
#######################################################
#                                                     #
#                        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  154 (  154),  selected  154 , name T0318TS168_3-D1
# Molecule2: number of CA atoms  154 ( 1200),  selected  154 , name T0318_D1.pdb
# PARAMETERS: T0318TS168_3-D1.T0318_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    T       2      T       2          3.500
LGA    Q       3      Q       3           #
LGA    V       4      V       4          4.255
LGA    L       5      L       5           #
LGA    V       6      V       6          3.514
LGA    R       7      R       7           #
LGA    N       8      -       -           -
LGA    G       9      -       -           -
LGA    I      10      -       -           -
LGA    Q      11      -       -           -
LGA    A      12      -       -           -
LGA    V      13      -       -           -
LGA    G      14      -       -           -
LGA    D      15      -       -           -
LGA    G      16      -       -           -
LGA    L      17      -       -           -
LGA    T      18      -       -           -
LGA    S      19      -       -           -
LGA    L      20      N       8           #
LGA    I      21      G       9          4.340
LGA    I      22      I      10          3.957
LGA    V      23      Q      11          2.989
LGA    G      24      A      12          5.157
LGA    K      25      V      13           -
LGA    K      26      G      14           -
LGA    S      27      D      15           -
LGA    V      28      G      16           -
LGA    L      29      L      17           -
LGA    K      30      T      18           -
LGA    N      31      S      19           -
LGA    V      32      L      20           -
LGA    T      33      I      21           -
LGA    F      34      I      22           -
LGA    E      35      V      23           -
LGA    G      36      G      24           -
LGA    K      37      K      25           -
LGA    F      38      K      26           -
LGA    K      39      S      27           -
LGA    E      40      V      28           -
LGA    V      41      L      29           -
LGA    A      42      -       -           -
LGA    Q      43      -       -           -
LGA    K      44      -       -           -
LGA    F      45      K      30           #
LGA    -       -      N      31           -
LGA    V      46      V      32          4.323
LGA    T      47      T      33           #
LGA    D      48      F      34           -
LGA    G      49      -       -           -
LGA    D      50      -       -           -
LGA    S      51      -       -           -
LGA    W      52      E      35          2.989
LGA    N      53      -       -           -
LGA    S      54      -       -           -
LGA    M      55      -       -           -
LGA    I      56      G      36          2.740
LGA    S      57      K      37          4.422
LGA    R      58      F      38           -
LGA    -       -      K      39           -
LGA    I      59      E      40           #
LGA    P      60      -       -           -
LGA    A      61      -       -           -
LGA    S      62      -       -           -
LGA    G      63      -       -           -
LGA    R      64      -       -           -
LGA    H      65      V      41          1.558
LGA    P      66      A      42          4.748
LGA    L      67      Q      43           -
LGA    H      68      K      44           -
LGA    Y      69      F      45           -
LGA    -       -      V      46           -
LGA    -       -      T      47           -
LGA    -       -      D      48           -
LGA    -       -      G      49           -
LGA    -       -      D      50           -
LGA    -       -      S      51           -
LGA    E      70      W      52           #
LGA    L      71      -       -           -
LGA    A      72      -       -           -
LGA    H      73      N      53           #
LGA    L      74      S      54           -
LGA    -       -      M      55           -
LGA    I      75      I      56          3.497
LGA    T      76      S      57           -
LGA    V      77      R      58           -
LGA    P      78      I      59           -
LGA    D      79      P      60           -
LGA    -       -      A      61           -
LGA    -       -      S      62           -
LGA    -       -      G      63           -
LGA    -       -      R      64           -
LGA    -       -      H      65           -
LGA    -       -      P      66           -
LGA    -       -      L      67           -
LGA    -       -      H      68           -
LGA    -       -      Y      69           -
LGA    -       -      E      70           -
LGA    A      80      L      71          4.275
LGA    S      81      A      72          1.447
LGA    S      82      -       -           -
LGA    R      83      -       -           -
LGA    G      84      -       -           -
LGA    N      85      -       -           -
LGA    T      86      -       -           -
LGA    P      87      H      73          2.424
LGA    T      88      L      74          2.037
LGA    N      89      -       -           -
LGA    A      90      I      75          2.553
LGA    H      91      T      76          3.010
LGA    S      92      -       -           -
LGA    I      93      -       -           -
LGA    Y      94      V      77          1.391
LGA    K      95      -       -           -
LGA    E      96      -       -           -
LGA    L      97      P      78          1.195
LGA    K      98      D      79          1.667
LGA    P      99      -       -           -
LGA    I     100      A      80          3.896
LGA    N     101      -       -           -
LGA    Y     102      -       -           -
LGA    P     103      S      81          1.765
LGA    E     104      S      82          1.995
LGA    D     105      R      83          2.873
LGA    T     106      G      84           #
LGA    K     107      N      85          4.482
LGA    N     108      T      86          3.713
LGA    V     109      P      87          2.751
LGA    H     110      T      88          4.123
LGA    -       -      N      89           -
LGA    F     111      A      90          2.402
LGA    V     112      H      91          1.822
LGA    -       -      S      92           -
LGA    L     113      I      93           #
LGA    F     114      Y      94          2.726
LGA    -       -      K      95           -
LGA    -       -      E      96           -
LGA    A     115      L      97          3.710
LGA    E     116      K      98          1.466
LGA    Y     117      P      99          1.540
LGA    P     118      I     100           #
LGA    D     119      N     101           -
LGA    V     120      Y     102           -
LGA    L     121      P     103           -
LGA    S     122      E     104           -
LGA    H     123      D     105           -
LGA    V     124      T     106           -
LGA    A     125      K     107           -
LGA    A     126      N     108           -
LGA    I     127      V     109           -
LGA    A     128      H     110           -
LGA    -       -      F     111           -
LGA    R     129      V     112           #
LGA    T     130      -       -           -
LGA    F     131      -       -           -
LGA    C     132      -       -           -
LGA    K     133      -       -           -
LGA    F     134      -       -           -
LGA    S     135      -       -           -
LGA    M     136      -       -           -
LGA    K     137      -       -           -
LGA    T     138      -       -           -
LGA    S     139      -       -           -
LGA    G     140      -       -           -
LGA    I     141      -       -           -
LGA    R     142      -       -           -
LGA    E     143      -       -           -
LGA    L     144      -       -           -
LGA    N     145      -       -           -
LGA    V     146      L     113          3.937
LGA    N     147      F     114          4.125
LGA    -       -      A     115           -
LGA    -       -      E     116           -
LGA    -       -      Y     117           -
LGA    -       -      P     118           -
LGA    -       -      D     119           -
LGA    -       -      V     120           -
LGA    -       -      L     121           -
LGA    -       -      S     122           -
LGA    I     148      H     123           #
LGA    D     149      V     124          4.193
LGA    -       -      A     125           -
LGA    -       -      A     126           -
LGA    V     150      I     127          1.914
LGA    V     151      A     128          3.172
LGA    C     152      R     129          4.083
LGA    D     153      T     130           -
LGA    K     154      F     131           -
LGA    L     155      C     132           -
LGA    -       -      K     133           -
LGA    -       -      F     134           -
LGA    -       -      S     135           -
LGA    -       -      M     136           -
LGA    -       -      K     137           -
LGA    -       -      T     138           -
LGA    -       -      S     139           -
LGA    -       -      G     140           -
LGA    -       -      I     141           -
LGA    -       -      R     142           -
LGA    -       -      E     143           -
LGA    -       -      L     144           -
LGA    -       -      N     145           -
LGA    -       -      V     146           -
LGA    -       -      N     147           -
LGA    -       -      I     148           -
LGA    -       -      D     149           -
LGA    -       -      V     150           -
LGA    -       -      V     151           -
LGA    -       -      C     152           -
LGA    -       -      D     153           -
LGA    -       -      K     154           -
LGA    -       -      L     155           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  154  154    5.0     43    3.27    13.95     15.693     1.274

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.664525 * X  +  -0.200692 * Y  +  -0.719812 * Z  +  35.299492
  Y_new =  -0.403694 * X  +  -0.907016 * Y  +  -0.119801 * Z  +  26.809217
  Z_new =  -0.628838 * X  +   0.370195 * Y  +  -0.683753 * Z  +   4.438603 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.645364   -0.496228  [ DEG:   151.5682    -28.4318 ]
  Theta =   0.680058    2.461535  [ DEG:    38.9644    141.0356 ]
  Phi   =  -0.545911    2.595682  [ DEG:   -31.2784    148.7216 ]
 
# 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: T0318TS168_3-D1                               
REMARK     2: T0318_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0318TS168_3-D1.T0318_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  154  154   5.0   43   3.27   13.95  15.693
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS168_3-D1
PFRMAT TS
TARGET T0318
MODEL 3
PARENT N/A
ATOM      2  CA  THR     2      31.852  53.063  12.676  1.00 25.00           C
ATOM      3  CA  GLN     3      31.177  49.900  14.675  1.00 25.00           C
ATOM      4  CA  VAL     4      30.770  46.214  15.566  1.00 25.00           C
ATOM      5  CA  LEU     5      31.533  42.693  16.734  1.00 25.00           C
ATOM      6  CA  VAL     6      28.723  40.133  16.867  1.00 25.00           C
ATOM      7  CA  ARG     7      26.978  36.811  17.219  1.00 25.00           C
ATOM      8  CA  ASN     8      24.345  34.165  16.586  1.00 25.00           C
ATOM      9  CA  GLY     9      22.811  30.887  17.658  1.00 25.00           C
ATOM     10  CA  ILE    10      20.691  27.691  17.848  1.00 25.00           C
ATOM     11  CA  GLN    11      19.350  24.161  18.645  1.00 25.00           C
ATOM     12  CA  ALA    12      17.882  20.647  19.160  1.00 25.00           C
ATOM     13  CA  VAL    13      20.558  18.465  20.824  1.00 25.00           C
ATOM     14  CA  GLY    14      21.508  15.834  23.370  1.00 25.00           C
ATOM     15  CA  ASP    15      24.865  14.649  24.728  1.00 25.00           C
ATOM     16  CA  GLY    16      27.871  15.336  22.460  1.00 25.00           C
ATOM     17  CA  LEU    17      29.907  18.225  21.070  1.00 25.00           C
ATOM     18  CA  THR    18      33.024  20.363  20.382  1.00 25.00           C
ATOM     19  CA  SER    19      33.622  23.304  18.023  1.00 25.00           C
ATOM     20  CA  LEU    20      35.767  26.032  16.471  1.00 25.00           C
ATOM     21  CA  ILE    21      37.090  29.328  15.248  1.00 25.00           C
ATOM     22  CA  ILE    22      38.441  32.827  14.905  1.00 25.00           C
ATOM     23  CA  VAL    23      41.119  33.696  17.467  1.00 25.00           C
ATOM     24  CA  GLY    24      44.049  35.704  18.832  1.00 25.00           C
ATOM     25  CA  LYS    25      47.051  35.919  21.077  1.00 25.00           C
ATOM     26  CA  LYS    26      50.876  35.522  20.990  1.00 25.00           C
ATOM     27  CA  SER    27      54.446  36.789  20.425  1.00 25.00           C
ATOM     28  CA  VAL    28      56.139  35.352  23.567  1.00 25.00           C
ATOM     29  CA  LEU    29      58.244  38.472  23.274  1.00 25.00           C
ATOM     30  CA  LYS    30      61.414  36.705  24.591  1.00 25.00           C
ATOM     31  CA  ASN    31      60.962  33.492  26.637  1.00 25.00           C
ATOM     32  CA  VAL    32      58.176  34.399  28.973  1.00 25.00           C
ATOM     33  CA  THR    33      59.379  33.743  32.568  1.00 25.00           C
ATOM     34  CA  PHE    34      56.069  34.432  34.310  1.00 25.00           C
ATOM     35  CA  GLU    35      56.315  38.185  33.737  1.00 25.00           C
ATOM     36  CA  GLY    36      56.917  41.790  34.563  1.00 25.00           C
ATOM     37  CA  LYS    37      54.864  41.116  37.673  1.00 25.00           C
ATOM     38  CA  PHE    38      51.177  42.090  37.312  1.00 25.00           C
ATOM     39  CA  LYS    39      48.440  42.512  34.680  1.00 25.00           C
ATOM     40  CA  GLU    40      45.658  41.526  37.120  1.00 25.00           C
ATOM     41  CA  VAL    41      43.343  40.694  34.184  1.00 25.00           C
ATOM     42  CA  ALA    42      46.092  38.553  32.593  1.00 25.00           C
ATOM     43  CA  GLN    43      46.614  36.714  35.912  1.00 25.00           C
ATOM     44  CA  LYS    44      42.846  36.078  36.180  1.00 25.00           C
ATOM     45  CA  PHE    45      42.796  34.722  32.598  1.00 25.00           C
ATOM     46  CA  VAL    46      40.769  31.627  33.703  1.00 25.00           C
ATOM     47  CA  THR    47      43.560  30.665  36.116  1.00 25.00           C
ATOM     48  CA  ASP    48      42.721  27.023  35.393  1.00 25.00           C
ATOM     49  CA  GLY    49      45.065  27.209  32.430  1.00 25.00           C
ATOM     50  CA  ASP    50      42.663  24.657  30.910  1.00 25.00           C
ATOM     51  CA  SER    51      40.751  27.461  29.225  1.00 25.00           C
ATOM     52  CA  TRP    52      43.950  27.871  27.159  1.00 25.00           C
ATOM     53  CA  ASN    53      42.306  26.064  24.209  1.00 25.00           C
ATOM     54  CA  SER    54      39.246  28.350  24.484  1.00 25.00           C
ATOM     55  CA  MET    55      41.519  31.432  24.522  1.00 25.00           C
ATOM     56  CA  ILE    56      43.698  31.302  21.386  1.00 25.00           C
ATOM     57  CA  SER    57      47.261  31.866  20.034  1.00 25.00           C
ATOM     58  CA  ARG    58      48.091  33.633  16.729  1.00 25.00           C
ATOM     59  CA  ILE    59      48.188  37.420  16.290  1.00 25.00           C
ATOM     60  CA  PRO    60      48.407  40.302  18.822  1.00 25.00           C
ATOM     61  CA  ALA    61      49.805  43.616  17.584  1.00 25.00           C
ATOM     62  CA  SER    62      47.513  46.351  18.923  1.00 25.00           C
ATOM     63  CA  GLY    63      44.611  43.956  18.607  1.00 25.00           C
ATOM     64  CA  ARG    64      44.448  42.199  21.931  1.00 25.00           C
ATOM     65  CA  HIS    65      42.985  38.952  23.229  1.00 25.00           C
ATOM     66  CA  PRO    66      40.668  36.393  24.747  1.00 25.00           C
ATOM     67  CA  LEU    67      37.584  37.026  26.953  1.00 25.00           C
ATOM     68  CA  HIS    68      35.053  34.156  26.819  1.00 25.00           C
ATOM     69  CA  TYR    69      37.130  32.173  29.353  1.00 25.00           C
ATOM     70  CA  GLU    70      37.268  35.223  31.664  1.00 25.00           C
ATOM     71  CA  LEU    71      33.471  35.639  31.383  1.00 25.00           C
ATOM     72  CA  ALA    72      32.979  31.935  32.226  1.00 25.00           C
ATOM     73  CA  HIS    73      35.275  32.298  35.270  1.00 25.00           C
ATOM     74  CA  LEU    74      33.297  35.368  36.427  1.00 25.00           C
ATOM     75  CA  ILE    75      35.600  38.253  35.376  1.00 25.00           C
ATOM     76  CA  THR    76      36.508  40.597  32.521  1.00 25.00           C
ATOM     77  CA  VAL    77      37.627  41.741  29.039  1.00 25.00           C
ATOM     78  CA  PRO    78      37.130  41.879  25.264  1.00 25.00           C
ATOM     79  CA  ASP    79      39.915  44.229  24.280  1.00 25.00           C
ATOM     80  CA  ALA    80      42.420  47.018  23.387  1.00 25.00           C
ATOM     81  CA  SER    81      39.718  49.249  24.851  1.00 25.00           C
ATOM     82  CA  SER    82      40.698  48.758  28.498  1.00 25.00           C
ATOM     83  CA  ARG    83      40.618  49.567  32.266  1.00 25.00           C
ATOM     84  CA  GLY    84      38.690  52.605  33.520  1.00 25.00           C
ATOM     85  CA  ASN    85      36.716  52.355  30.298  1.00 25.00           C
ATOM     86  CA  THR    86      33.319  51.281  29.011  1.00 25.00           C
ATOM     87  CA  PRO    87      34.942  48.093  27.753  1.00 25.00           C
ATOM     88  CA  THR    88      36.601  46.458  30.793  1.00 25.00           C
ATOM     89  CA  ASN    89      34.240  48.357  33.135  1.00 25.00           C
ATOM     90  CA  ALA    90      31.227  47.211  31.065  1.00 25.00           C
ATOM     91  CA  HIS    91      32.463  43.590  31.226  1.00 25.00           C
ATOM     92  CA  SER    92      32.873  43.872  35.023  1.00 25.00           C
ATOM     93  CA  ILE    93      29.323  45.274  35.327  1.00 25.00           C
ATOM     94  CA  TYR    94      27.973  42.385  33.207  1.00 25.00           C
ATOM     95  CA  LYS    95      29.821  39.865  35.423  1.00 25.00           C
ATOM     96  CA  GLU    96      28.357  41.510  38.557  1.00 25.00           C
ATOM     97  CA  LEU    97      24.846  41.337  37.036  1.00 25.00           C
ATOM     98  CA  LYS    98      25.357  37.632  36.214  1.00 25.00           C
ATOM     99  CA  PRO    99      26.518  36.970  39.803  1.00 25.00           C
ATOM    100  CA  ILE   100      23.430  38.785  41.162  1.00 25.00           C
ATOM    101  CA  ASN   101      21.210  41.818  40.760  1.00 25.00           C
ATOM    102  CA  TYR   102      18.402  43.681  38.974  1.00 25.00           C
ATOM    103  CA  PRO   103      16.870  40.854  36.993  1.00 25.00           C
ATOM    104  CA  GLU   104      13.320  41.757  38.188  1.00 25.00           C
ATOM    105  CA  ASP   105      12.632  38.121  39.007  1.00 25.00           C
ATOM    106  CA  THR   106      14.661  35.904  36.615  1.00 25.00           C
ATOM    107  CA  LYS   107      12.174  37.363  34.072  1.00 25.00           C
ATOM    108  CA  ASN   108      14.612  35.894  31.596  1.00 25.00           C
ATOM    109  CA  VAL   109      17.299  37.707  29.552  1.00 25.00           C
ATOM    110  CA  HIS   110      17.820  38.496  25.903  1.00 25.00           C
ATOM    111  CA  PHE   111      19.014  42.038  26.514  1.00 25.00           C
ATOM    112  CA  VAL   112      19.081  45.814  27.088  1.00 25.00           C
ATOM    113  CA  LEU   113      20.714  46.540  23.693  1.00 25.00           C
ATOM    114  CA  PHE   114      23.153  49.492  23.641  1.00 25.00           C
ATOM    115  CA  ALA   115      26.757  50.562  23.037  1.00 25.00           C
ATOM    116  CA  GLU   116      28.137  53.745  24.635  1.00 25.00           C
ATOM    117  CA  TYR   117      29.448  55.384  27.876  1.00 25.00           C
ATOM    118  CA  PRO   118      27.817  56.538  31.132  1.00 25.00           C
ATOM    119  CA  ASP   119      27.800  53.803  33.812  1.00 25.00           C
ATOM    120  CA  VAL   120      24.236  52.816  32.819  1.00 25.00           C
ATOM    121  CA  LEU   121      25.283  52.647  29.139  1.00 25.00           C
ATOM    122  CA  SER   122      28.276  50.444  30.065  1.00 25.00           C
ATOM    123  CA  HIS   123      25.982  48.131  32.079  1.00 25.00           C
ATOM    124  CA  VAL   124      23.577  47.890  29.109  1.00 25.00           C
ATOM    125  CA  ALA   125      26.498  47.039  26.782  1.00 25.00           C
ATOM    126  CA  ALA   126      27.681  44.330  29.216  1.00 25.00           C
ATOM    127  CA  ILE   127      24.141  42.873  29.353  1.00 25.00           C
ATOM    128  CA  ALA   128      23.980  42.841  25.527  1.00 25.00           C
ATOM    129  CA  ARG   129      27.368  41.061  25.374  1.00 25.00           C
ATOM    130  CA  THR   130      26.145  38.464  27.908  1.00 25.00           C
ATOM    131  CA  PHE   131      22.974  37.898  25.836  1.00 25.00           C
ATOM    132  CA  CYS   132      25.091  37.444  22.676  1.00 25.00           C
ATOM    133  CA  LYS   133      27.318  34.921  24.502  1.00 25.00           C
ATOM    134  CA  PHE   134      24.220  33.003  25.683  1.00 25.00           C
ATOM    135  CA  SER   135      23.403  29.518  27.023  1.00 25.00           C
ATOM    136  CA  MET   136      24.230  28.106  30.457  1.00 25.00           C
ATOM    137  CA  LYS   137      23.881  27.457  34.188  1.00 25.00           C
ATOM    138  CA  THR   138      26.243  27.232  37.123  1.00 25.00           C
ATOM    139  CA  SER   139      23.127  27.445  39.218  1.00 25.00           C
ATOM    140  CA  GLY   140      19.651  26.435  37.902  1.00 25.00           C
ATOM    141  CA  ILE   141      17.227  28.529  35.929  1.00 25.00           C
ATOM    142  CA  ARG   142      18.499  31.530  33.978  1.00 25.00           C
ATOM    143  CA  GLU   143      21.579  32.142  31.803  1.00 25.00           C
ATOM    144  CA  LEU   144      24.781  33.828  30.876  1.00 25.00           C
ATOM    145  CA  ASN   145      28.241  34.061  29.373  1.00 25.00           C
ATOM    146  CA  VAL   146      30.202  36.399  27.141  1.00 25.00           C
ATOM    147  CA  ASN   147      31.135  38.626  24.162  1.00 25.00           C
ATOM    148  CA  ILE   148      30.198  41.259  21.598  1.00 25.00           C
ATOM    149  CA  ASP   149      27.587  43.772  20.442  1.00 25.00           C
ATOM    150  CA  VAL   150      24.532  45.922  20.122  1.00 25.00           C
ATOM    151  CA  VAL   151      22.417  48.100  17.910  1.00 25.00           C
ATOM    152  CA  CYS   152      18.704  47.960  18.714  1.00 25.00           C
ATOM    153  CA  ASP   153      15.445  47.553  20.628  1.00 25.00           C
ATOM    154  CA  LYS   154      12.741  45.418  18.992  1.00 25.00           C
ATOM    155  CA  LEU   155      12.693  41.871  17.549  1.00 25.00           C
TER
END
