
#######################################################
#                                                     #
#                        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  128 (  128),  selected  128 , name T0322TS393_4-D1
# Molecule2: number of CA atoms  128 (  980),  selected  128 , name T0322_D1.pdb
# PARAMETERS: T0322TS393_4-D1.T0322_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G      16      G      16           -
LGA    F      17      F      17           -
LGA    S      18      S      18           -
LGA    Q      19      Q      19           -
LGA    L      20      L      20           -
LGA    N      21      N      21           -
LGA    W      22      -       -           -
LGA    S      23      W      22          4.943
LGA    R      24      S      23          3.141
LGA    G      25      R      24          2.707
LGA    -       -      G      25           -
LGA    F      26      F      26          3.522
LGA    G      27      G      27          2.872
LGA    R      28      R      28          3.100
LGA    Q      29      Q      29          2.870
LGA    I      30      I      30          1.821
LGA    G      31      G      31          1.797
LGA    -       -      P      32           -
LGA    P      32      L      33          0.719
LGA    L      33      F      34          3.828
LGA    F      34      E      35          1.301
LGA    E      35      H      36          1.974
LGA    -       -      R      37           -
LGA    -       -      E      38           -
LGA    -       -      G      39           -
LGA    H      36      P      40           #
LGA    R      37      G      41          2.807
LGA    E      38      -       -           -
LGA    G      39      -       -           -
LGA    P      40      -       -           -
LGA    G      41      -       -           -
LGA    Q      42      Q      42           #
LGA    A      43      A      43          2.548
LGA    R      44      R      44          2.851
LGA    L      45      L      45          2.148
LGA    A      46      A      46          1.822
LGA    F      47      F      47          1.749
LGA    R      48      R      48          1.800
LGA    V      49      V      49          1.480
LGA    E      50      E      50          0.846
LGA    E      51      E      51          1.617
LGA    H      52      H      52          2.209
LGA    H      53      H      53          1.408
LGA    T      54      T      54          0.822
LGA    N      55      N      55          0.633
LGA    G      56      G      56          4.332
LGA    L      57      L      57          3.588
LGA    G      58      G      58          2.036
LGA    N      59      N      59          0.643
LGA    C      60      C      60          0.857
LGA    H      61      H      61          1.422
LGA    G      62      G      62          1.640
LGA    G      63      -       -           -
LGA    M      64      G      63          1.599
LGA    L      65      M      64          1.855
LGA    M      66      L      65          2.395
LGA    S      67      M      66          1.878
LGA    F      68      S      67          1.152
LGA    A      69      F      68          1.504
LGA    D      70      A      69          2.247
LGA    M      71      D      70          2.164
LGA    A      72      M      71          1.472
LGA    W      73      A      72          2.420
LGA    G      74      W      73          4.462
LGA    R      75      G      74          4.607
LGA    I      76      R      75          2.824
LGA    I      77      I      76          2.772
LGA    S      78      I      77          3.173
LGA    L      79      S      78          2.743
LGA    -       -      L      79           -
LGA    -       -      Q      80           -
LGA    -       -      K      81           -
LGA    Q      80      S      82          2.313
LGA    K      81      Y      83          4.495
LGA    S      82      -       -           -
LGA    Y      83      -       -           -
LGA    S      84      S      84          2.022
LGA    W      85      W      85          0.658
LGA    V      86      V      86          0.833
LGA    T      87      T      87          1.147
LGA    V      88      V      88          1.399
LGA    R      89      R      89          2.103
LGA    L      90      L      90          1.828
LGA    M      91      M      91          1.898
LGA    C      92      C      92          2.394
LGA    D      93      D      93          1.057
LGA    F      94      F      94          1.016
LGA    L      95      L      95          2.094
LGA    S      96      S      96          1.902
LGA    G      97      G      97          1.345
LGA    A      98      A      98          0.821
LGA    K      99      K      99          2.431
LGA    L     100      L     100          2.018
LGA    G     101      G     101          1.848
LGA    D     102      D     102          1.093
LGA    W     103      W     103          0.970
LGA    V     104      V     104          1.934
LGA    E     105      E     105          1.668
LGA    G     106      G     106          1.672
LGA    E     107      E     107          1.148
LGA    G     108      G     108          2.184
LGA    E     109      E     109          1.952
LGA    L     110      L     110          1.144
LGA    I     111      I     111          1.380
LGA    S     112      S     112          1.321
LGA    E     113      E     113          2.134
LGA    E     114      E     114          3.680
LGA    D     115      D     115          5.057
LGA    -       -      M     116           -
LGA    M     116      L     117          2.537
LGA    L     117      F     118          0.711
LGA    F     118      T     119          2.422
LGA    T     119      V     120          2.005
LGA    V     120      R     121          3.280
LGA    R     121      G     122          0.956
LGA    G     122      R     123          3.230
LGA    R     123      I     124          2.246
LGA    I     124      W     125          1.433
LGA    W     125      A     126          3.938
LGA    A     126      G     127          1.499
LGA    G     127      -       -           -
LGA    E     128      E     128          1.378
LGA    R     129      R     129          1.314
LGA    T     130      T     130          1.555
LGA    L     131      L     131          1.800
LGA    I     132      I     132          1.323
LGA    T     133      T     133          1.267
LGA    G     134      G     134          3.001
LGA    T     135      T     135          2.602
LGA    G     136      G     136          1.455
LGA    V     137      V     137          4.167
LGA    F     138      F     138          1.999
LGA    K     139      K     139          2.018
LGA    A     140      A     140          1.853
LGA    L     141      L     141          2.537
LGA    S     142      -       -           -
LGA    A     143      S     142           #
LGA    -       -      A     143           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  128  128    5.0    109    2.32    66.97     60.804     4.503

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.075475 * X  +  -0.765204 * Y  +  -0.639348 * Z  +  10.461805
  Y_new =  -0.430432 * X  +  -0.553363 * Y  +   0.713105 * Z  +  -5.707389
  Z_new =  -0.899462 * X  +   0.329017 * Y  +  -0.287603 * Z  + -15.432803 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.289132   -0.852461  [ DEG:   131.1576    -48.8424 ]
  Theta =   1.118537    2.023056  [ DEG:    64.0875    115.9125 ]
  Phi   =  -1.744379    1.397214  [ DEG:   -99.9455     80.0545 ]
 
# 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: T0322TS393_4-D1                               
REMARK     2: T0322_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0322TS393_4-D1.T0322_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  128  128   5.0  109   2.32   66.97  60.804
REMARK  ---------------------------------------------------------- 
MOLECULE T0322TS393_4-D1
PFRMAT TS
TARGET T0322
MODEL 4
PARENT N/A
ATOM     16  CA  GLY    16      22.599  -1.858   8.301  1.00 25.00           C
ATOM     17  CA  PHE    17      19.839   0.661   8.039  1.00 25.00           C
ATOM     18  CA  SER    18      18.361   4.003   7.049  1.00 25.00           C
ATOM     19  CA  GLN    19      17.291   6.145   4.059  1.00 25.00           C
ATOM     20  CA  LEU    20      14.562   5.490   1.465  1.00 25.00           C
ATOM     21  CA  ASN    21      11.658   3.998   3.528  1.00 25.00           C
ATOM     22  CA  TRP    22      10.020   0.624   4.206  1.00 25.00           C
ATOM     23  CA  SER    23      11.482  -0.314   0.820  1.00 25.00           C
ATOM     24  CA  ARG    24       8.880  -1.688  -1.558  1.00 25.00           C
ATOM     25  CA  GLY    25       7.528   1.479  -3.211  1.00 25.00           C
ATOM     26  CA  PHE    26       9.264   0.809  -6.512  1.00 25.00           C
ATOM     27  CA  GLY    27       9.971  -2.431  -8.429  1.00 25.00           C
ATOM     28  CA  ARG    28       7.907  -4.416  -5.886  1.00 25.00           C
ATOM     29  CA  GLN    29       5.021  -1.925  -6.247  1.00 25.00           C
ATOM     30  CA  ILE    30       3.028  -5.038  -7.211  1.00 25.00           C
ATOM     31  CA  GLY    31       4.122  -8.175  -5.265  1.00 25.00           C
ATOM     32  CA  PRO    32       6.069  -9.442  -8.322  1.00 25.00           C
ATOM     33  CA  LEU    33       9.456  -9.390 -10.074  1.00 25.00           C
ATOM     34  CA  PHE    34      10.416 -12.948 -11.162  1.00 25.00           C
ATOM     35  CA  GLU    35      10.846 -16.548 -12.312  1.00 25.00           C
ATOM     36  CA  HIS    36      11.304 -18.099 -15.763  1.00 25.00           C
ATOM     37  CA  ARG    37      12.029 -16.635 -19.166  1.00 25.00           C
ATOM     38  CA  GLU    38      12.926 -19.403 -21.552  1.00 25.00           C
ATOM     39  CA  GLY    39      15.050 -17.702 -24.190  1.00 25.00           C
ATOM     40  CA  PRO    40      18.693 -17.218 -23.343  1.00 25.00           C
ATOM     41  CA  GLY    41      18.081 -13.471 -23.939  1.00 25.00           C
ATOM     42  CA  GLN    42      15.061 -12.743 -21.686  1.00 25.00           C
ATOM     43  CA  ALA    43      15.293 -11.521 -18.091  1.00 25.00           C
ATOM     44  CA  ARG    44      12.200 -12.306 -15.971  1.00 25.00           C
ATOM     45  CA  LEU    45       8.504 -11.380 -15.920  1.00 25.00           C
ATOM     46  CA  ALA    46       5.937 -12.091 -13.244  1.00 25.00           C
ATOM     47  CA  PHE    47       2.643 -11.682 -11.287  1.00 25.00           C
ATOM     48  CA  ARG    48       1.035 -12.461  -7.936  1.00 25.00           C
ATOM     49  CA  VAL    49      -2.344 -10.908  -8.754  1.00 25.00           C
ATOM     50  CA  GLU    50      -4.181 -11.230  -5.381  1.00 25.00           C
ATOM     51  CA  GLU    51      -7.510  -9.908  -4.078  1.00 25.00           C
ATOM     52  CA  HIS    52      -5.444  -6.915  -2.875  1.00 25.00           C
ATOM     53  CA  HIS    53      -4.267  -6.255  -6.458  1.00 25.00           C
ATOM     54  CA  THR    54      -7.758  -6.297  -7.923  1.00 25.00           C
ATOM     55  CA  ASN    55     -10.495  -4.735 -10.028  1.00 25.00           C
ATOM     56  CA  GLY    56     -14.196  -3.931 -10.197  1.00 25.00           C
ATOM     57  CA  LEU    57     -14.982  -7.371 -11.553  1.00 25.00           C
ATOM     58  CA  GLY    58     -13.281 -10.176  -9.609  1.00 25.00           C
ATOM     59  CA  ASN    59     -10.148  -9.631 -11.646  1.00 25.00           C
ATOM     60  CA  CYS    60      -6.377  -9.078 -12.203  1.00 25.00           C
ATOM     61  CA  HIS    61      -6.007  -5.329 -12.630  1.00 25.00           C
ATOM     62  CA  GLY    62      -6.007  -6.118 -16.390  1.00 25.00           C
ATOM     63  CA  GLY    63      -4.442  -3.968 -19.146  1.00 25.00           C
ATOM     64  CA  MET    64      -2.762  -1.761 -16.504  1.00 25.00           C
ATOM     65  CA  LEU    65      -1.395  -4.874 -14.739  1.00 25.00           C
ATOM     66  CA  MET    66      -0.035  -6.195 -18.065  1.00 25.00           C
ATOM     67  CA  SER    67       1.641  -2.819 -18.749  1.00 25.00           C
ATOM     68  CA  PHE    68       3.213  -2.866 -15.257  1.00 25.00           C
ATOM     69  CA  ALA    69       4.506  -6.421 -15.859  1.00 25.00           C
ATOM     70  CA  ASP    70       6.000  -5.335 -19.215  1.00 25.00           C
ATOM     71  CA  MET    71       7.702  -2.353 -17.519  1.00 25.00           C
ATOM     72  CA  ALA    72       9.133  -4.670 -14.825  1.00 25.00           C
ATOM     73  CA  TRP    73      10.447  -7.043 -17.529  1.00 25.00           C
ATOM     74  CA  GLY    74      12.076  -4.097 -19.356  1.00 25.00           C
ATOM     75  CA  ARG    75      13.710  -2.943 -16.091  1.00 25.00           C
ATOM     76  CA  ILE    76      15.028  -6.485 -15.470  1.00 25.00           C
ATOM     77  CA  ILE    77      16.451  -6.604 -19.024  1.00 25.00           C
ATOM     78  CA  SER    78      18.153  -3.217 -18.483  1.00 25.00           C
ATOM     79  CA  LEU    79      19.654  -4.469 -15.189  1.00 25.00           C
ATOM     80  CA  GLN    80      22.139  -1.591 -15.761  1.00 25.00           C
ATOM     81  CA  LYS    81      25.034  -2.961 -17.751  1.00 25.00           C
ATOM     82  CA  SER    82      24.120  -1.000 -20.914  1.00 25.00           C
ATOM     83  CA  TYR    83      21.479   1.453 -19.807  1.00 25.00           C
ATOM     84  CA  SER    84      18.989   3.557 -17.880  1.00 25.00           C
ATOM     85  CA  TRP    85      16.073   1.677 -19.479  1.00 25.00           C
ATOM     86  CA  VAL    86      12.995   3.662 -20.618  1.00 25.00           C
ATOM     87  CA  THR    87       9.299   2.677 -20.793  1.00 25.00           C
ATOM     88  CA  VAL    88       9.289   3.561 -24.497  1.00 25.00           C
ATOM     89  CA  ARG    89       5.614   2.520 -24.508  1.00 25.00           C
ATOM     90  CA  LEU    90       2.936  -0.099 -23.570  1.00 25.00           C
ATOM     91  CA  MET    91       0.018  -0.650 -25.973  1.00 25.00           C
ATOM     92  CA  CYS    92      -2.153  -3.002 -23.885  1.00 25.00           C
ATOM     93  CA  ASP    93      -3.840  -5.678 -25.997  1.00 25.00           C
ATOM     94  CA  PHE    94      -6.510  -7.280 -23.811  1.00 25.00           C
ATOM     95  CA  LEU    95      -8.736 -10.210 -24.647  1.00 25.00           C
ATOM     96  CA  SER    96     -10.160 -12.292 -21.859  1.00 25.00           C
ATOM     97  CA  GLY    97      -9.288 -13.128 -18.201  1.00 25.00           C
ATOM     98  CA  ALA    98      -7.596 -13.692 -14.889  1.00 25.00           C
ATOM     99  CA  LYS    99      -9.719 -15.808 -12.555  1.00 25.00           C
ATOM    100  CA  LEU   100      -8.405 -15.149  -9.030  1.00 25.00           C
ATOM    101  CA  GLY   101      -5.751 -17.612  -8.109  1.00 25.00           C
ATOM    102  CA  ASP   102      -3.599 -17.629 -11.216  1.00 25.00           C
ATOM    103  CA  TRP   103      -0.022 -16.493 -11.675  1.00 25.00           C
ATOM    104  CA  VAL   104      -1.181 -13.838 -14.188  1.00 25.00           C
ATOM    105  CA  GLU   105       2.182 -14.252 -15.890  1.00 25.00           C
ATOM    106  CA  GLY   106       5.062 -14.105 -18.371  1.00 25.00           C
ATOM    107  CA  GLU   107       7.804 -13.565 -20.871  1.00 25.00           C
ATOM    108  CA  GLY   108       9.729 -10.394 -21.461  1.00 25.00           C
ATOM    109  CA  GLU   109      11.511 -10.901 -24.780  1.00 25.00           C
ATOM    110  CA  LEU   110      14.522  -9.551 -26.665  1.00 25.00           C
ATOM    111  CA  ILE   111      14.039  -9.623 -30.448  1.00 25.00           C
ATOM    112  CA  SER   112      15.759  -7.029 -32.536  1.00 25.00           C
ATOM    113  CA  GLU   113      17.525  -3.706 -33.017  1.00 25.00           C
ATOM    114  CA  GLU   114      17.087  -1.141 -35.843  1.00 25.00           C
ATOM    115  CA  ASP   115      16.416   1.576 -33.204  1.00 25.00           C
ATOM    116  CA  MET   116      14.518   0.318 -30.160  1.00 25.00           C
ATOM    117  CA  LEU   117      14.829  -2.666 -27.828  1.00 25.00           C
ATOM    118  CA  PHE   118      11.733  -4.731 -27.200  1.00 25.00           C
ATOM    119  CA  THR   119       9.735  -7.624 -28.626  1.00 25.00           C
ATOM    120  CA  VAL   120       7.694  -7.259 -25.439  1.00 25.00           C
ATOM    121  CA  ARG   121       5.170 -10.013 -24.792  1.00 25.00           C
ATOM    122  CA  GLY   122       3.789 -10.198 -21.265  1.00 25.00           C
ATOM    123  CA  ARG   123       1.965 -13.412 -22.338  1.00 25.00           C
ATOM    124  CA  ILE   124      -0.778 -14.557 -19.968  1.00 25.00           C
ATOM    125  CA  TRP   125       1.032 -17.865 -19.397  1.00 25.00           C
ATOM    126  CA  ALA   126      -0.387 -20.187 -16.766  1.00 25.00           C
ATOM    127  CA  GLY   127      -1.028 -23.930 -17.261  1.00 25.00           C
ATOM    128  CA  GLU   128      -3.474 -22.884 -19.979  1.00 25.00           C
ATOM    129  CA  ARG   129      -3.463 -19.547 -21.785  1.00 25.00           C
ATOM    130  CA  THR   130      -3.864 -16.417 -23.793  1.00 25.00           C
ATOM    131  CA  LEU   131      -5.201 -13.222 -22.252  1.00 25.00           C
ATOM    132  CA  ILE   132      -2.775 -10.342 -22.293  1.00 25.00           C
ATOM    133  CA  THR   133      -0.706 -10.423 -25.557  1.00 25.00           C
ATOM    134  CA  GLY   134       1.013  -7.223 -24.539  1.00 25.00           C
ATOM    135  CA  THR   135       2.959  -4.869 -26.709  1.00 25.00           C
ATOM    136  CA  GLY   136       6.089  -2.630 -26.640  1.00 25.00           C
ATOM    137  CA  VAL   137       8.223  -1.735 -23.604  1.00 25.00           C
ATOM    138  CA  PHE   138      12.030  -1.191 -23.663  1.00 25.00           C
ATOM    139  CA  LYS   139      14.553   1.359 -24.794  1.00 25.00           C
ATOM    140  CA  ALA   140      18.240   1.154 -24.102  1.00 25.00           C
ATOM    141  CA  LEU   141      19.602   4.652 -23.268  1.00 25.00           C
ATOM    142  CA  SER   142      20.421   8.347 -22.814  1.00 25.00           C
ATOM    143  CA  ALA   143      22.536  10.104 -20.184  1.00 25.00           C
TER
END
