
#######################################################
#                                                     #
#                        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_2-D1
# Molecule2: number of CA atoms  154 ( 1200),  selected  154 , name T0318_D1.pdb
# PARAMETERS: T0318TS168_2-D1.T0318_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    T       2      -       -           -
LGA    Q       3      T       2           #
LGA    V       4      Q       3          3.302
LGA    L       5      V       4          2.770
LGA    V       6      L       5          2.482
LGA    R       7      V       6           #
LGA    N       8      R       7           -
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      -       -           -
LGA    I      21      N       8           #
LGA    I      22      G       9          3.488
LGA    V      23      I      10           #
LGA    G      24      Q      11           -
LGA    K      25      A      12           -
LGA    K      26      V      13           -
LGA    S      27      G      14           -
LGA    V      28      D      15           -
LGA    L      29      G      16           -
LGA    K      30      L      17           -
LGA    N      31      T      18           -
LGA    V      32      S      19           -
LGA    T      33      L      20           -
LGA    F      34      I      21           -
LGA    E      35      I      22           -
LGA    G      36      V      23           -
LGA    K      37      G      24           -
LGA    F      38      -       -           -
LGA    K      39      -       -           -
LGA    E      40      -       -           -
LGA    V      41      K      25          4.107
LGA    A      42      K      26          3.893
LGA    Q      43      S      27          3.033
LGA    K      44      V      28          1.405
LGA    F      45      L      29          1.108
LGA    -       -      K      30           -
LGA    V      46      N      31          3.518
LGA    T      47      V      32          3.196
LGA    D      48      T      33          1.014
LGA    -       -      F      34           -
LGA    -       -      E      35           -
LGA    -       -      G      36           -
LGA    -       -      K      37           -
LGA    -       -      F      38           -
LGA    -       -      K      39           -
LGA    -       -      E      40           -
LGA    -       -      V      41           -
LGA    -       -      A      42           -
LGA    -       -      Q      43           -
LGA    -       -      K      44           -
LGA    -       -      F      45           -
LGA    -       -      V      46           -
LGA    -       -      T      47           -
LGA    -       -      D      48           -
LGA    G      49      G      49          4.447
LGA    D      50      D      50          4.439
LGA    S      51      -       -           -
LGA    W      52      -       -           -
LGA    N      53      -       -           -
LGA    S      54      -       -           -
LGA    M      55      -       -           -
LGA    I      56      -       -           -
LGA    S      57      -       -           -
LGA    R      58      -       -           -
LGA    I      59      -       -           -
LGA    P      60      -       -           -
LGA    A      61      S      51          4.407
LGA    S      62      W      52           -
LGA    G      63      N      53           -
LGA    -       -      S      54           -
LGA    -       -      M      55           -
LGA    -       -      I      56           -
LGA    R      64      S      57           #
LGA    H      65      R      58          1.277
LGA    P      66      I      59          4.522
LGA    L      67      P      60           #
LGA    H      68      A      61           #
LGA    -       -      S      62           -
LGA    Y      69      G      63           #
LGA    E      70      -       -           -
LGA    L      71      R      64          4.970
LGA    A      72      H      65          4.671
LGA    -       -      P      66           -
LGA    -       -      L      67           -
LGA    -       -      H      68           -
LGA    -       -      Y      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      A      72           -
LGA    H      73      H      73          2.996
LGA    L      74      L      74          3.679
LGA    I      75      I      75           #
LGA    -       -      T      76           -
LGA    T      76      V      77          5.120
LGA    V      77      -       -           -
LGA    P      78      -       -           -
LGA    D      79      -       -           -
LGA    A      80      -       -           -
LGA    S      81      -       -           -
LGA    S      82      -       -           -
LGA    R      83      P      78          2.820
LGA    G      84      D      79           -
LGA    N      85      A      80           -
LGA    -       -      S      81           -
LGA    -       -      S      82           -
LGA    -       -      R      83           -
LGA    -       -      G      84           -
LGA    -       -      N      85           -
LGA    -       -      T      86           -
LGA    -       -      P      87           -
LGA    T      86      T      88           #
LGA    P      87      N      89          2.230
LGA    T      88      A      90          3.649
LGA    N      89      H      91          2.529
LGA    A      90      S      92          1.892
LGA    H      91      I      93          3.562
LGA    S      92      Y      94          3.566
LGA    I      93      K      95          2.072
LGA    Y      94      E      96          3.669
LGA    K      95      L      97           #
LGA    E      96      K      98          3.831
LGA    L      97      P      99          1.486
LGA    K      98      I     100          3.767
LGA    P      99      -       -           -
LGA    I     100      -       -           -
LGA    N     101      -       -           -
LGA    Y     102      -       -           -
LGA    P     103      N     101          5.897
LGA    E     104      -       -           -
LGA    D     105      -       -           -
LGA    T     106      -       -           -
LGA    K     107      -       -           -
LGA    N     108      -       -           -
LGA    V     109      Y     102          4.335
LGA    H     110      P     103           -
LGA    -       -      E     104           -
LGA    -       -      D     105           -
LGA    -       -      T     106           -
LGA    -       -      K     107           -
LGA    -       -      N     108           -
LGA    F     111      V     109           #
LGA    V     112      H     110          2.124
LGA    L     113      F     111          2.009
LGA    -       -      V     112           -
LGA    F     114      L     113          3.097
LGA    A     115      F     114          4.965
LGA    E     116      A     115           #
LGA    -       -      E     116           -
LGA    -       -      Y     117           -
LGA    Y     117      P     118          4.909
LGA    P     118      D     119          2.078
LGA    -       -      V     120           -
LGA    D     119      L     121          3.330
LGA    V     120      S     122          4.459
LGA    L     121      H     123          3.404
LGA    S     122      V     124          2.114
LGA    H     123      A     125          4.273
LGA    V     124      A     126           #
LGA    A     125      I     127          4.525
LGA    A     126      -       -           -
LGA    I     127      A     128           #
LGA    A     128      R     129           -
LGA    R     129      T     130           -
LGA    T     130      F     131          4.025
LGA    F     131      C     132           -
LGA    C     132      K     133           -
LGA    K     133      F     134           -
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      S     135           #
LGA    E     143      M     136           -
LGA    L     144      K     137           -
LGA    N     145      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      V     146           #
LGA    N     147      N     147           -
LGA    I     148      I     148           #
LGA    D     149      D     149           -
LGA    V     150      V     150           #
LGA    V     151      V     151           -
LGA    C     152      C     152           -
LGA    D     153      D     153           -
LGA    K     154      K     154           #
LGA    L     155      L     155           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  154  154    5.0     49    3.55     8.16     17.927     1.342

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.120080 * X  +   0.111314 * Y  +   0.986504 * Z  +  49.076878
  Y_new =   0.395211 * X  +   0.916921 * Y  +  -0.055356 * Z  +  40.723984
  Z_new =  -0.910708 * X  +   0.383230 * Y  +  -0.154097 * Z  +  12.312010 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.953112   -1.188481  [ DEG:   111.9051    -68.0949 ]
  Theta =   1.144995    1.996598  [ DEG:    65.6034    114.3966 ]
  Phi   =   1.865771   -1.275821  [ DEG:   106.9008    -73.0992 ]
 
# 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_2-D1                               
REMARK     2: T0318_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0318TS168_2-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   49   3.55    8.16  17.927
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS168_2-D1
PFRMAT TS
TARGET T0318
MODEL 2
PARENT N/A
ATOM      2  CA  THR     2      26.977  46.151   0.851  1.00 25.00           C
ATOM      3  CA  GLN     3      29.222  45.496   3.848  1.00 25.00           C
ATOM      4  CA  VAL     4      31.360  45.077   6.908  1.00 25.00           C
ATOM      5  CA  LEU     5      30.592  42.973   9.936  1.00 25.00           C
ATOM      6  CA  VAL     6      28.444  41.731  12.823  1.00 25.00           C
ATOM      7  CA  ARG     7      25.304  41.131  10.761  1.00 25.00           C
ATOM      8  CA  ASN     8      21.786  40.839   9.476  1.00 25.00           C
ATOM      9  CA  GLY     9      17.988  41.022   8.898  1.00 25.00           C
ATOM     10  CA  ILE    10      16.896  39.065  12.004  1.00 25.00           C
ATOM     11  CA  GLN    11      13.101  38.793  11.437  1.00 25.00           C
ATOM     12  CA  ALA    12      10.494  36.212  12.326  1.00 25.00           C
ATOM     13  CA  VAL    13      10.249  34.443  15.749  1.00 25.00           C
ATOM     14  CA  GLY    14       8.612  31.511  17.601  1.00 25.00           C
ATOM     15  CA  ASP    15      10.084  28.853  19.795  1.00 25.00           C
ATOM     16  CA  GLY    16      13.564  27.380  20.512  1.00 25.00           C
ATOM     17  CA  LEU    17      17.352  27.719  20.542  1.00 25.00           C
ATOM     18  CA  THR    18      20.817  27.690  22.115  1.00 25.00           C
ATOM     19  CA  SER    19      24.191  28.388  20.645  1.00 25.00           C
ATOM     20  CA  LEU    20      27.939  28.899  20.496  1.00 25.00           C
ATOM     21  CA  ILE    21      31.747  29.037  20.108  1.00 25.00           C
ATOM     22  CA  ILE    22      35.234  30.444  20.793  1.00 25.00           C
ATOM     23  CA  VAL    23      37.205  30.018  24.086  1.00 25.00           C
ATOM     24  CA  GLY    24      37.378  28.195  27.429  1.00 25.00           C
ATOM     25  CA  LYS    25      37.765  24.841  29.186  1.00 25.00           C
ATOM     26  CA  LYS    26      37.796  23.877  32.844  1.00 25.00           C
ATOM     27  CA  SER    27      36.281  20.701  34.327  1.00 25.00           C
ATOM     28  CA  VAL    28      34.850  23.059  36.924  1.00 25.00           C
ATOM     29  CA  LEU    29      32.954  23.883  40.138  1.00 25.00           C
ATOM     30  CA  LYS    30      35.633  21.570  41.657  1.00 25.00           C
ATOM     31  CA  ASN    31      37.738  20.687  44.743  1.00 25.00           C
ATOM     32  CA  VAL    32      40.562  23.250  44.687  1.00 25.00           C
ATOM     33  CA  THR    33      38.536  25.307  47.222  1.00 25.00           C
ATOM     34  CA  PHE    34      37.863  29.037  46.893  1.00 25.00           C
ATOM     35  CA  GLU    35      36.502  31.934  48.962  1.00 25.00           C
ATOM     36  CA  GLY    36      33.250  33.785  49.466  1.00 25.00           C
ATOM     37  CA  LYS    37      29.580  33.799  48.639  1.00 25.00           C
ATOM     38  CA  PHE    38      30.458  35.350  45.294  1.00 25.00           C
ATOM     39  CA  LYS    39      30.061  36.687  41.790  1.00 25.00           C
ATOM     40  CA  GLU    40      27.981  35.098  38.995  1.00 25.00           C
ATOM     41  CA  VAL    41      29.852  37.182  36.384  1.00 25.00           C
ATOM     42  CA  ALA    42      33.205  36.090  37.878  1.00 25.00           C
ATOM     43  CA  GLN    43      32.091  32.427  37.765  1.00 25.00           C
ATOM     44  CA  LYS    44      31.046  32.833  34.102  1.00 25.00           C
ATOM     45  CA  PHE    45      34.444  34.396  33.282  1.00 25.00           C
ATOM     46  CA  VAL    46      35.333  31.473  30.949  1.00 25.00           C
ATOM     47  CA  THR    47      37.402  29.190  33.238  1.00 25.00           C
ATOM     48  CA  ASP    48      40.898  29.792  31.865  1.00 25.00           C
ATOM     49  CA  GLY    49      44.047  30.795  33.806  1.00 25.00           C
ATOM     50  CA  ASP    50      45.976  34.051  33.359  1.00 25.00           C
ATOM     51  CA  SER    51      43.088  35.570  31.459  1.00 25.00           C
ATOM     52  CA  TRP    52      44.967  38.903  31.633  1.00 25.00           C
ATOM     53  CA  ASN    53      46.622  38.174  28.257  1.00 25.00           C
ATOM     54  CA  SER    54      43.205  37.353  26.733  1.00 25.00           C
ATOM     55  CA  MET    55      41.774  40.626  28.114  1.00 25.00           C
ATOM     56  CA  ILE    56      38.848  38.325  29.110  1.00 25.00           C
ATOM     57  CA  SER    57      38.235  37.715  32.808  1.00 25.00           C
ATOM     58  CA  ARG    58      41.153  38.446  35.144  1.00 25.00           C
ATOM     59  CA  ILE    59      42.684  41.966  35.492  1.00 25.00           C
ATOM     60  CA  PRO    60      46.271  40.951  36.287  1.00 25.00           C
ATOM     61  CA  ALA    61      46.699  42.574  39.681  1.00 25.00           C
ATOM     62  CA  SER    62      45.104  45.443  41.574  1.00 25.00           C
ATOM     63  CA  GLY    63      41.934  47.381  42.336  1.00 25.00           C
ATOM     64  CA  ARG    64      40.634  44.147  43.803  1.00 25.00           C
ATOM     65  CA  HIS    65      38.623  41.793  41.578  1.00 25.00           C
ATOM     66  CA  PRO    66      39.540  44.173  38.793  1.00 25.00           C
ATOM     67  CA  LEU    67      37.179  42.027  36.633  1.00 25.00           C
ATOM     68  CA  HIS    68      34.016  44.141  37.073  1.00 25.00           C
ATOM     69  CA  TYR    69      35.755  47.129  35.425  1.00 25.00           C
ATOM     70  CA  GLU    70      36.844  44.914  32.498  1.00 25.00           C
ATOM     71  CA  LEU    71      33.258  43.631  32.103  1.00 25.00           C
ATOM     72  CA  ALA    72      31.944  47.228  32.108  1.00 25.00           C
ATOM     73  CA  HIS    73      34.517  48.198  29.443  1.00 25.00           C
ATOM     74  CA  LEU    74      33.467  45.199  27.303  1.00 25.00           C
ATOM     75  CA  ILE    75      33.547  41.410  27.244  1.00 25.00           C
ATOM     76  CA  THR    76      30.335  40.697  29.228  1.00 25.00           C
ATOM     77  CA  VAL    77      30.654  36.968  28.351  1.00 25.00           C
ATOM     78  CA  PRO    78      28.551  36.641  31.464  1.00 25.00           C
ATOM     79  CA  ASP    79      25.595  34.667  30.033  1.00 25.00           C
ATOM     80  CA  ALA    80      23.832  33.535  33.169  1.00 25.00           C
ATOM     81  CA  SER    81      22.636  37.114  33.487  1.00 25.00           C
ATOM     82  CA  SER    82      24.098  39.645  35.947  1.00 25.00           C
ATOM     83  CA  ARG    83      24.278  43.435  36.514  1.00 25.00           C
ATOM     84  CA  GLY    84      25.179  46.304  34.143  1.00 25.00           C
ATOM     85  CA  ASN    85      26.297  44.258  31.134  1.00 25.00           C
ATOM     86  CA  THR    86      23.520  41.636  31.081  1.00 25.00           C
ATOM     87  CA  PRO    87      20.177  42.734  29.492  1.00 25.00           C
ATOM     88  CA  THR    88      18.377  44.852  26.858  1.00 25.00           C
ATOM     89  CA  ASN    89      18.413  47.866  29.220  1.00 25.00           C
ATOM     90  CA  ALA    90      22.161  47.370  29.835  1.00 25.00           C
ATOM     91  CA  HIS    91      22.782  47.197  26.060  1.00 25.00           C
ATOM     92  CA  SER    92      20.779  50.422  25.557  1.00 25.00           C
ATOM     93  CA  ILE    93      22.813  52.143  28.309  1.00 25.00           C
ATOM     94  CA  TYR    94      26.069  50.988  26.657  1.00 25.00           C
ATOM     95  CA  LYS    95      24.864  52.336  23.281  1.00 25.00           C
ATOM     96  CA  GLU    96      23.986  55.691  24.907  1.00 25.00           C
ATOM     97  CA  LEU    97      27.456  55.846  26.519  1.00 25.00           C
ATOM     98  CA  LYS    98      29.088  55.107  23.136  1.00 25.00           C
ATOM     99  CA  PRO    99      27.011  57.877  21.499  1.00 25.00           C
ATOM    100  CA  ILE   100      28.059  60.323  24.253  1.00 25.00           C
ATOM    101  CA  ASN   101      26.831  60.649  27.856  1.00 25.00           C
ATOM    102  CA  TYR   102      30.507  60.861  28.883  1.00 25.00           C
ATOM    103  CA  PRO   103      33.657  59.042  27.771  1.00 25.00           C
ATOM    104  CA  GLU   104      36.618  60.965  29.186  1.00 25.00           C
ATOM    105  CA  ASP   105      37.712  63.351  26.475  1.00 25.00           C
ATOM    106  CA  THR   106      37.658  61.073  23.485  1.00 25.00           C
ATOM    107  CA  LYS   107      39.309  58.464  25.787  1.00 25.00           C
ATOM    108  CA  ASN   108      39.749  54.735  25.565  1.00 25.00           C
ATOM    109  CA  VAL   109      37.074  52.535  24.001  1.00 25.00           C
ATOM    110  CA  HIS   110      37.180  48.726  23.752  1.00 25.00           C
ATOM    111  CA  PHE   111      37.081  45.043  23.131  1.00 25.00           C
ATOM    112  CA  VAL   112      35.477  43.941  19.891  1.00 25.00           C
ATOM    113  CA  LEU   113      33.704  40.602  19.793  1.00 25.00           C
ATOM    114  CA  PHE   114      30.757  38.346  20.754  1.00 25.00           C
ATOM    115  CA  ALA   115      28.490  35.666  22.191  1.00 25.00           C
ATOM    116  CA  GLU   116      25.578  35.301  19.772  1.00 25.00           C
ATOM    117  CA  TYR   117      22.849  33.472  21.578  1.00 25.00           C
ATOM    118  CA  PRO   118      23.723  35.281  24.752  1.00 25.00           C
ATOM    119  CA  ASP   119      21.665  38.177  23.325  1.00 25.00           C
ATOM    120  CA  VAL   120      22.945  40.486  26.099  1.00 25.00           C
ATOM    121  CA  LEU   121      26.549  39.428  25.352  1.00 25.00           C
ATOM    122  CA  SER   122      26.008  40.126  21.625  1.00 25.00           C
ATOM    123  CA  HIS   123      24.581  43.582  22.455  1.00 25.00           C
ATOM    124  CA  VAL   124      27.608  44.323  24.682  1.00 25.00           C
ATOM    125  CA  ALA   125      29.972  43.250  21.868  1.00 25.00           C
ATOM    126  CA  ALA   126      28.115  45.522  19.407  1.00 25.00           C
ATOM    127  CA  ILE   127      28.385  48.446  21.864  1.00 25.00           C
ATOM    128  CA  ALA   128      32.139  47.799  22.260  1.00 25.00           C
ATOM    129  CA  ARG   129      32.555  47.739  18.454  1.00 25.00           C
ATOM    130  CA  THR   130      30.646  51.048  18.169  1.00 25.00           C
ATOM    131  CA  PHE   131      32.883  52.598  20.863  1.00 25.00           C
ATOM    132  CA  CYS   132      36.005  51.392  19.001  1.00 25.00           C
ATOM    133  CA  LYS   133      34.674  52.899  15.742  1.00 25.00           C
ATOM    134  CA  PHE   134      34.005  56.223  17.525  1.00 25.00           C
ATOM    135  CA  SER   135      36.605  58.208  19.461  1.00 25.00           C
ATOM    136  CA  MET   136      34.372  61.207  18.773  1.00 25.00           C
ATOM    137  CA  LYS   137      33.376  62.101  15.201  1.00 25.00           C
ATOM    138  CA  THR   138      29.794  61.742  16.240  1.00 25.00           C
ATOM    139  CA  SER   139      28.207  63.632  13.358  1.00 25.00           C
ATOM    140  CA  GLY   140      27.569  60.301  11.556  1.00 25.00           C
ATOM    141  CA  ILE   141      23.881  60.880  12.488  1.00 25.00           C
ATOM    142  CA  ARG   142      20.901  58.541  12.827  1.00 25.00           C
ATOM    143  CA  GLU   143      22.908  55.437  13.708  1.00 25.00           C
ATOM    144  CA  LEU   144      25.476  53.089  15.172  1.00 25.00           C
ATOM    145  CA  ASN   145      24.119  49.829  13.782  1.00 25.00           C
ATOM    146  CA  VAL   146      25.132  46.469  15.245  1.00 25.00           C
ATOM    147  CA  ASN   147      23.005  43.877  17.012  1.00 25.00           C
ATOM    148  CA  ILE   148      23.627  40.136  17.130  1.00 25.00           C
ATOM    149  CA  ASP   149      20.847  37.838  15.789  1.00 25.00           C
ATOM    150  CA  VAL   150      22.268  34.325  16.112  1.00 25.00           C
ATOM    151  CA  VAL   151      20.966  30.743  16.240  1.00 25.00           C
ATOM    152  CA  CYS   152      20.759  27.021  16.893  1.00 25.00           C
ATOM    153  CA  ASP   153      21.561  23.280  17.087  1.00 25.00           C
ATOM    154  CA  LYS   154      23.605  20.182  16.255  1.00 25.00           C
ATOM    155  CA  LEU   155      25.200  19.960  12.781  1.00 25.00           C
TER
END
