
#######################################################
#                                                     #
#                        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   97 (   97),  selected   97 , name T0328TS464_2_1
# Molecule2: number of CA atoms  307 ( 2453),  selected  307 , name T0328.pdb
# PARAMETERS: T0328TS464_2_1.T0328.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    Y      48      N       5           -
LGA    E      49      M       6           -
LGA    L      50      P       7           -
LGA    T      51      R       8           -
LGA    D      52      E       9           -
LGA    Q      53      Q      10           -
LGA    Y      54      L      11           -
LGA    S      55      G      12           -
LGA    D      56      V      13           -
LGA    S      57      C      14           -
LGA    A      58      A      15           -
LGA    F      59      E      16           -
LGA    N      60      G      17           -
LGA    G      61      N      18           -
LGA    E      80      L      19           -
LGA    M      81      H      20           -
LGA    L      82      S      21           -
LGA    -       -      V      22           -
LGA    -       -      Y      23           -
LGA    -       -      L      24           -
LGA    -       -      M      25           -
LGA    -       -      F      26           -
LGA    -       -      N      27           -
LGA    -       -      A      28           -
LGA    -       -      N      29           -
LGA    -       -      D      30           -
LGA    K      83      N      31           #
LGA    -       -      V      32           -
LGA    P      84      E      33          3.386
LGA    -       -      S      34           -
LGA    -       -      Q      35           -
LGA    -       -      L      36           -
LGA    -       -      R      37           -
LGA    -       -      P      38           -
LGA    -       -      C      39           -
LGA    -       -      I      40           -
LGA    -       -      A      41           -
LGA    -       -      N      42           -
LGA    -       -      V      43           -
LGA    -       -      A      44           -
LGA    L     102      Q      45          1.197
LGA    F     103      Y      46          4.077
LGA    -       -      I      47           -
LGA    -       -      Y      48           -
LGA    V     104      E      49          1.963
LGA    -       -      L      50           -
LGA    -       -      T      51           -
LGA    H     105      D      52          4.555
LGA    L     106      Q      53          3.222
LGA    R     107      Y      54           -
LGA    C     108      -       -           -
LGA    D     109      -       -           -
LGA    R     110      -       -           -
LGA    Y     111      -       -           -
LGA    D     112      S      55          4.932
LGA    I     113      D      56          2.956
LGA    L     114      S      57           #
LGA    H     115      A      58          1.141
LGA    L     116      F      59          1.946
LGA    V     117      -       -           -
LGA    A     118      N      60          1.011
LGA    N     119      -       -           -
LGA    E     120      -       -           -
LGA    I     121      -       -           -
LGA    S     122      G      61          1.592
LGA    Q     123      F      62          4.679
LGA    M     124      -       -           -
LGA    F     125      V      63          1.393
LGA    E     126      A      64          2.415
LGA    D     127      I      65          3.883
LGA    L     128      G      66          1.725
LGA    V     129      A      67          3.340
LGA    E     130      -       -           -
LGA    L     131      N      68           #
LGA    V     132      Y      69           #
LGA    -       -      W      70           -
LGA    -       -      D      71           -
LGA    -       -      S      72           -
LGA    -       -      L      73           -
LGA    -       -      Y      74           -
LGA    -       -      P      75           -
LGA    -       -      E      76           -
LGA    -       -      S      77           -
LGA    -       -      R      78           -
LGA    -       -      P      79           -
LGA    -       -      E      80           -
LGA    -       -      M      81           -
LGA    -       -      L      82           -
LGA    -       -      K      83           -
LGA    E     133      P      84          2.743
LGA    -       -      F      85           -
LGA    -       -      P      86           -
LGA    -       -      A      87           -
LGA    -       -      M      88           -
LGA    -       -      Q      89           -
LGA    -       -      E      90           -
LGA    -       -      G      91           -
LGA    -       -      N      92           -
LGA    -       -      R      93           -
LGA    -       -      E      94           -
LGA    -       -      A      95           -
LGA    E     134      P      96           #
LGA    E     135      A      97          4.169
LGA    R     136      I      98           #
LGA    G     137      -       -           -
LGA    F     138      E      99          3.398
LGA    R     139      Y     100          3.513
LGA    F     140      -       -           -
LGA    M     141      -       -           -
LGA    D     142      -       -           -
LGA    G     205      -       -           -
LGA    R     206      D     101           #
LGA    T     207      L     102          4.351
LGA    -       -      F     103           -
LGA    -       -      V     104           -
LGA    -       -      H     105           -
LGA    -       -      L     106           -
LGA    -       -      R     107           -
LGA    -       -      C     108           -
LGA    -       -      D     109           -
LGA    -       -      R     110           -
LGA    -       -      Y     111           -
LGA    -       -      D     112           -
LGA    -       -      I     113           -
LGA    -       -      L     114           -
LGA    -       -      H     115           -
LGA    -       -      L     116           -
LGA    -       -      V     117           -
LGA    -       -      A     118           -
LGA    -       -      N     119           -
LGA    -       -      E     120           -
LGA    -       -      I     121           -
LGA    -       -      S     122           -
LGA    -       -      Q     123           -
LGA    -       -      M     124           -
LGA    -       -      F     125           -
LGA    -       -      E     126           -
LGA    -       -      D     127           -
LGA    -       -      L     128           -
LGA    K     208      V     129          4.548
LGA    Q     209      E     130          4.570
LGA    -       -      L     131           -
LGA    N     229      V     132           #
LGA    L     230      E     133          3.808
LGA    K     231      E     134           #
LGA    D     232      -       -           -
LGA    E     233      -       -           -
LGA    N     234      -       -           -
LGA    G     235      -       -           -
LGA    K     236      -       -           -
LGA    S     237      -       -           -
LGA    I     238      -       -           -
LGA    E     239      E     135          2.414
LGA    S     249      R     136           -
LGA    L     250      G     137           -
LGA    K     251      F     138           -
LGA    -       -      R     139           -
LGA    -       -      F     140           -
LGA    -       -      M     141           -
LGA    -       -      D     142           -
LGA    -       -      S     143           -
LGA    -       -      R     144           -
LGA    -       -      D     145           -
LGA    -       -      L     146           -
LGA    -       -      T     147           -
LGA    -       -      G     148           -
LGA    -       -      F     149           -
LGA    -       -      V     150           -
LGA    -       -      D     151           -
LGA    -       -      G     152           -
LGA    -       -      T     153           -
LGA    -       -      E     154           -
LGA    -       -      N     155           -
LGA    -       -      P     156           -
LGA    -       -      K     157           -
LGA    -       -      G     158           -
LGA    -       -      R     159           -
LGA    -       -      H     160           -
LGA    -       -      R     161           -
LGA    E     252      Q     162          4.557
LGA    -       -      E     163           -
LGA    -       -      V     164           -
LGA    -       -      A     165           -
LGA    Q     253      L     166          2.367
LGA    G     254      V     167          1.545
LGA    -       -      G     168           -
LGA    -       -      S     169           -
LGA    -       -      E     170           -
LGA    -       -      D     171           -
LGA    -       -      P     172           -
LGA    -       -      E     173           -
LGA    L     255      F     174          4.193
LGA    M     256      K     175          2.060
LGA    F     257      G     176          5.518
LGA    I     258      G     177           -
LGA    S     259      S     178           -
LGA    -       -      Y     179           -
LGA    -       -      I     180           -
LGA    -       -      H     181           -
LGA    -       -      V     182           -
LGA    -       -      Q     183           -
LGA    -       -      K     184           -
LGA    -       -      Y     185           -
LGA    -       -      A     186           -
LGA    -       -      H     187           -
LGA    -       -      N     188           -
LGA    -       -      L     189           -
LGA    -       -      S     190           -
LGA    -       -      K     191           -
LGA    -       -      W     192           -
LGA    -       -      H     193           -
LGA    -       -      R     194           -
LGA    -       -      L     195           -
LGA    -       -      P     196           -
LGA    -       -      L     197           -
LGA    -       -      K     198           -
LGA    -       -      K     199           -
LGA    -       -      Q     200           -
LGA    -       -      E     201           -
LGA    -       -      D     202           -
LGA    -       -      I     203           -
LGA    -       -      I     204           -
LGA    -       -      G     205           -
LGA    -       -      R     206           -
LGA    -       -      T     207           -
LGA    -       -      K     208           -
LGA    -       -      Q     209           -
LGA    -       -      D     210           -
LGA    -       -      N     211           -
LGA    -       -      I     212           -
LGA    -       -      E     213           -
LGA    -       -      Y     214           -
LGA    -       -      E     215           -
LGA    -       -      S     216           -
LGA    -       -      E     217           -
LGA    -       -      D     218           -
LGA    -       -      K     219           -
LGA    -       -      P     220           -
LGA    -       -      L     221           -
LGA    -       -      T     222           -
LGA    -       -      S     223           -
LGA    -       -      H     224           -
LGA    -       -      I     225           -
LGA    -       -      K     226           -
LGA    -       -      R     227           -
LGA    -       -      V     228           -
LGA    -       -      N     229           -
LGA    -       -      L     230           -
LGA    -       -      K     231           -
LGA    -       -      D     232           -
LGA    -       -      E     233           -
LGA    -       -      N     234           -
LGA    -       -      G     235           -
LGA    -       -      K     236           -
LGA    -       -      S     237           -
LGA    -       -      I     238           -
LGA    -       -      E     239           -
LGA    -       -      I     240           -
LGA    -       -      L     241           -
LGA    -       -      R     242           -
LGA    -       -      Q     243           -
LGA    -       -      S     244           -
LGA    -       -      M     245           -
LGA    -       -      P     246           -
LGA    -       -      Y     247           -
LGA    -       -      G     248           -
LGA    -       -      S     249           -
LGA    -       -      L     250           -
LGA    -       -      K     251           -
LGA    -       -      E     252           -
LGA    -       -      Q     253           -
LGA    -       -      G     254           -
LGA    -       -      L     255           -
LGA    -       -      M     256           -
LGA    -       -      F     257           -
LGA    -       -      I     258           -
LGA    -       -      S     259           -
LGA    -       -      T     260           -
LGA    -       -      C     261           -
LGA    -       -      R     262           -
LGA    -       -      T     263           -
LGA    -       -      P     264           -
LGA    -       -      D     265           -
LGA    -       -      H     266           -
LGA    -       -      F     267           -
LGA    -       -      E     268           -
LGA    -       -      K     269           -
LGA    -       -      M     270           -
LGA    -       -      L     271           -
LGA    -       -      H     272           -
LGA    -       -      S     273           -
LGA    -       -      M     274           -
LGA    -       -      V     275           -
LGA    -       -      F     276           -
LGA    -       -      G     277           -
LGA    -       -      D     278           -
LGA    -       -      G     279           -
LGA    -       -      A     280           -
LGA    -       -      G     281           -
LGA    -       -      N     282           -
LGA    -       -      H     283           -
LGA    -       -      D     284           -
LGA    -       -      H     285           -
LGA    -       -      L     286           -
LGA    -       -      M     287           -
LGA    -       -      H     288           -
LGA    -       -      F     289           -
LGA    -       -      T     290           -
LGA    -       -      S     291           -
LGA    -       -      A     292           -
LGA    -       -      L     293           -
LGA    -       -      T     294           -
LGA    -       -      G     295           -
LGA    -       -      S     296           -
LGA    -       -      S     297           -
LGA    -       -      F     298           -
LGA    D     284      F     299          4.945
LGA    -       -      A     300           -
LGA    H     285      P     301          2.711
LGA    L     286      S     302           #
LGA    -       -      L     303           -
LGA    -       -      D     304           -
LGA    -       -      F     305           -
LGA    M     287      L     306          2.334
LGA    H     288      M     307           #
LGA    S     302      -       -           -
LGA    L     303      -       -           -
LGA    D     304      -       -           -
LGA    F     305      -       -           -
LGA    L     306      Q     308           #
LGA    -       -      F     309           -
LGA    -       -      D     310           -
LGA    -       -      N     311           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   97  307    5.0     36    3.39     2.78      6.624     1.032

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.285209 * X  +   0.879908 * Y  +  -0.380023 * Z  +  33.940372
  Y_new =   0.958465 * X  +  -0.261445 * Y  +   0.113980 * Z  +  -9.861109
  Z_new =   0.000937 * X  +  -0.396747 * Y  +  -0.917928 * Z  +  51.622593 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.733623    0.407970  [ DEG:  -156.6250     23.3750 ]
  Theta =  -0.000937   -3.140656  [ DEG:    -0.0537   -179.9463 ]
  Phi   =   1.281572   -1.860021  [ DEG:    73.4287   -106.5713 ]
 
# 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: T0328TS464_2_1                                
REMARK     2: T0328.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0328TS464_2_1.T0328.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   97  307   5.0   36   3.39    2.78   6.624
REMARK  ---------------------------------------------------------- 
MOLECULE T0328TS464_2_1
REMARK PARENT number 1
PFRMAT TS
TARGET T0328
PARENT N/A
ATOM      1  CA  TYR    48      46.975  21.097  27.307  1.00  0.00
ATOM      2  CA  GLU    49      43.409  20.985  25.721  1.00  0.00
ATOM      3  CA  LEU    50      42.633  24.411  27.402  1.00  0.00
ATOM      4  CA  THR    51      45.727  25.840  25.769  1.00  0.00
ATOM      5  CA  ASP    52      44.416  24.835  22.346  1.00  0.00
ATOM      6  CA  GLN    53      40.940  26.152  23.159  1.00  0.00
ATOM      7  CA  TYR    54      41.849  29.616  24.461  1.00  0.00
ATOM      8  CA  SER    55      44.339  31.098  21.941  1.00  0.00
ATOM      9  CA  ASP    56      44.107  34.343  23.818  1.00  0.00
ATOM     10  CA  SER    57      45.413  32.996  27.210  1.00  0.00
ATOM     11  CA  ALA    58      49.064  31.967  27.832  1.00  0.00
ATOM     12  CA  PHE    59      49.558  28.579  29.604  1.00  0.00
ATOM     13  CA  ASN    60      52.869  27.883  31.345  1.00  0.00
ATOM     14  CA  GLY    61      54.077  24.693  33.100  1.00  0.00
ATOM     15  CA  GLU    80      43.840  32.888  31.680  1.00  0.00
ATOM     16  CA  MET    81      47.346  32.025  32.853  1.00  0.00
ATOM     17  CA  LEU    82      47.872  28.713  34.608  1.00  0.00
ATOM     18  CA  LYS    83      50.938  27.186  36.240  1.00  0.00
ATOM     19  CA  PRO    84      50.599  23.511  37.220  1.00  0.00
ATOM     20  CA  LEU   102      36.837  10.179  42.224  1.00  0.00
ATOM     21  CA  PHE   103      34.682   7.269  43.280  1.00  0.00
ATOM     22  CA  VAL   104      32.058   6.587  45.958  1.00  0.00
ATOM     23  CA  HIS   105      31.056   2.947  46.481  1.00  0.00
ATOM     24  CA  LEU   106      27.639   2.903  48.121  1.00  0.00
ATOM     25  CA  ARG   107      26.767   0.350  50.813  1.00  0.00
ATOM     26  CA  CYS   108      23.091  -0.442  51.166  1.00  0.00
ATOM     27  CA  ASP   109      20.160   1.367  49.630  1.00  0.00
ATOM     28  CA  ARG   110      19.695   4.637  51.530  1.00  0.00
ATOM     29  CA  TYR   111      17.112   6.887  49.880  1.00  0.00
ATOM     30  CA  ASP   112      19.570   9.775  50.104  1.00  0.00
ATOM     31  CA  ILE   113      22.684   8.148  48.560  1.00  0.00
ATOM     32  CA  LEU   114      22.562   9.724  45.093  1.00  0.00
ATOM     33  CA  HIS   115      22.042  13.131  46.690  1.00  0.00
ATOM     34  CA  LEU   116      24.981  12.930  49.061  1.00  0.00
ATOM     35  CA  VAL   117      27.274  11.233  46.551  1.00  0.00
ATOM     36  CA  ALA   118      26.466  14.078  44.221  1.00  0.00
ATOM     37  CA  ASN   119      27.153  16.624  46.927  1.00  0.00
ATOM     38  CA  GLU   120      30.479  15.104  47.974  1.00  0.00
ATOM     39  CA  ILE   121      31.794  14.710  44.446  1.00  0.00
ATOM     40  CA  SER   122      30.466  18.234  43.755  1.00  0.00
ATOM     41  CA  GLN   123      33.597  20.357  44.339  1.00  0.00
ATOM     42  CA  MET   124      36.392  18.518  42.498  1.00  0.00
ATOM     43  CA  PHE   125      36.229  20.067  38.999  1.00  0.00
ATOM     44  CA  GLU   126      34.673  22.868  36.897  1.00  0.00
ATOM     45  CA  ASP   127      37.252  25.171  38.527  1.00  0.00
ATOM     46  CA  LEU   128      40.298  25.689  36.266  1.00  0.00
ATOM     47  CA  VAL   129      38.163  26.647  33.316  1.00  0.00
ATOM     48  CA  GLU   130      35.673  28.617  35.371  1.00  0.00
ATOM     49  CA  LEU   131      38.520  30.721  36.787  1.00  0.00
ATOM     50  CA  VAL   132      39.988  31.320  33.293  1.00  0.00
ATOM     51  CA  GLU   133      36.572  32.566  32.137  1.00  0.00
ATOM     52  CA  GLU   134      36.256  34.881  35.158  1.00  0.00
ATOM     53  CA  GLU   135      39.728  36.388  34.601  1.00  0.00
ATOM     54  CA  ARG   136      43.048  35.144  36.143  1.00  0.00
ATOM     55  CA  GLY   137      44.495  34.462  39.574  1.00  0.00
ATOM     56  CA  PHE   138      41.161  33.681  41.211  1.00  0.00
ATOM     57  CA  ARG   139      41.666  30.817  43.665  1.00  0.00
ATOM     58  CA  PHE   140      39.830  27.527  44.049  1.00  0.00
ATOM     59  CA  MET   141      40.051  26.384  47.668  1.00  0.00
ATOM     60  CA  ASP   142      39.355  22.660  47.876  1.00  0.00
ATOM     61  CA  GLY   205      49.540  29.177  41.403  1.00  0.00
ATOM     62  CA  ARG   206      46.247  30.007  43.152  1.00  0.00
ATOM     63  CA  THR   207      44.457  27.360  41.062  1.00  0.00
ATOM     64  CA  LYS   208      46.992  24.671  42.054  1.00  0.00
ATOM     65  CA  GLN   209      44.966  24.197  45.274  1.00  0.00
ATOM     66  CA  ASN   229      35.659  28.044  48.051  1.00  0.00
ATOM     67  CA  LEU   230      37.022  30.179  45.231  1.00  0.00
ATOM     68  CA  LYS   231      38.751  33.388  46.256  1.00  0.00
ATOM     69  CA  ASP   232      39.659  36.127  43.801  1.00  0.00
ATOM     70  CA  GLU   233      42.601  38.538  43.909  1.00  0.00
ATOM     71  CA  ASN   234      40.432  41.179  45.577  1.00  0.00
ATOM     72  CA  GLY   235      39.932  38.608  48.357  1.00  0.00
ATOM     73  CA  LYS   236      36.259  37.939  47.669  1.00  0.00
ATOM     74  CA  SER   237      34.978  34.426  48.362  1.00  0.00
ATOM     75  CA  ILE   238      32.427  32.425  46.372  1.00  0.00
ATOM     76  CA  GLU   239      31.216  29.251  48.113  1.00  0.00
ATOM     77  CA  SER   249      29.851  16.295  35.528  1.00  0.00
ATOM     78  CA  LEU   250      32.128  17.874  32.912  1.00  0.00
ATOM     79  CA  LYS   251      30.975  15.269  30.377  1.00  0.00
ATOM     80  CA  GLU   252      27.363  16.200  31.241  1.00  0.00
ATOM     81  CA  GLN   253      28.264  19.747  30.223  1.00  0.00
ATOM     82  CA  GLY   254      29.618  18.743  26.864  1.00  0.00
ATOM     83  CA  LEU   255      33.218  17.931  27.752  1.00  0.00
ATOM     84  CA  MET   256      35.203  15.428  25.728  1.00  0.00
ATOM     85  CA  PHE   257      36.850  12.718  27.826  1.00  0.00
ATOM     86  CA  ILE   258      39.996  11.071  26.487  1.00  0.00
ATOM     87  CA  SER   259      41.975   8.152  27.819  1.00  0.00
ATOM     88  CA  ASP   284      36.072  21.230  27.945  1.00  0.00
ATOM     89  CA  HIS   285      37.590  18.239  29.980  1.00  0.00
ATOM     90  CA  LEU   286      39.685  18.496  33.118  1.00  0.00
ATOM     91  CA  MET   287      41.722  15.775  34.816  1.00  0.00
ATOM     92  CA  HIS   288      42.346  15.034  38.472  1.00  0.00
ATOM     93  CA  SER   302      33.368   6.417  29.926  1.00  0.00
ATOM     94  CA  LEU   303      35.547   8.151  27.375  1.00  0.00
ATOM     95  CA  ASP   304      34.654   9.704  24.059  1.00  0.00
ATOM     96  CA  PHE   305      38.124   8.774  22.747  1.00  0.00
ATOM     97  CA  LEU   306      40.254   5.845  23.870  1.00  0.00
TER
END
