
#######################################################
#                                                     #
#                        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_4-D2
# Molecule2: number of CA atoms  116 (  868),  selected  116 , name T0323_D2.pdb
# PARAMETERS: T0323TS168_4-D2.T0323_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    P      34      -       -           -
LGA    T      35      -       -           -
LGA    K      36      -       -           -
LGA    P      37      -       -           -
LGA    N      38      P      34           #
LGA    -       -      T      35           -
LGA    P      39      K      36          2.661
LGA    F      40      P      37           #
LGA    Q      41      N      38           -
LGA    S      42      P      39           -
LGA    -       -      F      40           -
LGA    -       -      Q      41           -
LGA    -       -      S      42           -
LGA    -       -      L      43           -
LGA    L      43      V      44           #
LGA    V      44      S      45          1.830
LGA    S      45      -       -           -
LGA    S      46      S      46          4.645
LGA    I      47      I      47          3.566
LGA    V      48      V      48          3.542
LGA    E      49      E      49          3.633
LGA    Q      50      Q      50          2.115
LGA    Q      51      Q      51          3.091
LGA    L      52      L      52          2.169
LGA    S      53      S      53          3.065
LGA    I      54      I      54          1.645
LGA    K      55      K      55          1.933
LGA    A      56      A      56          2.366
LGA    A      57      A      57          1.612
LGA    S      58      S      58          1.478
LGA    A      59      A      59          1.908
LGA    I      60      I      60          2.079
LGA    Y      61      Y      61          2.180
LGA    G      62      G      62          1.907
LGA    R      63      R      63          1.630
LGA    V      64      V      64          2.057
LGA    E      65      E      65          2.014
LGA    Q      66      Q      66          1.753
LGA    L      67      L      67          1.957
LGA    V      68      V      68          1.998
LGA    G      69      G      69          2.577
LGA    G      70      G      70           -
LGA    A      71      A      71           -
LGA    L      72      L      72           -
LGA    E      73      E      73           -
LGA    K      74      K      74           -
LGA    -       -      P      75           -
LGA    -       -      E      76           -
LGA    -       -      Q      77           -
LGA    -       -      L      78           -
LGA    P      75      Y      79          6.460
LGA    E      76      R      80          2.180
LGA    Q      77      V      81          2.217
LGA    L      78      S      82          5.189
LGA    Y      79      -       -           -
LGA    R      80      D      83          3.992
LGA    V      81      -       -           -
LGA    S      82      -       -           -
LGA    D      83      E      84          4.071
LGA    E      84      A      85          4.701
LGA    A      85      L      86          1.170
LGA    L      86      R      87          4.016
LGA    R      87      Q      88           #
LGA    Q      88      A      89          3.989
LGA    A      89      G      90          3.547
LGA    G      90      V      91          4.571
LGA    V      91      S      92          3.782
LGA    S      92      K      93          3.075
LGA    K      93      R      94          1.899
LGA    R      94      -       -           -
LGA    K      95      -       -           -
LGA    I      96      K      95          1.521
LGA    E      97      I      96           -
LGA    Y      98      E      97           -
LGA    I      99      Y      98           -
LGA    R     100      I      99          3.183
LGA    H     101      R     100           -
LGA    V     102      H     101           -
LGA    C     103      V     102           #
LGA    E     104      -       -           -
LGA    H     105      -       -           -
LGA    V     106      -       -           -
LGA    E     107      -       -           -
LGA    S     108      -       -           -
LGA    G     109      -       -           -
LGA    R     110      -       -           -
LGA    L     111      C     103          4.732
LGA    D     112      E     104           #
LGA    F     113      H     105          4.334
LGA    -       -      V     106           -
LGA    T     114      E     107          1.559
LGA    E     115      S     108          1.942
LGA    L     116      G     109          2.698
LGA    -       -      R     110           -
LGA    E     117      L     111           #
LGA    G     118      -       -           -
LGA    A     119      D     112          3.595
LGA    E     120      F     113          2.517
LGA    A     121      T     114          4.093
LGA    -       -      E     115           -
LGA    T     122      L     116          3.284
LGA    T     123      E     117           -
LGA    V     124      G     118           -
LGA    -       -      A     119           -
LGA    -       -      E     120           -
LGA    -       -      A     121           -
LGA    -       -      T     122           -
LGA    -       -      T     123           -
LGA    I     125      V     124          3.263
LGA    E     126      I     125           #
LGA    -       -      E     126           -
LGA    K     127      K     127          3.485
LGA    L     128      L     128          1.270
LGA    T     129      T     129          2.719
LGA    A     130      A     130          1.403
LGA    I     131      I     131          2.032
LGA    K     132      K     132          2.389
LGA    G     133      G     133          2.940
LGA    I     134      I     134          2.801
LGA    G     135      G     135          3.931
LGA    Q     136      Q     136          3.315
LGA    W     137      -       -           -
LGA    T     138      -       -           -
LGA    A     139      -       -           -
LGA    E     140      W     137          0.782
LGA    M     141      T     138          2.290
LGA    F     142      A     139          3.755
LGA    M     143      E     140          2.548
LGA    M     144      M     141          2.162
LGA    -       -      F     142           -
LGA    -       -      M     143           -
LGA    -       -      M     144           -
LGA    F     145      F     145          5.119
LGA    S     146      S     146          3.240
LGA    -       -      L     147           -
LGA    L     147      G     148           #
LGA    G     148      R     149           -
LGA    R     149      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  116  116    5.0     70    3.06    52.86     35.057     2.215

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.270711 * X  +   0.614122 * Y  +   0.741330 * Z  +  16.531429
  Y_new =  -0.199665 * X  +  -0.789157 * Y  +   0.580832 * Z  +  34.996529
  Z_new =   0.941727 * X  +   0.009220 * Y  +   0.336252 * Z  +  -4.594129 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.027413   -3.114180  [ DEG:     1.5707   -178.4294 ]
  Theta =  -1.227728   -1.913865  [ DEG:   -70.3436   -109.6564 ]
  Phi   =  -2.506103    0.635490  [ DEG:  -143.5891     36.4109 ]
 
# 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_4-D2                               
REMARK     2: T0323_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0323TS168_4-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   70   3.06   52.86  35.057
REMARK  ---------------------------------------------------------- 
MOLECULE T0323TS168_4-D2
PFRMAT TS
TARGET T0323
MODEL 4
PARENT N/A
ATOM     34  CA  PRO    34      15.220  17.893   7.705  1.00 25.00           C
ATOM     35  CA  THR    35      11.867  19.506   6.912  1.00 25.00           C
ATOM     36  CA  LYS    36      12.847  21.687   4.016  1.00 25.00           C
ATOM     37  CA  PRO    37      12.961  24.196   1.103  1.00 25.00           C
ATOM     38  CA  ASN    38      13.812  26.944  -1.427  1.00 25.00           C
ATOM     39  CA  PRO    39      15.063  30.205  -3.040  1.00 25.00           C
ATOM     40  CA  PHE    40      12.817  32.193  -5.422  1.00 25.00           C
ATOM     41  CA  GLN    41       9.753  30.254  -4.191  1.00 25.00           C
ATOM     42  CA  SER    42      10.728  30.970  -0.557  1.00 25.00           C
ATOM     43  CA  LEU    43      11.119  34.692  -1.370  1.00 25.00           C
ATOM     44  CA  VAL    44       7.674  34.713  -3.042  1.00 25.00           C
ATOM     45  CA  SER    45       6.144  33.015   0.031  1.00 25.00           C
ATOM     46  CA  SER    46       7.786  35.615   2.314  1.00 25.00           C
ATOM     47  CA  ILE    47       6.410  38.442   0.127  1.00 25.00           C
ATOM     48  CA  VAL    48       2.911  36.891   0.282  1.00 25.00           C
ATOM     49  CA  GLU    49       3.167  36.635   4.095  1.00 25.00           C
ATOM     50  CA  GLN    50       4.242  40.306   4.294  1.00 25.00           C
ATOM     51  CA  GLN    51       1.278  41.318   2.091  1.00 25.00           C
ATOM     52  CA  LEU    52      -0.530  38.022   2.436  1.00 25.00           C
ATOM     53  CA  SER    53      -0.065  34.192   2.552  1.00 25.00           C
ATOM     54  CA  ILE    54       1.779  30.829   2.549  1.00 25.00           C
ATOM     55  CA  LYS    55      -0.533  28.446   0.641  1.00 25.00           C
ATOM     56  CA  ALA    56      -1.999  31.395  -1.313  1.00 25.00           C
ATOM     57  CA  ALA    57       1.529  32.612  -2.173  1.00 25.00           C
ATOM     58  CA  SER    58       2.477  29.098  -3.366  1.00 25.00           C
ATOM     59  CA  ALA    59      -0.674  28.960  -5.538  1.00 25.00           C
ATOM     60  CA  ILE    60       0.179  32.378  -7.037  1.00 25.00           C
ATOM     61  CA  TYR    61       3.740  31.187  -7.791  1.00 25.00           C
ATOM     62  CA  GLY    62       2.357  28.040  -9.477  1.00 25.00           C
ATOM     63  CA  ARG    63      -0.018  30.182 -11.584  1.00 25.00           C
ATOM     64  CA  VAL    64       2.897  32.443 -12.612  1.00 25.00           C
ATOM     65  CA  GLU    65       4.965  29.373 -13.594  1.00 25.00           C
ATOM     66  CA  GLN    66       2.039  28.036 -15.672  1.00 25.00           C
ATOM     67  CA  LEU    67       1.694  31.428 -17.414  1.00 25.00           C
ATOM     68  CA  VAL    68       5.447  31.445 -18.179  1.00 25.00           C
ATOM     69  CA  GLY    69       4.596  28.726 -20.613  1.00 25.00           C
ATOM     70  CA  GLY    70       1.772  28.885 -23.220  1.00 25.00           C
ATOM     71  CA  ALA    71      -1.599  27.439 -22.217  1.00 25.00           C
ATOM     72  CA  LEU    72      -2.542  30.713 -20.522  1.00 25.00           C
ATOM     73  CA  GLU    73      -1.562  32.953 -23.361  1.00 25.00           C
ATOM     74  CA  LYS    74       1.040  35.619 -24.033  1.00 25.00           C
ATOM     75  CA  PRO    75       2.780  36.439 -20.720  1.00 25.00           C
ATOM     76  CA  GLU    76       1.618  40.057 -21.197  1.00 25.00           C
ATOM     77  CA  GLN    77      -0.889  39.656 -18.330  1.00 25.00           C
ATOM     78  CA  LEU    78       1.869  38.234 -16.085  1.00 25.00           C
ATOM     79  CA  TYR    79       4.144  41.186 -16.968  1.00 25.00           C
ATOM     80  CA  ARG    80       1.321  43.639 -16.142  1.00 25.00           C
ATOM     81  CA  VAL    81       0.054  47.162 -15.373  1.00 25.00           C
ATOM     82  CA  SER    82      -3.528  46.121 -16.367  1.00 25.00           C
ATOM     83  CA  ASP    83      -4.142  44.934 -12.797  1.00 25.00           C
ATOM     84  CA  GLU    84      -6.291  41.782 -12.464  1.00 25.00           C
ATOM     85  CA  ALA    85      -3.157  39.687 -11.788  1.00 25.00           C
ATOM     86  CA  LEU    86      -2.030  42.189  -9.116  1.00 25.00           C
ATOM     87  CA  ARG    87      -5.490  42.038  -7.480  1.00 25.00           C
ATOM     88  CA  GLN    88      -5.349  38.210  -7.481  1.00 25.00           C
ATOM     89  CA  ALA    89      -2.080  38.436  -5.545  1.00 25.00           C
ATOM     90  CA  GLY    90      -4.241  39.178  -2.529  1.00 25.00           C
ATOM     91  CA  VAL    91      -2.743  42.456  -1.266  1.00 25.00           C
ATOM     92  CA  SER    92      -2.180  44.631  -4.317  1.00 25.00           C
ATOM     93  CA  LYS    93      -0.152  47.468  -2.755  1.00 25.00           C
ATOM     94  CA  ARG    94       2.349  46.568   0.002  1.00 25.00           C
ATOM     95  CA  LYS    95       2.429  42.940  -1.220  1.00 25.00           C
ATOM     96  CA  ILE    96       3.046  44.136  -4.806  1.00 25.00           C
ATOM     97  CA  GLU    97       5.897  46.385  -3.590  1.00 25.00           C
ATOM     98  CA  TYR    98       7.436  43.444  -1.680  1.00 25.00           C
ATOM     99  CA  ILE    99       7.196  41.253  -4.812  1.00 25.00           C
ATOM    100  CA  ARG   100       8.888  43.991  -6.887  1.00 25.00           C
ATOM    101  CA  HIS   101      11.686  44.268  -4.288  1.00 25.00           C
ATOM    102  CA  VAL   102      12.169  40.470  -4.368  1.00 25.00           C
ATOM    103  CA  CYS   103      12.349  40.548  -8.193  1.00 25.00           C
ATOM    104  CA  GLU   104      14.950  43.356  -8.037  1.00 25.00           C
ATOM    105  CA  HIS   105      17.013  41.338  -5.520  1.00 25.00           C
ATOM    106  CA  VAL   106      16.842  38.268  -7.802  1.00 25.00           C
ATOM    107  CA  GLU   107      17.985  40.388 -10.780  1.00 25.00           C
ATOM    108  CA  SER   108      19.974  37.192 -11.597  1.00 25.00           C
ATOM    109  CA  GLY   109      17.869  37.303 -14.805  1.00 25.00           C
ATOM    110  CA  ARG   110      14.590  37.295 -12.858  1.00 25.00           C
ATOM    111  CA  LEU   111      12.230  40.309 -13.195  1.00 25.00           C
ATOM    112  CA  ASP   112      15.230  42.152 -14.636  1.00 25.00           C
ATOM    113  CA  PHE   113      16.911  45.243 -13.172  1.00 25.00           C
ATOM    114  CA  THR   114      16.825  47.091 -16.525  1.00 25.00           C
ATOM    115  CA  GLU   115      16.315  50.422 -14.705  1.00 25.00           C
ATOM    116  CA  LEU   116      19.273  49.643 -12.400  1.00 25.00           C
ATOM    117  CA  GLU   117      21.452  48.810 -15.438  1.00 25.00           C
ATOM    118  CA  GLY   118      21.606  45.593 -17.407  1.00 25.00           C
ATOM    119  CA  ALA   119      21.707  43.905 -14.046  1.00 25.00           C
ATOM    120  CA  GLU   120      22.397  43.405 -10.353  1.00 25.00           C
ATOM    121  CA  ALA   121      24.261  43.840  -7.103  1.00 25.00           C
ATOM    122  CA  THR   122      25.038  47.453  -6.097  1.00 25.00           C
ATOM    123  CA  THR   123      22.411  48.734  -8.572  1.00 25.00           C
ATOM    124  CA  VAL   124      19.837  46.283  -7.145  1.00 25.00           C
ATOM    125  CA  ILE   125      20.649  47.459  -3.592  1.00 25.00           C
ATOM    126  CA  GLU   126      20.231  51.108  -4.679  1.00 25.00           C
ATOM    127  CA  LYS   127      16.855  50.270  -6.280  1.00 25.00           C
ATOM    128  CA  LEU   128      15.735  48.519  -3.065  1.00 25.00           C
ATOM    129  CA  THR   129      16.791  51.571  -1.005  1.00 25.00           C
ATOM    130  CA  ALA   130      14.834  53.869  -3.364  1.00 25.00           C
ATOM    131  CA  ILE   131      12.078  52.023  -5.305  1.00 25.00           C
ATOM    132  CA  LYS   132       9.172  49.544  -5.685  1.00 25.00           C
ATOM    133  CA  GLY   133       8.493  50.448  -2.053  1.00 25.00           C
ATOM    134  CA  ILE   134      11.965  49.507  -0.730  1.00 25.00           C
ATOM    135  CA  GLY   135      12.829  51.937   2.075  1.00 25.00           C
ATOM    136  CA  GLN   136      11.966  50.718   5.542  1.00 25.00           C
ATOM    137  CA  TRP   137       9.418  47.965   6.316  1.00 25.00           C
ATOM    138  CA  THR   138       9.663  46.691   2.713  1.00 25.00           C
ATOM    139  CA  ALA   139      13.485  46.648   2.963  1.00 25.00           C
ATOM    140  CA  GLU   140      13.273  44.696   6.251  1.00 25.00           C
ATOM    141  CA  MET   141      10.884  42.178   4.632  1.00 25.00           C
ATOM    142  CA  PHE   142      13.286  41.764   1.677  1.00 25.00           C
ATOM    143  CA  MET   143      16.199  41.186   4.094  1.00 25.00           C
ATOM    144  CA  MET   144      14.145  38.561   5.981  1.00 25.00           C
ATOM    145  CA  PHE   145      13.305  36.811   2.680  1.00 25.00           C
ATOM    146  CA  SER   146      17.010  36.804   1.711  1.00 25.00           C
ATOM    147  CA  LEU   147      17.745  33.060   2.246  1.00 25.00           C
ATOM    148  CA  GLY   148      16.784  30.892   5.213  1.00 25.00           C
ATOM    149  CA  ARG   149      19.798  29.422   7.018  1.00 25.00           C
TER
END
