
#######################################################
#                                                     #
#                        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   94 (   94),  selected   94 , name T0320TS464_4_1
# Molecule2: number of CA atoms  287 ( 2364),  selected  287 , name T0320.pdb
# PARAMETERS: T0320TS464_4_1.T0320.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    Q       2      -       -           -
LGA    L       3      -       -           -
LGA    S       4      M       1           #
LGA    K       5      -       -           -
LGA    A       6      -       -           -
LGA    A       7      Q       2          3.971
LGA    E       8      L       3          2.944
LGA    M       9      S       4          1.701
LGA    C      10      K       5           -
LGA    Y      11      A       6           -
LGA    E      12      A       7           -
LGA    I      13      E       8           -
LGA    T      14      M       9           -
LGA    N      15      C      10           -
LGA    S      16      Y      11           -
LGA    Y      17      E      12           -
LGA    L      18      I      13           -
LGA    H      19      T      14           -
LGA    I      20      N      15           -
LGA    D      21      S      16           -
LGA    Q      22      Y      17           -
LGA    K      23      L      18           -
LGA    S      24      H      19           -
LGA    Q      25      I      20           -
LGA    I      26      D      21           -
LGA    F      58      Q      22           -
LGA    S      59      K      23           -
LGA    Y      60      S      24           -
LGA    N      61      Q      25           -
LGA    -       -      I      26           -
LGA    -       -      I      27           -
LGA    -       -      A      28           -
LGA    -       -      S      29           -
LGA    -       -      T      30           -
LGA    -       -      Q      31           -
LGA    -       -      E      32           -
LGA    -       -      A      33           -
LGA    -       -      I      34           -
LGA    -       -      R      35           -
LGA    G      62      L      36          2.890
LGA    G      63      T      37          2.469
LGA    K      64      R      38          3.223
LGA    -       -      K      39           -
LGA    D      65      Y      40          2.880
LGA    C      66      L      41          2.141
LGA    Q      67      L      42          2.247
LGA    V      68      S      43          2.511
LGA    L      69      E      44          2.915
LGA    L      70      I      45           #
LGA    L      71      F      46           #
LGA    L      72      -       -           -
LGA    Y      73      V      47          2.045
LGA    T     112      R      48           -
LGA    F     113      W      49           -
LGA    -       -      S      50           -
LGA    -       -      P      51           -
LGA    P     114      L      52           #
LGA    T     115      -       -           -
LGA    L     116      -       -           -
LGA    E     117      -       -           -
LGA    N     118      N      53          4.237
LGA    F     119      -       -           -
LGA    V     120      G      54          5.471
LGA    L     121      E      55          5.055
LGA    E     122      I      56          3.344
LGA    T     123      S      57          1.940
LGA    S     124      F      58          5.099
LGA    -       -      S      59           -
LGA    -       -      Y      60           -
LGA    -       -      N      61           -
LGA    -       -      G      62           -
LGA    -       -      G      63           -
LGA    -       -      K      64           -
LGA    -       -      D      65           -
LGA    -       -      C      66           -
LGA    -       -      Q      67           -
LGA    A     140      V      68          4.744
LGA    S     141      L      69          2.402
LGA    -       -      L      70           -
LGA    V     142      L      71          4.173
LGA    N     143      L      72          3.472
LGA    M     144      Y      73          2.959
LGA    A     145      L      74          3.399
LGA    D     146      S      75          2.399
LGA    A     147      C      76          1.638
LGA    F     148      L      77          2.162
LGA    R     149      W      78          2.595
LGA    D     150      E      79          1.801
LGA    F     151      Y      80          1.816
LGA    I     152      F      81          2.007
LGA    K     153      F      82          1.912
LGA    I     154      I      83          2.082
LGA    Y     155      K      84          3.295
LGA    P     156      -       -           -
LGA    E     157      A      85          3.931
LGA    -       -      Q      86           -
LGA    T     158      N      87           #
LGA    E     159      S      88          2.186
LGA    S     223      F      97           -
LGA    I     224      P      98           -
LGA    G     225      M      99           -
LGA    G     226      Q     100           -
LGA    I     227      R     101           -
LGA    -       -      L     102           -
LGA    -       -      P     103           -
LGA    -       -      T     104           -
LGA    -       -      V     105           -
LGA    -       -      F     106           -
LGA    -       -      I     107           -
LGA    -       -      D     108           -
LGA    -       -      Q     109           -
LGA    -       -      E     110           -
LGA    -       -      E     111           -
LGA    -       -      T     112           -
LGA    -       -      F     113           -
LGA    -       -      P     114           -
LGA    -       -      T     115           -
LGA    -       -      L     116           -
LGA    Y     292      E     117          2.852
LGA    L     293      N     118           #
LGA    -       -      F     119           -
LGA    V     294      V     120          3.929
LGA    D     295      L     121          2.468
LGA    D     296      E     122          2.393
LGA    T     297      T     123          2.574
LGA    L     298      S     124          2.513
LGA    E     299      E     125          1.861
LGA    R     300      R     126          1.729
LGA    A     301      Y     127          3.724
LGA    G     302      C     128          5.343
LGA    R     303      L     129           #
LGA    I     304      S     130           #
LGA    K     305      L     131           -
LGA    -       -      Y     132           -
LGA    -       -      E     133           -
LGA    -       -      S     134           -
LGA    -       -      Q     135           -
LGA    -       -      R     136           -
LGA    -       -      V     142           -
LGA    -       -      N     143           -
LGA    -       -      M     144           -
LGA    -       -      A     145           -
LGA    -       -      D     146           -
LGA    -       -      A     147           -
LGA    -       -      F     148           -
LGA    -       -      R     149           -
LGA    -       -      D     150           -
LGA    -       -      F     151           -
LGA    -       -      I     152           -
LGA    -       -      K     153           -
LGA    -       -      I     154           -
LGA    -       -      Y     155           -
LGA    -       -      P     156           -
LGA    -       -      E     157           -
LGA    -       -      T     158           -
LGA    -       -      E     159           -
LGA    -       -      A     160           -
LGA    -       -      I     161           -
LGA    -       -      V     162           -
LGA    -       -      I     163           -
LGA    -       -      G     164           -
LGA    -       -      I     165           -
LGA    -       -      R     166           -
LGA    -       -      H     167           -
LGA    -       -      T     168           -
LGA    -       -      D     169           -
LGA    -       -      P     170           -
LGA    -       -      F     171           -
LGA    -       -      G     172           -
LGA    -       -      E     173           -
LGA    -       -      A     174           -
LGA    -       -      L     175           -
LGA    -       -      K     176           -
LGA    -       -      P     177           -
LGA    -       -      I     178           -
LGA    -       -      Q     179           -
LGA    -       -      R     180           -
LGA    -       -      T     181           -
LGA    -       -      D     182           -
LGA    -       -      S     183           -
LGA    -       -      N     184           -
LGA    -       -      W     185           -
LGA    -       -      P     186           -
LGA    -       -      D     187           -
LGA    -       -      F     188           -
LGA    -       -      M     189           -
LGA    -       -      R     190           -
LGA    -       -      L     191           -
LGA    -       -      Q     192           -
LGA    -       -      P     193           -
LGA    -       -      L     194           -
LGA    -       -      L     195           -
LGA    -       -      H     196           -
LGA    -       -      W     197           -
LGA    -       -      D     198           -
LGA    -       -      L     199           -
LGA    -       -      T     200           -
LGA    -       -      N     201           -
LGA    -       -      I     202           -
LGA    -       -      W     203           -
LGA    -       -      S     204           -
LGA    -       -      F     205           -
LGA    -       -      L     206           -
LGA    -       -      L     207           -
LGA    -       -      Y     208           -
LGA    -       -      S     209           -
LGA    -       -      N     210           -
LGA    -       -      E     211           -
LGA    -       -      P     212           -
LGA    -       -      I     213           -
LGA    -       -      C     214           -
LGA    -       -      G     215           -
LGA    -       -      L     216           -
LGA    -       -      Y     217           -
LGA    -       -      G     218           -
LGA    -       -      K     219           -
LGA    -       -      G     220           -
LGA    -       -      F     221           -
LGA    -       -      T     222           -
LGA    -       -      S     223           -
LGA    -       -      I     224           -
LGA    -       -      G     225           -
LGA    -       -      G     226           -
LGA    -       -      I     227           -
LGA    -       -      N     228           -
LGA    -       -      N     229           -
LGA    -       -      S     230           -
LGA    -       -      L     231           -
LGA    -       -      P     232           -
LGA    -       -      N     233           -
LGA    -       -      P     234           -
LGA    -       -      H     235           -
LGA    -       -      L     236           -
LGA    -       -      R     237           -
LGA    -       -      K     238           -
LGA    -       -      D     239           -
LGA    -       -      S     240           -
LGA    -       -      N     241           -
LGA    -       -      N     242           -
LGA    -       -      P     243           -
LGA    -       -      A     244           -
LGA    -       -      L     245           -
LGA    -       -      H     246           -
LGA    -       -      F     247           -
LGA    -       -      E     248           -
LGA    -       -      W     249           -
LGA    -       -      E     250           -
LGA    -       -      I     251           -
LGA    -       -      I     252           -
LGA    -       -      H     253           -
LGA    -       -      A     254           -
LGA    -       -      F     255           -
LGA    -       -      G     256           -
LGA    -       -      K     257           -
LGA    -       -      D     258           -
LGA    -       -      R     263           -
LGA    -       -      S     264           -
LGA    -       -      S     265           -
LGA    -       -      A     266           -
LGA    -       -      I     267           -
LGA    -       -      N     268           -
LGA    -       -      T     269           -
LGA    -       -      S     270           -
LGA    -       -      P     271           -
LGA    -       -      I     272           -
LGA    -       -      S     273           -
LGA    -       -      V     274           -
LGA    -       -      V     275           -
LGA    -       -      D     276           -
LGA    -       -      K     277           -
LGA    -       -      E     278           -
LGA    -       -      R     279           -
LGA    -       -      F     280           -
LGA    -       -      S     281           -
LGA    -       -      K     282           -
LGA    -       -      Y     283           -
LGA    -       -      H     284           -
LGA    -       -      D     285           -
LGA    -       -      N     286           -
LGA    -       -      Y     287           -
LGA    -       -      Y     288           -
LGA    -       -      P     289           -
LGA    -       -      G     290           -
LGA    -       -      W     291           -
LGA    -       -      Y     292           -
LGA    -       -      L     293           -
LGA    -       -      V     294           -
LGA    -       -      D     295           -
LGA    -       -      D     296           -
LGA    -       -      T     297           -
LGA    -       -      L     298           -
LGA    -       -      E     299           -
LGA    -       -      R     300           -
LGA    -       -      A     301           -
LGA    -       -      G     302           -
LGA    -       -      R     303           -
LGA    -       -      I     304           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   94  287    5.0     46    3.12    13.04     10.037     1.428

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.803326 * X  +  -0.585330 * Y  +  -0.109794 * Z  +  83.914162
  Y_new =   0.590298 * X  +   0.758204 * Y  +   0.276901 * Z  + -101.114365
  Z_new =  -0.078832 * X  +  -0.287253 * Y  +   0.954605 * Z  +  42.423309 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.292294    2.849298  [ DEG:   -16.7472    163.2528 ]
  Theta =   0.078914    3.062679  [ DEG:     4.5214    175.4786 ]
  Phi   =   0.633713   -2.507879  [ DEG:    36.3091   -143.6909 ]
 
# 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: T0320TS464_4_1                                
REMARK     2: T0320.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS464_4_1.T0320.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   94  287   5.0   46   3.12   13.04  10.037
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS464_4_1
REMARK PARENT number 1
PFRMAT TS
TARGET T0320
PARENT N/A
ATOM      1  CA  MET     1       9.884  31.139  25.511  1.00  0.00
ATOM      2  CA  GLN     2      11.983  32.587  28.365  1.00  0.00
ATOM      3  CA  LEU     3      13.181  35.694  26.476  1.00  0.00
ATOM      4  CA  SER     4       9.532  36.270  25.555  1.00  0.00
ATOM      5  CA  LYS     5       8.554  36.192  29.241  1.00  0.00
ATOM      6  CA  ALA     6      11.482  38.416  30.265  1.00  0.00
ATOM      7  CA  ALA     7      10.542  40.998  27.625  1.00  0.00
ATOM      8  CA  GLU     8       6.969  41.267  28.963  1.00  0.00
ATOM      9  CA  MET     9       4.801  38.609  30.596  1.00  0.00
ATOM     10  CA  CYS    10       6.903  38.638  33.748  1.00  0.00
ATOM     11  CA  TYR    11       6.824  42.435  34.047  1.00  0.00
ATOM     12  CA  GLU    12       3.630  42.822  36.245  1.00  0.00
ATOM     13  CA  ILE    13       2.259  40.961  39.255  1.00  0.00
ATOM     14  CA  THR    14       4.327  42.718  41.850  1.00  0.00
ATOM     15  CA  ASN    15       7.811  41.336  42.199  1.00  0.00
ATOM     16  CA  SER    16      10.721  43.677  42.358  1.00  0.00
ATOM     17  CA  TYR    17      13.761  43.057  40.202  1.00  0.00
ATOM     18  CA  LEU    18      15.530  40.925  42.793  1.00  0.00
ATOM     19  CA  HIS    19      12.560  38.761  43.666  1.00  0.00
ATOM     20  CA  ILE    20      11.788  38.419  39.950  1.00  0.00
ATOM     21  CA  ASP    21      15.362  37.321  39.242  1.00  0.00
ATOM     22  CA  GLN    22      15.364  34.939  42.181  1.00  0.00
ATOM     23  CA  LYS    23      12.280  33.182  40.737  1.00  0.00
ATOM     24  CA  SER    24      13.838  32.979  37.276  1.00  0.00
ATOM     25  CA  GLN    25      16.929  31.474  38.853  1.00  0.00
ATOM     26  CA  ILE    26      14.874  28.792  40.637  1.00  0.00
ATOM     27  CA  PHE    58      17.557  22.384  36.147  1.00  0.00
ATOM     28  CA  SER    59      15.974  21.318  32.899  1.00  0.00
ATOM     29  CA  TYR    60      13.199  18.811  33.516  1.00  0.00
ATOM     30  CA  ASN    61      12.152  16.406  30.769  1.00  0.00
ATOM     31  CA  GLY    62       8.626  17.669  31.433  1.00  0.00
ATOM     32  CA  GLY    63       7.206  21.157  31.800  1.00  0.00
ATOM     33  CA  LYS    64       4.643  19.608  34.121  1.00  0.00
ATOM     34  CA  ASP    65       7.562  18.618  36.341  1.00  0.00
ATOM     35  CA  CYS    66       8.941  22.151  36.070  1.00  0.00
ATOM     36  CA  GLN    67       5.557  23.604  37.028  1.00  0.00
ATOM     37  CA  VAL    68       5.567  21.490  40.168  1.00  0.00
ATOM     38  CA  LEU    69       9.176  22.402  41.006  1.00  0.00
ATOM     39  CA  LEU    70       8.163  26.053  40.958  1.00  0.00
ATOM     40  CA  LEU    71       5.582  26.738  43.663  1.00  0.00
ATOM     41  CA  LEU    72       7.949  23.975  45.098  1.00  0.00
ATOM     42  CA  TYR    73      10.592  26.647  44.543  1.00  0.00
ATOM     43  CA  THR   112      10.760  44.592  38.529  1.00  0.00
ATOM     44  CA  PHE   113      10.644  43.794  34.813  1.00  0.00
ATOM     45  CA  PRO   114      13.851  42.337  33.386  1.00  0.00
ATOM     46  CA  THR   115      16.847  44.346  32.173  1.00  0.00
ATOM     47  CA  LEU   116      18.879  42.902  29.320  1.00  0.00
ATOM     48  CA  GLU   117      21.491  41.987  31.924  1.00  0.00
ATOM     49  CA  ASN   118      19.247  39.754  34.021  1.00  0.00
ATOM     50  CA  PHE   119      17.611  38.137  30.992  1.00  0.00
ATOM     51  CA  VAL   120      21.070  36.796  30.057  1.00  0.00
ATOM     52  CA  LEU   121      21.751  35.291  33.463  1.00  0.00
ATOM     53  CA  GLU   122      18.408  33.581  33.310  1.00  0.00
ATOM     54  CA  THR   123      19.255  32.097  29.910  1.00  0.00
ATOM     55  CA  SER   124      22.605  30.850  31.224  1.00  0.00
ATOM     56  CA  ALA   140      10.110  20.506  24.349  1.00  0.00
ATOM     57  CA  SER   141       9.813  24.130  23.161  1.00  0.00
ATOM     58  CA  VAL   142       6.066  24.424  23.697  1.00  0.00
ATOM     59  CA  ASN   143       5.960  22.594  27.039  1.00  0.00
ATOM     60  CA  MET   144       8.650  25.118  28.087  1.00  0.00
ATOM     61  CA  ALA   145       6.588  28.111  26.964  1.00  0.00
ATOM     62  CA  ASP   146       3.234  27.409  28.519  1.00  0.00
ATOM     63  CA  ALA   147       4.851  27.156  31.953  1.00  0.00
ATOM     64  CA  PHE   148       5.963  30.786  31.558  1.00  0.00
ATOM     65  CA  ARG   149       2.274  31.683  31.099  1.00  0.00
ATOM     66  CA  ASP   150       1.224  29.718  34.190  1.00  0.00
ATOM     67  CA  PHE   151       4.068  31.133  36.280  1.00  0.00
ATOM     68  CA  ILE   152       6.328  33.874  37.099  1.00  0.00
ATOM     69  CA  LYS   153       3.124  33.923  39.179  1.00  0.00
ATOM     70  CA  ILE   154       4.443  31.539  41.783  1.00  0.00
ATOM     71  CA  TYR   155       8.071  32.585  42.144  1.00  0.00
ATOM     72  CA  PRO   156       8.401  36.061  40.630  1.00  0.00
ATOM     73  CA  GLU   157       6.104  37.813  43.131  1.00  0.00
ATOM     74  CA  THR   158       6.441  39.218  46.609  1.00  0.00
ATOM     75  CA  GLU   159       6.500  35.848  48.353  1.00  0.00
ATOM     76  CA  SER   223      11.906  14.367  43.238  1.00  0.00
ATOM     77  CA  ILE   224       9.687  16.319  40.837  1.00  0.00
ATOM     78  CA  GLY   225      10.617  14.140  37.872  1.00  0.00
ATOM     79  CA  GLY   226      13.356  13.343  35.371  1.00  0.00
ATOM     80  CA  ILE   227      15.794  16.202  34.976  1.00  0.00
ATOM     81  CA  TYR   292      22.865  34.765  14.661  1.00  0.00
ATOM     82  CA  LEU   293      19.936  32.740  16.048  1.00  0.00
ATOM     83  CA  VAL   294      19.868  34.572  19.385  1.00  0.00
ATOM     84  CA  ASP   295      19.924  37.940  17.530  1.00  0.00
ATOM     85  CA  ASP   296      16.712  36.867  15.773  1.00  0.00
ATOM     86  CA  THR   297      15.012  35.892  19.023  1.00  0.00
ATOM     87  CA  LEU   298      15.926  39.210  20.649  1.00  0.00
ATOM     88  CA  GLU   299      14.448  41.052  17.640  1.00  0.00
ATOM     89  CA  ARG   300      11.319  38.882  17.714  1.00  0.00
ATOM     90  CA  ALA   301      10.656  39.995  21.295  1.00  0.00
ATOM     91  CA  GLY   302      11.503  43.665  20.886  1.00  0.00
ATOM     92  CA  ARG   303      14.739  43.479  22.893  1.00  0.00
ATOM     93  CA  ILE   304      17.397  43.978  20.159  1.00  0.00
ATOM     94  CA  LYS   305      19.230  46.705  22.145  1.00  0.00
TER
END
