
#######################################################
#                                                     #
#                        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  143 (  143),  selected  143 , name T0338TS393_5-D1
# Molecule2: number of CA atoms  143 ( 1129),  selected  143 , name T0338_D1.pdb
# PARAMETERS: T0338TS393_5-D1.T0338_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A       1      A       1           -
LGA    S       2      S       2           -
LGA    S       3      S       3           -
LGA    R       4      R       4           -
LGA    W       5      W       5           -
LGA    F       6      F       6           -
LGA    F       7      F       7           -
LGA    T       8      T       8           -
LGA    R       9      R       9           -
LGA    E      10      E      10           -
LGA    Q      11      Q      11           -
LGA    -       -      L      12           -
LGA    -       -      E      13           -
LGA    -       -      N      14           -
LGA    -       -      T      15           -
LGA    -       -      P      16           -
LGA    -       -      S      17           -
LGA    -       -      R      18           -
LGA    -       -      R      19           -
LGA    -       -      C      20           -
LGA    -       -      G      21           -
LGA    -       -      V      22           -
LGA    -       -      E      23           -
LGA    -       -      A      24           -
LGA    -       -      D      25           -
LGA    -       -      K      26           -
LGA    -       -      E      27           -
LGA    -       -      L      28           -
LGA    -       -      S      29           -
LGA    -       -      C      30           -
LGA    -       -      R      31           -
LGA    -       -      Q      32           -
LGA    -       -      Q      33           -
LGA    -       -      A      34           -
LGA    -       -      A      35           -
LGA    -       -      N      36           -
LGA    -       -      L      37           -
LGA    -       -      I      38           -
LGA    -       -      Q      39           -
LGA    -       -      E      40           -
LGA    -       -      M      41           -
LGA    -       -      G      42           -
LGA    -       -      Q      43           -
LGA    L      12      R      44          5.211
LGA    E      13      L      45           -
LGA    N      14      N      46           -
LGA    T      15      V      47           -
LGA    P      16      -       -           -
LGA    S      17      -       -           -
LGA    R      18      -       -           -
LGA    R      19      -       -           -
LGA    C      20      -       -           -
LGA    G      21      -       -           -
LGA    V      22      -       -           -
LGA    E      23      -       -           -
LGA    A      24      S      48          4.287
LGA    D      25      Q      49          4.369
LGA    K      26      L      50          2.607
LGA    E      27      T      51          3.968
LGA    L      28      I      52           #
LGA    S      29      N      53          5.765
LGA    -       -      T      54           -
LGA    C      30      A      55           #
LGA    R      31      -       -           -
LGA    Q      32      -       -           -
LGA    Q      33      I      56          5.730
LGA    A      34      V      57           -
LGA    A      35      Y      58           -
LGA    N      36      -       -           -
LGA    L      37      M      59           #
LGA    I      38      H      60           -
LGA    Q      39      R      61           -
LGA    -       -      F      62           -
LGA    -       -      Y      63           -
LGA    -       -      M      64           -
LGA    -       -      H      65           -
LGA    -       -      H      66           -
LGA    -       -      S      67           -
LGA    -       -      F      68           -
LGA    -       -      T      69           -
LGA    -       -      K      70           -
LGA    -       -      F      71           -
LGA    -       -      N      72           -
LGA    E      40      K      73          5.603
LGA    M      41      N      74          1.888
LGA    G      42      -       -           -
LGA    Q      43      -       -           -
LGA    R      44      -       -           -
LGA    L      45      -       -           -
LGA    N      46      -       -           -
LGA    V      47      -       -           -
LGA    S      48      -       -           -
LGA    Q      49      -       -           -
LGA    L      50      -       -           -
LGA    T      51      -       -           -
LGA    I      52      -       -           -
LGA    N      53      -       -           -
LGA    T      54      -       -           -
LGA    A      55      I      75          2.205
LGA    I      56      -       -           -
LGA    V      57      -       -           -
LGA    Y      58      I      76          0.944
LGA    M      59      S      77          3.110
LGA    H      60      S      78           #
LGA    R      61      T      79          4.672
LGA    F      62      A      80          2.193
LGA    Y      63      L      81          2.711
LGA    -       -      F      82           -
LGA    M      64      L      83          4.152
LGA    H      65      A      84           #
LGA    H      66      A      85           -
LGA    -       -      K      86           -
LGA    S      67      V      87          4.590
LGA    F      68      E      88          1.406
LGA    T      69      -       -           -
LGA    K      70      E      89          1.775
LGA    F      71      -       -           -
LGA    N      72      Q      90          2.453
LGA    K      73      A      91          2.764
LGA    N      74      R      92           #
LGA    I      75      -       -           -
LGA    I      76      K      93          2.993
LGA    S      77      -       -           -
LGA    S      78      L      94          5.163
LGA    T      79      E      95          4.515
LGA    A      80      H      96          3.900
LGA    L      81      V      97          4.059
LGA    F      82      I      98          3.401
LGA    L      83      K      99          3.313
LGA    -       -      V     100           -
LGA    A      84      A     101          1.877
LGA    A      85      H     102          4.310
LGA    K      86      -       -           -
LGA    V      87      -       -           -
LGA    E      88      -       -           -
LGA    E      89      A     103           #
LGA    Q      90      C     104          0.674
LGA    A      91      L     105           #
LGA    R      92      H     106           -
LGA    K      93      P     107           -
LGA    L      94      L     108           -
LGA    E      95      E     109           -
LGA    H      96      -       -           -
LGA    V      97      -       -           -
LGA    I      98      -       -           -
LGA    K      99      -       -           -
LGA    V     100      -       -           -
LGA    A     101      -       -           -
LGA    H     102      -       -           -
LGA    A     103      -       -           -
LGA    C     104      P     110           #
LGA    L     105      L     111          3.389
LGA    H     106      L     112           -
LGA    P     107      -       -           -
LGA    L     108      -       -           -
LGA    E     109      -       -           -
LGA    P     110      -       -           -
LGA    L     111      -       -           -
LGA    L     112      -       -           -
LGA    D     113      -       -           -
LGA    T     114      D     113           #
LGA    K     115      T     114           #
LGA    -       -      K     115           -
LGA    C     116      C     116          1.843
LGA    D     117      D     117          1.688
LGA    A     118      A     118          2.056
LGA    Y     119      Y     119          1.629
LGA    L     120      L     120          0.552
LGA    Q     121      Q     121          1.240
LGA    Q     122      Q     122          1.602
LGA    T     123      T     123          0.846
LGA    R     124      R     124          0.520
LGA    E     125      E     125          1.246
LGA    L     126      L     126          1.371
LGA    V     127      V     127          0.877
LGA    I     128      I     128          0.695
LGA    L     129      L     129          1.381
LGA    E     130      E     130          1.934
LGA    T     131      T     131          1.904
LGA    I     132      I     132          1.525
LGA    M     133      M     133          2.997
LGA    L     134      L     134          3.752
LGA    Q     135      Q     135          3.070
LGA    T     136      T     136          3.560
LGA    -       -      L     137           -
LGA    -       -      G     138           -
LGA    L     137      F     139          2.020
LGA    G     138      E     140          2.586
LGA    F     139      I     141          3.291
LGA    E     140      T     142           #
LGA    I     141      I     143           -
LGA    T     142      -       -           -
LGA    I     143      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  143  143    5.0     56    3.11    41.07     25.339     1.746

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.918234 * X  +   0.263056 * Y  +  -0.296053 * Z  + -18.209309
  Y_new =   0.263503 * X  +  -0.963863 * Y  +  -0.039159 * Z  +  41.115669
  Z_new =  -0.295656 * X  +  -0.042054 * Y  +  -0.954368 * Z  +  46.952553 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.097556    0.044036  [ DEG:  -177.4769      2.5231 ]
  Theta =   0.300142    2.841451  [ DEG:    17.1969    162.8031 ]
  Phi   =   0.279458   -2.862135  [ DEG:    16.0117   -163.9883 ]
 
# 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: T0338TS393_5-D1                               
REMARK     2: T0338_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0338TS393_5-D1.T0338_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  143  143   5.0   56   3.11   41.07  25.339
REMARK  ---------------------------------------------------------- 
MOLECULE T0338TS393_5-D1
PFRMAT TS
TARGET T0338
MODEL 5
PARENT N/A
ATOM      1  CA  ALA     1     -30.680  61.702  61.383  1.00 25.00           C
ATOM      2  CA  SER     2     -30.388  60.694  57.687  1.00 25.00           C
ATOM      3  CA  SER     3     -26.772  59.549  57.872  1.00 25.00           C
ATOM      4  CA  ARG     4     -27.044  55.816  58.671  1.00 25.00           C
ATOM      5  CA  TRP     5     -24.202  54.872  56.429  1.00 25.00           C
ATOM      6  CA  PHE     6     -22.054  53.375  59.117  1.00 25.00           C
ATOM      7  CA  PHE     7     -22.034  51.799  62.561  1.00 25.00           C
ATOM      8  CA  THR     8     -20.720  48.440  63.761  1.00 25.00           C
ATOM      9  CA  ARG     9     -20.530  47.329  67.406  1.00 25.00           C
ATOM     10  CA  GLU    10     -23.006  47.473  70.323  1.00 25.00           C
ATOM     11  CA  GLN    11     -25.898  46.684  67.940  1.00 25.00           C
ATOM     12  CA  LEU    12     -23.947  43.713  66.516  1.00 25.00           C
ATOM     13  CA  GLU    13     -23.261  42.432  70.060  1.00 25.00           C
ATOM     14  CA  ASN    14     -25.040  43.785  73.117  1.00 25.00           C
ATOM     15  CA  THR    15     -28.225  43.308  71.095  1.00 25.00           C
ATOM     16  CA  PRO    16     -31.975  43.143  71.439  1.00 25.00           C
ATOM     17  CA  SER    17     -34.946  42.644  73.734  1.00 25.00           C
ATOM     18  CA  ARG    18     -38.045  43.018  71.611  1.00 25.00           C
ATOM     19  CA  ARG    19     -39.036  40.357  69.026  1.00 25.00           C
ATOM     20  CA  CYS    20     -39.837  37.672  66.372  1.00 25.00           C
ATOM     21  CA  GLY    21     -38.600  34.064  65.906  1.00 25.00           C
ATOM     22  CA  VAL    22     -37.001  31.653  63.392  1.00 25.00           C
ATOM     23  CA  GLU    23     -34.824  29.150  65.208  1.00 25.00           C
ATOM     24  CA  ALA    24     -31.724  31.349  65.487  1.00 25.00           C
ATOM     25  CA  ASP    25     -29.240  29.510  67.749  1.00 25.00           C
ATOM     26  CA  LYS    26     -27.875  27.590  64.729  1.00 25.00           C
ATOM     27  CA  GLU    27     -27.476  30.870  62.793  1.00 25.00           C
ATOM     28  CA  LEU    28     -25.622  32.426  65.762  1.00 25.00           C
ATOM     29  CA  SER    29     -23.307  29.380  65.943  1.00 25.00           C
ATOM     30  CA  CYS    30     -22.607  29.657  62.187  1.00 25.00           C
ATOM     31  CA  ARG    31     -21.807  33.380  62.587  1.00 25.00           C
ATOM     32  CA  GLN    32     -19.427  32.585  65.480  1.00 25.00           C
ATOM     33  CA  GLN    33     -17.696  29.911  63.353  1.00 25.00           C
ATOM     34  CA  ALA    34     -17.320  32.410  60.475  1.00 25.00           C
ATOM     35  CA  ALA    35     -15.824  34.990  62.878  1.00 25.00           C
ATOM     36  CA  ASN    36     -13.362  32.370  64.197  1.00 25.00           C
ATOM     37  CA  LEU    37     -12.356  31.475  60.612  1.00 25.00           C
ATOM     38  CA  ILE    38     -11.809  35.180  59.814  1.00 25.00           C
ATOM     39  CA  GLN    39      -9.648  35.563  62.952  1.00 25.00           C
ATOM     40  CA  GLU    40      -7.587  32.498  61.937  1.00 25.00           C
ATOM     41  CA  MET    41      -7.106  33.955  58.427  1.00 25.00           C
ATOM     42  CA  GLY    42      -5.977  37.288  59.939  1.00 25.00           C
ATOM     43  CA  GLN    43      -3.492  35.449  62.200  1.00 25.00           C
ATOM     44  CA  ARG    44      -2.127  33.529  59.180  1.00 25.00           C
ATOM     45  CA  LEU    45       0.031  36.659  58.731  1.00 25.00           C
ATOM     46  CA  ASN    46       2.617  38.629  56.766  1.00 25.00           C
ATOM     47  CA  VAL    47       0.214  40.081  54.146  1.00 25.00           C
ATOM     48  CA  SER    48       0.622  41.012  50.466  1.00 25.00           C
ATOM     49  CA  GLN    49      -2.331  40.828  48.079  1.00 25.00           C
ATOM     50  CA  LEU    50      -1.965  37.052  47.553  1.00 25.00           C
ATOM     51  CA  THR    51      -2.373  36.463  51.315  1.00 25.00           C
ATOM     52  CA  ILE    52      -5.518  38.648  51.341  1.00 25.00           C
ATOM     53  CA  ASN    53      -6.937  36.684  48.376  1.00 25.00           C
ATOM     54  CA  THR    54      -6.219  33.385  50.185  1.00 25.00           C
ATOM     55  CA  ALA    55      -7.970  34.700  53.327  1.00 25.00           C
ATOM     56  CA  ILE    56     -10.999  35.747  51.232  1.00 25.00           C
ATOM     57  CA  VAL    57     -11.117  32.274  49.623  1.00 25.00           C
ATOM     58  CA  TYR    58     -10.966  30.639  53.083  1.00 25.00           C
ATOM     59  CA  MET    59     -13.821  32.885  54.296  1.00 25.00           C
ATOM     60  CA  HIS    60     -15.900  31.945  51.220  1.00 25.00           C
ATOM     61  CA  ARG    61     -15.244  28.231  51.881  1.00 25.00           C
ATOM     62  CA  PHE    62     -16.313  28.666  55.533  1.00 25.00           C
ATOM     63  CA  TYR    63     -19.518  30.435  54.410  1.00 25.00           C
ATOM     64  CA  MET    64     -20.256  27.590  51.953  1.00 25.00           C
ATOM     65  CA  HIS    65     -19.715  25.015  54.736  1.00 25.00           C
ATOM     66  CA  HIS    66     -23.397  24.376  55.113  1.00 25.00           C
ATOM     67  CA  SER    67     -26.936  25.083  54.037  1.00 25.00           C
ATOM     68  CA  PHE    68     -28.162  28.438  55.349  1.00 25.00           C
ATOM     69  CA  THR    69     -31.800  27.914  56.334  1.00 25.00           C
ATOM     70  CA  LYS    70     -32.862  31.129  54.710  1.00 25.00           C
ATOM     71  CA  PHE    71     -29.847  32.276  52.617  1.00 25.00           C
ATOM     72  CA  ASN    72     -28.011  34.778  54.863  1.00 25.00           C
ATOM     73  CA  LYS    73     -26.383  35.799  51.530  1.00 25.00           C
ATOM     74  CA  ASN    74     -23.237  33.710  50.897  1.00 25.00           C
ATOM     75  CA  ILE    75     -21.665  36.618  48.964  1.00 25.00           C
ATOM     76  CA  ILE    76     -22.493  39.008  51.838  1.00 25.00           C
ATOM     77  CA  SER    77     -20.912  36.582  54.345  1.00 25.00           C
ATOM     78  CA  SER    78     -17.768  36.346  52.170  1.00 25.00           C
ATOM     79  CA  THR    79     -17.576  40.166  51.990  1.00 25.00           C
ATOM     80  CA  ALA    80     -17.921  40.388  55.797  1.00 25.00           C
ATOM     81  CA  LEU    81     -15.128  37.802  56.226  1.00 25.00           C
ATOM     82  CA  PHE    82     -12.888  39.791  53.840  1.00 25.00           C
ATOM     83  CA  LEU    83     -13.593  42.997  55.812  1.00 25.00           C
ATOM     84  CA  ALA    84     -12.724  41.208  59.084  1.00 25.00           C
ATOM     85  CA  ALA    85      -9.456  39.934  57.547  1.00 25.00           C
ATOM     86  CA  LYS    86      -8.595  43.479  56.379  1.00 25.00           C
ATOM     87  CA  VAL    87      -9.298  44.833  59.892  1.00 25.00           C
ATOM     88  CA  GLU    88      -7.049  42.130  61.411  1.00 25.00           C
ATOM     89  CA  GLU    89      -8.182  41.524  64.961  1.00 25.00           C
ATOM     90  CA  GLN    90     -11.888  40.589  64.424  1.00 25.00           C
ATOM     91  CA  ALA    91     -15.543  39.819  65.295  1.00 25.00           C
ATOM     92  CA  ARG    92     -18.643  40.291  63.242  1.00 25.00           C
ATOM     93  CA  LYS    93     -20.694  38.958  60.274  1.00 25.00           C
ATOM     94  CA  LEU    94     -22.582  40.439  57.323  1.00 25.00           C
ATOM     95  CA  GLU    95     -24.175  43.870  57.921  1.00 25.00           C
ATOM     96  CA  HIS    96     -21.880  44.438  60.934  1.00 25.00           C
ATOM     97  CA  VAL    97     -18.831  43.477  58.825  1.00 25.00           C
ATOM     98  CA  ILE    98     -19.934  45.909  56.080  1.00 25.00           C
ATOM     99  CA  LYS    99     -20.348  48.693  58.678  1.00 25.00           C
ATOM    100  CA  VAL   100     -16.851  47.960  60.055  1.00 25.00           C
ATOM    101  CA  ALA   101     -15.400  48.099  56.514  1.00 25.00           C
ATOM    102  CA  HIS   102     -17.150  51.449  55.902  1.00 25.00           C
ATOM    103  CA  ALA   103     -15.742  52.815  59.191  1.00 25.00           C
ATOM    104  CA  CYS   104     -12.230  51.657  58.197  1.00 25.00           C
ATOM    105  CA  LEU   105      -9.074  53.338  59.497  1.00 25.00           C
ATOM    106  CA  HIS   106     -10.454  56.600  60.715  1.00 25.00           C
ATOM    107  CA  PRO   107      -9.225  58.795  57.886  1.00 25.00           C
ATOM    108  CA  LEU   108      -8.118  62.304  58.952  1.00 25.00           C
ATOM    109  CA  GLU   109      -6.696  62.457  55.408  1.00 25.00           C
ATOM    110  CA  PRO   110      -3.541  60.368  54.642  1.00 25.00           C
ATOM    111  CA  LEU   111      -4.980  56.982  53.643  1.00 25.00           C
ATOM    112  CA  LEU   112      -8.672  57.019  52.627  1.00 25.00           C
ATOM    113  CA  ASP   113      -7.725  56.022  49.053  1.00 25.00           C
ATOM    114  CA  THR   114      -5.573  53.154  50.397  1.00 25.00           C
ATOM    115  CA  LYS   115      -8.480  51.969  52.591  1.00 25.00           C
ATOM    116  CA  CYS   116     -10.833  52.072  49.572  1.00 25.00           C
ATOM    117  CA  ASP   117      -8.320  50.043  47.513  1.00 25.00           C
ATOM    118  CA  ALA   118      -8.050  47.467  50.335  1.00 25.00           C
ATOM    119  CA  TYR   119     -11.868  47.213  50.500  1.00 25.00           C
ATOM    120  CA  LEU   120     -12.024  46.700  46.709  1.00 25.00           C
ATOM    121  CA  GLN   121      -9.363  43.955  46.947  1.00 25.00           C
ATOM    122  CA  GLN   122     -11.343  42.244  49.743  1.00 25.00           C
ATOM    123  CA  THR   123     -14.527  42.406  47.622  1.00 25.00           C
ATOM    124  CA  ARG   124     -12.653  40.883  44.649  1.00 25.00           C
ATOM    125  CA  GLU   125     -11.331  38.073  46.891  1.00 25.00           C
ATOM    126  CA  LEU   126     -14.876  37.394  48.171  1.00 25.00           C
ATOM    127  CA  VAL   127     -16.177  37.262  44.572  1.00 25.00           C
ATOM    128  CA  ILE   128     -13.392  34.809  43.629  1.00 25.00           C
ATOM    129  CA  LEU   129     -14.269  32.615  46.643  1.00 25.00           C
ATOM    130  CA  GLU   130     -17.961  32.653  45.626  1.00 25.00           C
ATOM    131  CA  THR   131     -17.014  31.656  42.052  1.00 25.00           C
ATOM    132  CA  ILE   132     -14.861  28.787  43.397  1.00 25.00           C
ATOM    133  CA  MET   133     -17.768  27.603  45.591  1.00 25.00           C
ATOM    134  CA  LEU   134     -20.122  27.705  42.572  1.00 25.00           C
ATOM    135  CA  GLN   135     -17.609  25.677  40.513  1.00 25.00           C
ATOM    136  CA  THR   136     -17.340  23.101  43.335  1.00 25.00           C
ATOM    137  CA  LEU   137     -21.157  22.847  43.500  1.00 25.00           C
ATOM    138  CA  GLY   138     -21.448  21.600  47.085  1.00 25.00           C
ATOM    139  CA  PHE   139     -22.869  25.011  47.894  1.00 25.00           C
ATOM    140  CA  GLU   140     -26.111  24.990  45.877  1.00 25.00           C
ATOM    141  CA  ILE   141     -25.118  27.411  43.137  1.00 25.00           C
ATOM    142  CA  THR   142     -28.521  28.167  41.573  1.00 25.00           C
ATOM    143  CA  ILE   143     -27.013  31.689  41.176  1.00 25.00           C
TER
END
