
#######################################################
#                                                     #
#                        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  151 (  151),  selected  151 , name T0362TS393_2
# Molecule2: number of CA atoms  144 ( 1169),  selected  144 , name T0362.pdb
# PARAMETERS: T0362TS393_2.T0362.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           #
LGA    N       2      N       2           -
LGA    P       3      P       3           -
LGA    E       4      -       -           -
LGA    N       5      E       4          4.867
LGA    W       6      N       5          2.072
LGA    L       7      W       6           -
LGA    -       -      L       7           -
LGA    L       8      L       8          3.001
LGA    L       9      L       9          1.059
LGA    R      10      R      10          1.939
LGA    R      11      R      11          2.125
LGA    V      12      V      12          2.499
LGA    V      13      V      13          4.042
LGA    R      14      R      14          3.250
LGA    F      15      F      15           #
LGA    G      16      G      16          1.987
LGA    D      17      D      17          1.397
LGA    T      18      T      18          1.666
LGA    D      19      D      19          2.641
LGA    A      20      A      20           #
LGA    A      21      A      21           #
LGA    G      22      G      22           #
LGA    V      23      V      23          3.263
LGA    M      24      M      24          3.002
LGA    H      25      H      25          2.241
LGA    F      26      F      26          2.471
LGA    H      27      H      27          1.753
LGA    Q      28      Q      28          0.690
LGA    L      29      L      29          1.161
LGA    F      30      F      30          1.209
LGA    R      31      R      31          0.735
LGA    W      32      W      32          1.047
LGA    C      33      C      33          1.288
LGA    H      34      H      34          0.991
LGA    E      35      E      35          1.128
LGA    S      36      S      36          1.649
LGA    W      37      W      37          1.579
LGA    E      38      E      38          1.334
LGA    E      39      E      39          1.661
LGA    S      40      S      40          2.114
LGA    L      41      L      41          2.120
LGA    E      42      E      42          1.982
LGA    S      43      S      43          2.841
LGA    Y      44      Y      44          3.366
LGA    G      45      G      45          3.326
LGA    L      46      L      46          2.460
LGA    N      47      N      47          2.812
LGA    P      48      P      48          1.782
LGA    A      49      A      49          6.164
LGA    D      50      -       -           -
LGA    I      51      -       -           -
LGA    F      52      -       -           -
LGA    P      53      -       -           -
LGA    G      54      -       -           -
LGA    S      55      D      50          4.408
LGA    R      56      -       -           -
LGA    K      57      -       -           -
LGA    S      58      -       -           -
LGA    E      59      -       -           -
LGA    V      60      -       -           -
LGA    T      61      -       -           -
LGA    P      62      -       -           -
LGA    E      63      -       -           -
LGA    V      64      I      51          3.453
LGA    A      65      F      52          3.774
LGA    L      66      P      53           -
LGA    -       -      G      54           -
LGA    -       -      S      55           -
LGA    -       -      R      56           -
LGA    -       -      K      57           -
LGA    -       -      S      58           -
LGA    -       -      E      59           -
LGA    -       -      V      60           -
LGA    -       -      T      61           -
LGA    -       -      P      62           -
LGA    -       -      E      63           -
LGA    -       -      V      64           -
LGA    -       -      A      65           -
LGA    -       -      L      66           -
LGA    P      67      P      67          3.983
LGA    I      68      I      68          3.611
LGA    I      69      I      69          4.423
LGA    H      70      H      70          1.485
LGA    C      71      C      71          1.348
LGA    Q      72      Q      72          1.566
LGA    A      73      A      73          1.106
LGA    D      74      D      74          1.328
LGA    F      75      F      75          1.367
LGA    R      76      R      76          1.170
LGA    R      77      R      77          1.922
LGA    P      78      P      78          0.358
LGA    I      79      I      79          0.362
LGA    H      80      H      80          1.301
LGA    T      81      T      81          1.940
LGA    G      82      G      82          0.665
LGA    D      83      D      83          0.803
LGA    A      84      A      84          1.944
LGA    L      85      L      85          1.610
LGA    A      86      A      86          1.285
LGA    M      87      M      87          0.937
LGA    E      88      E      88          1.126
LGA    L      89      L      89          2.166
LGA    R      90      R      90          2.766
LGA    P      91      P      91          2.047
LGA    E      92      E      92          3.145
LGA    R      93      R      93          4.757
LGA    L      94      L      94          2.326
LGA    N      95      N      95          2.898
LGA    P      96      P      96           #
LGA    -       -      N      97           -
LGA    N      97      S      98          1.252
LGA    S      98      F      99          2.268
LGA    F      99      Q     100          3.857
LGA    Q     100      V     101          2.798
LGA    V     101      H     102          2.355
LGA    H     102      F     103          2.387
LGA    F     103      E     104          2.486
LGA    E     104      F     105          3.860
LGA    F     105      R     106          2.171
LGA    R     106      C     107          2.140
LGA    C     107      E     108          1.182
LGA    E     108      -       -           -
LGA    E     109      E     109          5.151
LGA    Q     110      Q     110          1.728
LGA    I     111      I     111          2.203
LGA    A     112      A     112          1.000
LGA    A     113      A     113          1.792
LGA    H     114      H     114          2.917
LGA    A     115      A     115          1.115
LGA    L     116      L     116          1.235
LGA    I     117      I     117          2.400
LGA    R     118      R     118          4.015
LGA    H     119      H     119          5.861
LGA    L     120      L     120          5.287
LGA    A     121      A     121          6.092
LGA    I     122      I     122          6.006
LGA    N     123      -       -           -
LGA    A     124      -       -           -
LGA    Q     125      -       -           -
LGA    T     126      -       -           -
LGA    R     127      N     123          4.454
LGA    H     128      A     124           #
LGA    -       -      Q     125           -
LGA    -       -      T     126           -
LGA    -       -      R     127           -
LGA    -       -      H     128           -
LGA    R     129      R     129          2.298
LGA    C     130      C     130          1.658
LGA    A     131      A     131          1.500
LGA    L     132      L     132          1.582
LGA    P     133      P     133          1.981
LGA    E     134      E     134          3.967
LGA    G     135      G     135           -
LGA    I     136      I     136          3.690
LGA    D     137      D     137          3.280
LGA    -       -      R     138           -
LGA    R     138      W     139          2.721
LGA    W     139      L     140          2.267
LGA    L     140      E     141          2.643
LGA    E     141      A     142          1.952
LGA    -       -      S     143           -
LGA    A     142      G     144          3.567
LGA    S     143      -       -           -
LGA    G     144      -       -           -
LGA    V     145      -       -           -
LGA    G     146      -       -           -
LGA    K     147      -       -           -
LGA    I     148      -       -           -
LGA    G     149      -       -           -
LGA    S     150      -       -           -
LGA    I     151      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  151  144    5.0    111    2.73    80.18     47.207     3.919

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.175524 * X  +  -0.810184 * Y  +  -0.559279 * Z  +  39.745461
  Y_new =  -0.739095 * X  +   0.266833 * Y  +  -0.618497 * Z  +  46.035122
  Z_new =   0.650331 * X  +   0.521921 * Y  +  -0.551967 * Z  +  12.937762 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.384166   -0.757427  [ DEG:   136.6026    -43.3974 ]
  Theta =  -0.708020   -2.433572  [ DEG:   -40.5666   -139.4334 ]
  Phi   =  -1.337631    1.803962  [ DEG:   -76.6406    103.3594 ]
 
# 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: T0362TS393_2                                  
REMARK     2: T0362.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0362TS393_2.T0362.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  151  144   5.0  111   2.73   80.18  47.207
REMARK  ---------------------------------------------------------- 
MOLECULE T0362TS393_2
PFRMAT TS
TARGET T0362
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1      42.938  45.829  37.538  1.00 25.00           C
ATOM      2  CA  ASN     2      44.865  47.777  34.905  1.00 25.00           C
ATOM      3  CA  PRO     3      45.851  51.063  33.291  1.00 25.00           C
ATOM      4  CA  GLU     4      42.534  51.400  31.480  1.00 25.00           C
ATOM      5  CA  ASN     5      39.666  49.939  29.519  1.00 25.00           C
ATOM      6  CA  TRP     6      39.550  48.941  25.862  1.00 25.00           C
ATOM      7  CA  LEU     7      38.840  52.511  24.588  1.00 25.00           C
ATOM      8  CA  LEU     8      42.223  52.098  22.836  1.00 25.00           C
ATOM      9  CA  LEU     9      42.752  51.343  19.181  1.00 25.00           C
ATOM     10  CA  ARG    10      45.812  53.413  18.231  1.00 25.00           C
ATOM     11  CA  ARG    11      48.278  54.318  15.491  1.00 25.00           C
ATOM     12  CA  VAL    12      49.721  57.198  13.426  1.00 25.00           C
ATOM     13  CA  VAL    13      47.630  56.859  10.343  1.00 25.00           C
ATOM     14  CA  ARG    14      50.572  58.371   8.567  1.00 25.00           C
ATOM     15  CA  PHE    15      51.347  55.688   6.008  1.00 25.00           C
ATOM     16  CA  GLY    16      53.486  58.076   3.964  1.00 25.00           C
ATOM     17  CA  ASP    17      50.227  60.042   3.704  1.00 25.00           C
ATOM     18  CA  THR    18      49.336  63.269   1.934  1.00 25.00           C
ATOM     19  CA  ASP    19      50.921  61.784  -1.190  1.00 25.00           C
ATOM     20  CA  ALA    20      49.801  64.209  -3.849  1.00 25.00           C
ATOM     21  CA  ALA    21      46.223  63.105  -3.285  1.00 25.00           C
ATOM     22  CA  GLY    22      44.454  64.368  -0.198  1.00 25.00           C
ATOM     23  CA  VAL    23      44.529  63.747   3.589  1.00 25.00           C
ATOM     24  CA  MET    24      44.854  59.903   3.510  1.00 25.00           C
ATOM     25  CA  HIS    25      44.931  59.269  -0.281  1.00 25.00           C
ATOM     26  CA  PHE    26      41.857  56.982  -0.176  1.00 25.00           C
ATOM     27  CA  HIS    27      44.608  54.317  -0.200  1.00 25.00           C
ATOM     28  CA  GLN    28      46.011  55.701   3.083  1.00 25.00           C
ATOM     29  CA  LEU    29      42.514  55.613   4.645  1.00 25.00           C
ATOM     30  CA  PHE    30      42.066  51.987   3.496  1.00 25.00           C
ATOM     31  CA  ARG    31      45.460  51.062   5.012  1.00 25.00           C
ATOM     32  CA  TRP    32      44.471  52.737   8.311  1.00 25.00           C
ATOM     33  CA  CYS    33      41.162  50.808   8.326  1.00 25.00           C
ATOM     34  CA  HIS    34      43.042  47.530   7.699  1.00 25.00           C
ATOM     35  CA  GLU    35      45.439  48.326  10.579  1.00 25.00           C
ATOM     36  CA  SER    36      42.468  49.054  12.883  1.00 25.00           C
ATOM     37  CA  TRP    37      40.845  45.734  11.880  1.00 25.00           C
ATOM     38  CA  GLU    38      44.121  43.886  12.601  1.00 25.00           C
ATOM     39  CA  GLU    39      44.348  45.577  16.031  1.00 25.00           C
ATOM     40  CA  SER    40      40.735  44.565  16.796  1.00 25.00           C
ATOM     41  CA  LEU    41      41.504  40.954  15.778  1.00 25.00           C
ATOM     42  CA  GLU    42      44.592  40.948  18.043  1.00 25.00           C
ATOM     43  CA  SER    43      42.492  42.288  20.952  1.00 25.00           C
ATOM     44  CA  TYR    44      39.875  39.557  20.353  1.00 25.00           C
ATOM     45  CA  GLY    45      42.544  36.879  20.465  1.00 25.00           C
ATOM     46  CA  LEU    46      43.804  35.355  17.209  1.00 25.00           C
ATOM     47  CA  ASN    47      46.774  33.588  15.560  1.00 25.00           C
ATOM     48  CA  PRO    48      48.322  37.054  15.721  1.00 25.00           C
ATOM     49  CA  ALA    49      51.536  36.766  17.782  1.00 25.00           C
ATOM     50  CA  ASP    50      49.743  34.514  20.308  1.00 25.00           C
ATOM     51  CA  ILE    51      46.621  33.437  22.270  1.00 25.00           C
ATOM     52  CA  PHE    52      43.841  31.439  20.579  1.00 25.00           C
ATOM     53  CA  PRO    53      44.812  28.148  22.213  1.00 25.00           C
ATOM     54  CA  GLY    54      48.202  28.862  20.759  1.00 25.00           C
ATOM     55  CA  SER    55      46.671  28.572  17.329  1.00 25.00           C
ATOM     56  CA  ARG    56      48.036  26.942  14.173  1.00 25.00           C
ATOM     57  CA  LYS    57      46.868  23.652  15.688  1.00 25.00           C
ATOM     58  CA  SER    58      44.288  23.330  18.399  1.00 25.00           C
ATOM     59  CA  GLU    59      42.006  25.662  16.363  1.00 25.00           C
ATOM     60  CA  VAL    60      41.336  22.933  13.759  1.00 25.00           C
ATOM     61  CA  THR    61      42.616  25.218  10.942  1.00 25.00           C
ATOM     62  CA  PRO    62      42.839  28.854   9.948  1.00 25.00           C
ATOM     63  CA  GLU    63      45.610  30.704   8.000  1.00 25.00           C
ATOM     64  CA  VAL    64      43.206  33.654   8.476  1.00 25.00           C
ATOM     65  CA  ALA    65      44.316  37.106   7.530  1.00 25.00           C
ATOM     66  CA  LEU    66      43.349  40.714   6.608  1.00 25.00           C
ATOM     67  CA  PRO    67      41.540  40.918   3.271  1.00 25.00           C
ATOM     68  CA  ILE    68      39.481  44.086   3.717  1.00 25.00           C
ATOM     69  CA  ILE    69      37.979  44.294   0.292  1.00 25.00           C
ATOM     70  CA  HIS    70      34.540  45.623   1.147  1.00 25.00           C
ATOM     71  CA  CYS    71      35.837  49.147   1.905  1.00 25.00           C
ATOM     72  CA  GLN    72      32.732  51.215   2.737  1.00 25.00           C
ATOM     73  CA  ALA    73      33.699  54.838   3.657  1.00 25.00           C
ATOM     74  CA  ASP    74      33.422  58.207   5.420  1.00 25.00           C
ATOM     75  CA  PHE    75      36.427  60.543   5.446  1.00 25.00           C
ATOM     76  CA  ARG    76      34.311  63.254   7.023  1.00 25.00           C
ATOM     77  CA  ARG    77      37.112  65.738   6.270  1.00 25.00           C
ATOM     78  CA  PRO    78      40.652  66.841   7.055  1.00 25.00           C
ATOM     79  CA  ILE    79      43.327  64.507   8.465  1.00 25.00           C
ATOM     80  CA  HIS    80      46.150  66.859   9.622  1.00 25.00           C
ATOM     81  CA  THR    81      49.861  66.530  10.549  1.00 25.00           C
ATOM     82  CA  GLY    82      50.525  64.552  13.741  1.00 25.00           C
ATOM     83  CA  ASP    83      46.740  63.894  13.826  1.00 25.00           C
ATOM     84  CA  ALA    84      46.645  60.572  15.677  1.00 25.00           C
ATOM     85  CA  LEU    85      43.414  58.723  14.858  1.00 25.00           C
ATOM     86  CA  ALA    86      42.263  57.137  18.084  1.00 25.00           C
ATOM     87  CA  MET    87      40.617  54.555  15.897  1.00 25.00           C
ATOM     88  CA  GLU    88      37.779  53.575  18.210  1.00 25.00           C
ATOM     89  CA  LEU    89      38.096  50.039  16.940  1.00 25.00           C
ATOM     90  CA  ARG    90      35.116  47.622  17.175  1.00 25.00           C
ATOM     91  CA  PRO    91      32.751  44.621  16.808  1.00 25.00           C
ATOM     92  CA  GLU    92      30.038  45.827  14.429  1.00 25.00           C
ATOM     93  CA  ARG    93      27.475  43.734  12.497  1.00 25.00           C
ATOM     94  CA  LEU    94      28.222  40.255  11.133  1.00 25.00           C
ATOM     95  CA  ASN    95      26.624  38.031   8.534  1.00 25.00           C
ATOM     96  CA  PRO    96      27.454  35.885   5.442  1.00 25.00           C
ATOM     97  CA  ASN    97      30.977  35.602   6.832  1.00 25.00           C
ATOM     98  CA  SER    98      32.951  38.165   8.840  1.00 25.00           C
ATOM     99  CA  PHE    99      34.582  41.045  10.817  1.00 25.00           C
ATOM    100  CA  GLN   100      35.653  44.296  12.492  1.00 25.00           C
ATOM    101  CA  VAL   101      34.072  47.642  11.693  1.00 25.00           C
ATOM    102  CA  HIS   102      36.993  50.034  12.019  1.00 25.00           C
ATOM    103  CA  PHE   103      35.541  53.227  13.460  1.00 25.00           C
ATOM    104  CA  GLU   104      35.017  56.766  14.687  1.00 25.00           C
ATOM    105  CA  PHE   105      38.017  58.990  15.463  1.00 25.00           C
ATOM    106  CA  ARG   106      39.765  62.139  16.595  1.00 25.00           C
ATOM    107  CA  CYS   107      40.246  65.565  18.290  1.00 25.00           C
ATOM    108  CA  GLU   108      39.962  68.770  20.294  1.00 25.00           C
ATOM    109  CA  GLU   109      36.511  69.851  18.994  1.00 25.00           C
ATOM    110  CA  GLN   110      35.183  66.602  17.424  1.00 25.00           C
ATOM    111  CA  ILE   111      35.280  64.676  14.183  1.00 25.00           C
ATOM    112  CA  ALA   112      36.891  62.463  11.503  1.00 25.00           C
ATOM    113  CA  ALA   113      35.430  59.231  10.222  1.00 25.00           C
ATOM    114  CA  HIS   114      37.508  56.629   8.421  1.00 25.00           C
ATOM    115  CA  ALA   115      35.434  53.428   8.223  1.00 25.00           C
ATOM    116  CA  LEU   116      32.869  50.617   7.729  1.00 25.00           C
ATOM    117  CA  ILE   117      36.026  48.602   6.931  1.00 25.00           C
ATOM    118  CA  ARG   118      36.238  44.837   7.453  1.00 25.00           C
ATOM    119  CA  HIS   119      38.917  42.403   8.673  1.00 25.00           C
ATOM    120  CA  LEU   120      37.275  39.844   6.293  1.00 25.00           C
ATOM    121  CA  ALA   121      39.179  37.154   8.225  1.00 25.00           C
ATOM    122  CA  ILE   122      39.637  35.565   4.779  1.00 25.00           C
ATOM    123  CA  ASN   123      43.019  34.453   3.439  1.00 25.00           C
ATOM    124  CA  ALA   124      44.491  31.563   1.451  1.00 25.00           C
ATOM    125  CA  GLN   125      46.403  31.149  -1.776  1.00 25.00           C
ATOM    126  CA  THR   126      43.862  28.811  -3.265  1.00 25.00           C
ATOM    127  CA  ARG   127      40.698  28.499  -1.092  1.00 25.00           C
ATOM    128  CA  HIS   128      38.013  27.214   1.209  1.00 25.00           C
ATOM    129  CA  ARG   129      34.624  28.712   2.047  1.00 25.00           C
ATOM    130  CA  CYS   130      33.683  29.747   5.601  1.00 25.00           C
ATOM    131  CA  ALA   131      31.360  28.485   8.240  1.00 25.00           C
ATOM    132  CA  LEU   132      33.510  30.526  10.584  1.00 25.00           C
ATOM    133  CA  PRO   133      35.902  31.132  13.449  1.00 25.00           C
ATOM    134  CA  GLU   134      33.035  29.943  15.703  1.00 25.00           C
ATOM    135  CA  GLY   135      31.643  33.370  14.867  1.00 25.00           C
ATOM    136  CA  ILE   136      34.010  36.299  14.330  1.00 25.00           C
ATOM    137  CA  ASP   137      36.236  36.486  17.442  1.00 25.00           C
ATOM    138  CA  ARG   138      34.537  39.753  18.491  1.00 25.00           C
ATOM    139  CA  TRP   139      31.094  38.143  18.023  1.00 25.00           C
ATOM    140  CA  LEU   140      32.182  35.145  20.144  1.00 25.00           C
ATOM    141  CA  GLU   141      33.440  37.508  22.884  1.00 25.00           C
ATOM    142  CA  ALA   142      30.108  39.395  22.819  1.00 25.00           C
ATOM    143  CA  SER   143      28.200  36.088  23.110  1.00 25.00           C
ATOM    144  CA  GLY   144      26.534  33.646  25.416  1.00 25.00           C
ATOM    145  CA  VAL   145      23.607  32.846  27.630  1.00 25.00           C
ATOM    146  CA  GLY   146      25.177  34.700  30.554  1.00 25.00           C
ATOM    147  CA  LYS   147      27.695  33.614  33.186  1.00 25.00           C
ATOM    148  CA  ILE   148      29.128  36.713  34.886  1.00 25.00           C
ATOM    149  CA  GLY   149      26.336  39.141  35.482  1.00 25.00           C
ATOM    150  CA  SER   150      24.160  42.134  36.323  1.00 25.00           C
ATOM    151  CA  ILE   151      24.371  45.345  34.294  1.00 25.00           C
TER
END
