C
ATOM    111  CA  LEU   111      17.042  43.548  -8.302  1.00 25.00           C
ATOM    112  CA  ASP   112      19.329  40.562  -7.513  1.00 25.00           C
ATOM    113  CA  PHE   113      22.747  39.324  -8.636  1.00 25.00           C
ATOM    114  CA  THR   114      25.617  41.580  -9.792  1.00 25.00           C
ATOM    115  CA  GLU   115      23.867  44.629  -8.273  1.00 25.00           C
ATOM    116  CA  LEU   116      23.396  42.744  -4.973  1.00 25.00           C
ATOM    117  CA  GLU   117      27.102  41.780  -4.966  1.00 25.00           C
ATOM    118  CA  GLY   118      27.983  45.478  -4.691  1.00 25.00           C
ATOM    119  CA  ALA   119      26.328  46.313  -1.402  1.00 25.00           C
ATOM    120  CA  GLU   120      23.929  44.152   0.531  1.00 25.00           C
ATOM    121  CA  ALA   121      22.340  47.400   1.669  1.00 25.00           C
ATOM    122  CA  THR   122      22.822  50.361  -0.713  1.00 25.00           C
ATOM    123  CA  THR   123      22.202  48.073  -3.721  1.00 25.00           C
ATOM    124  CA  VAL   124      19.013  46.734  -2.076  1.00 25.00           C
ATOM    125  CA  ILE   125      17.818  50.314  -1.421  1.00 25.00           C
ATOM    126  CA  GLU   126      18.500  51.236  -5.075  1.00 25.00           C
ATOM    127  CA  LYS   127      16.535  48.163  -6.243  1.00 25.00           C
ATOM    128  CA  LEU   128      13.613  49.134  -3.966  1.00 25.00           C
ATOM    129  CA  THR   129      13.671  52.697  -5.369  1.00 25.00           C
ATOM    130  CA  ALA   130      13.650  51.315  -8.942  1.00 25.00           C
ATOM    131  CA  ILE   131      10.342  49.889  -7.827  1.00 25.00           C
ATOM    132  CA  LYS   132       7.565  52.263  -9.023  1.00 25.00           C
ATOM    133  CA  GLY   133       4.346  50.491  -7.914  1.00 25.00           C
ATOM    134  CA  ILE   134       5.056  50.490  -4.176  1.00 25.00           C
ATOM    135  CA  GLY   135       8.676  50.859  -2.976  1.00 25.00           C
ATOM    136  CA  GLN   136       7.307  51.298   0.553  1.00 25.00           C
ATOM    137  CA  TRP   137       6.086  47.799   1.522  1.00 25.00           C
ATOM    138  CA  THR   138       8.728  46.219  -0.757  1.00 25.00           C
ATOM    139  CA  ALA   139      11.442  48.405   0.834  1.00 25.00           C
ATOM    140  CA  GLU   140      10.267  47.364   4.327  1.00 25.00           C
ATOM    141  CA  MET   141      10.370  43.679   3.292  1.00 25.00           C
ATOM    142  CA  PHE   142      13.919  44.137   1.926  1.00 25.00           C
ATOM    143  CA  MET   143      14.992  45.802   5.204  1.00 25.00           C
ATOM    144  CA  MET   144      13.480  42.904   7.199  1.00 25.00           C
ATOM    145  CA  PHE   145      15.342  40.384   4.996  1.00 25.00           C
ATOM    146  CA  SER   146      18.617  42.296   5.534  1.00 25.00           C
ATOM    147  CA  LEU   147      19.562  45.429   7.417  1.00 25.00           C
ATOM    148  CA  GLY   148      22.268  47.894   8.622  1.00 25.00           C
ATOM    149  CA  ARG   149      21.287  47.353  12.251  1.00 25.00           C
TER
END
