
#######################################################
#                                                     #
#                        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   80 (   80),  selected   80 , name T0320TS464_4_1-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected  214 , name T0320_D1.pdb
# PARAMETERS: T0320TS464_4_1-D1.T0320_D1.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    M       1      -       -           -
LGA    Q       2      -       -           -
LGA    L       3      -       -           -
LGA    S       4      -       -           -
LGA    K       5      -       -           -
LGA    A       6      -       -           -
LGA    A       7      -       -           -
LGA    E       8      -       -           -
LGA    M       9      M       1          2.659
LGA    C      10      Q       2          4.358
LGA    Y      11      L       3          2.037
LGA    E      12      S       4          1.958
LGA    I      13      K       5          2.645
LGA    -       -      A       6           -
LGA    -       -      A       7           -
LGA    T      14      E       8          4.173
LGA    N      15      M       9           -
LGA    S      16      C      10           -
LGA    Y      17      Y      11           -
LGA    L      18      E      12           -
LGA    -       -      I      13           -
LGA    -       -      T      14           -
LGA    -       -      N      15           -
LGA    -       -      S      16           -
LGA    -       -      Y      17           -
LGA    -       -      L      18           -
LGA    -       -      H      19           -
LGA    -       -      I      20           -
LGA    -       -      D      21           -
LGA    -       -      Q      22           -
LGA    -       -      K      23           -
LGA    -       -      S      24           -
LGA    -       -      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    -       -      L      36           -
LGA    -       -      T      37           -
LGA    -       -      R      38           -
LGA    -       -      K      39           -
LGA    -       -      Y      40           -
LGA    -       -      L      41           -
LGA    -       -      L      42           -
LGA    -       -      S      43           -
LGA    -       -      E      44           -
LGA    -       -      I      45           -
LGA    -       -      F      46           -
LGA    -       -      V      47           -
LGA    -       -      R      48           -
LGA    -       -      W      49           -
LGA    -       -      S      50           -
LGA    H      19      P      51          3.811
LGA    I      20      L      52           #
LGA    D      21      N      53           #
LGA    -       -      G      54           -
LGA    -       -      E      55           -
LGA    Q      22      I      56           #
LGA    K      23      S      57           #
LGA    S      24      F      58          3.516
LGA    Q      25      S      59          2.917
LGA    I      26      Y      60          4.450
LGA    F      58      N      61          4.347
LGA    S      59      -       -           -
LGA    Y      60      -       -           -
LGA    N      61      -       -           -
LGA    G      62      -       -           -
LGA    G      63      -       -           -
LGA    K      64      -       -           -
LGA    D      65      -       -           -
LGA    C      66      G      62          2.713
LGA    Q      67      G      63          4.870
LGA    V      68      K      64          1.677
LGA    L      69      D      65          1.652
LGA    L      70      C      66          3.214
LGA    L      71      Q      67          4.670
LGA    L      72      V      68          3.464
LGA    Y      73      L      69          2.053
LGA    -       -      L      70           -
LGA    -       -      L      71           -
LGA    -       -      L      72           -
LGA    -       -      Y      73           -
LGA    -       -      L      74           -
LGA    -       -      S      75           -
LGA    -       -      C      76           -
LGA    -       -      L      77           -
LGA    -       -      W      78           -
LGA    -       -      E      79           -
LGA    -       -      Y      80           -
LGA    -       -      F      81           -
LGA    -       -      F      82           -
LGA    -       -      I      83           -
LGA    -       -      K      84           -
LGA    -       -      A      85           -
LGA    -       -      Q      86           -
LGA    -       -      N      87           -
LGA    -       -      S      88           -
LGA    -       -      F      97           -
LGA    -       -      P      98           -
LGA    T     112      M      99           #
LGA    F     113      Q     100          2.098
LGA    P     114      R     101          2.371
LGA    T     115      L     102           -
LGA    L     116      -       -           -
LGA    E     117      -       -           -
LGA    N     118      P     103          3.798
LGA    F     119      T     104           #
LGA    V     120      -       -           -
LGA    L     121      V     105           #
LGA    E     122      F     106           #
LGA    T     123      I     107           #
LGA    S     124      D     108           #
LGA    -       -      Q     109           -
LGA    -       -      E     110           -
LGA    -       -      E     111           -
LGA    -       -      T     112           -
LGA    -       -      F     113           -
LGA    -       -      P     114           -
LGA    A     140      T     115          3.653
LGA    -       -      L     116           -
LGA    S     141      E     117          4.288
LGA    V     142      N     118          2.828
LGA    N     143      F     119          2.846
LGA    M     144      V     120          2.695
LGA    A     145      L     121          2.972
LGA    D     146      E     122          3.194
LGA    A     147      T     123          3.079
LGA    -       -      S     124           -
LGA    -       -      E     125           -
LGA    F     148      R     126          3.838
LGA    R     149      Y     127           #
LGA    -       -      C     128           -
LGA    -       -      L     129           -
LGA    -       -      S     130           -
LGA    -       -      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    D     150      E     211          4.439
LGA    F     151      P     212           -
LGA    I     152      I     213           -
LGA    K     153      C     214           -
LGA    I     154      G     215           -
LGA    Y     155      L     216           -
LGA    P     156      Y     217           -
LGA    E     157      G     218           -
LGA    T     158      K     219           -
LGA    E     159      G     220           -
LGA    S     223      F     221           -
LGA    I     224      T     222          4.928
LGA    G     225      S     223          1.277
LGA    G     226      I     224          2.395
LGA    I     227      G     225          2.197
LGA    -       -      G     226           -
LGA    -       -      I     227           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   80  214    5.0     36    3.32     2.78      9.606     1.053

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.551870 * X  +  -0.618649 * Y  +  -0.559207 * Z  + 115.550255
  Y_new =   0.357042 * X  +   0.781283 * Y  +  -0.511974 * Z  + -68.612045
  Z_new =   0.753631 * X  +   0.082883 * Y  +   0.652051 * Z  + -29.311378 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.126434   -3.015159  [ DEG:     7.2441   -172.7559 ]
  Theta =  -0.853570   -2.288023  [ DEG:   -48.9059   -131.0941 ]
  Phi   =   0.574240   -2.567353  [ DEG:    32.9015   -147.0985 ]
 
# 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-D1                             
REMARK     2: T0320_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS464_4_1-D1.T0320_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   80  214   5.0   36   3.32    2.78   9.606
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS464_4_1-D1
REMARK PARENT number 1
PFRMAT TS
TARGET T0320
PARENT N/A
ATOM      1  CA  MET     1      18.707  39.853  16.667  1.00  0.00
ATOM      2  CA  GLN     2      18.953  38.455  20.222  1.00  0.00
ATOM      3  CA  LEU     3      19.820  41.774  21.922  1.00  0.00
ATOM      4  CA  SER     4      16.854  43.254  20.051  1.00  0.00
ATOM      5  CA  LYS     5      14.556  40.582  21.511  1.00  0.00
ATOM      6  CA  ALA     6      16.022  40.959  25.014  1.00  0.00
ATOM      7  CA  ALA     7      15.493  44.732  24.912  1.00  0.00
ATOM      8  CA  GLU     8      11.780  44.326  24.084  1.00  0.00
ATOM      9  CA  MET     9      10.041  41.605  22.083  1.00  0.00
ATOM     10  CA  CYS    10      10.595  39.047  24.822  1.00  0.00
ATOM     11  CA  TYR    11       9.275  41.346  27.560  1.00  0.00
ATOM     12  CA  GLU    12       5.512  40.338  27.461  1.00  0.00
ATOM     13  CA  ILE    13       3.677  37.032  27.137  1.00  0.00
ATOM     14  CA  THR    14       3.908  36.034  30.750  1.00  0.00
ATOM     15  CA  ASN    15       7.201  34.463  31.677  1.00  0.00
ATOM     16  CA  SER    16       8.961  35.560  34.787  1.00  0.00
ATOM     17  CA  TYR    17      12.643  36.401  34.673  1.00  0.00
ATOM     18  CA  LEU    18      13.777  32.869  35.461  1.00  0.00
ATOM     19  CA  HIS    19      11.499  31.130  33.001  1.00  0.00
ATOM     20  CA  ILE    20      12.416  33.746  30.387  1.00  0.00
ATOM     21  CA  ASP    21      16.124  33.137  30.984  1.00  0.00
ATOM     22  CA  GLN    22      15.662  29.382  30.930  1.00  0.00
ATOM     23  CA  LYS    23      14.089  29.643  27.446  1.00  0.00
ATOM     24  CA  SER    24      16.884  31.896  26.196  1.00  0.00
ATOM     25  CA  GLN    25      19.382  29.379  27.510  1.00  0.00
ATOM     26  CA  ILE    26      17.687  26.518  25.630  1.00  0.00
ATOM     27  CA  PHE    58      23.717  25.302  20.100  1.00  0.00
ATOM     28  CA  SER    59      23.961  27.185  16.846  1.00  0.00
ATOM     29  CA  TYR    60      22.057  25.386  14.108  1.00  0.00
ATOM     30  CA  ASN    61      22.963  25.952  10.462  1.00  0.00
ATOM     31  CA  GLY    62      19.265  26.698   9.979  1.00  0.00
ATOM     32  CA  GLY    63      16.847  28.895  11.888  1.00  0.00
ATOM     33  CA  LYS    64      14.160  26.443  10.830  1.00  0.00
ATOM     34  CA  ASP    65      16.098  23.809  12.762  1.00  0.00
ATOM     35  CA  CYS    66      16.349  26.189  15.717  1.00  0.00
ATOM     36  CA  GLN    67      12.599  26.826  15.592  1.00  0.00
ATOM     37  CA  VAL    68      11.983  23.100  15.833  1.00  0.00
ATOM     38  CA  LEU    69      14.505  22.669  18.665  1.00  0.00
ATOM     39  CA  LEU    70      12.558  25.235  20.660  1.00  0.00
ATOM     40  CA  LEU    71       9.036  23.978  21.338  1.00  0.00
ATOM     41  CA  LEU    72      11.337  20.816  21.359  1.00  0.00
ATOM     42  CA  TYR    73      13.053  22.693  24.181  1.00  0.00
ATOM     43  CA  THR   112      10.252  38.999  33.371  1.00  0.00
ATOM     44  CA  PHE   113      11.874  41.241  30.761  1.00  0.00
ATOM     45  CA  PRO   114      15.660  40.968  30.545  1.00  0.00
ATOM     46  CA  THR   115      18.142  42.854  32.728  1.00  0.00
ATOM     47  CA  LEU   116      21.474  43.781  31.182  1.00  0.00
ATOM     48  CA  GLU   117      22.971  40.947  33.224  1.00  0.00
ATOM     49  CA  ASN   118      20.853  38.172  31.729  1.00  0.00
ATOM     50  CA  PHE   119      21.128  39.535  28.189  1.00  0.00
ATOM     51  CA  VAL   120      24.900  38.946  28.440  1.00  0.00
ATOM     52  CA  LEU   121      24.578  35.348  29.571  1.00  0.00
ATOM     53  CA  GLU   122      22.251  34.712  26.690  1.00  0.00
ATOM     54  CA  THR   123      24.786  36.155  24.246  1.00  0.00
ATOM     55  CA  SER   124      27.537  33.973  25.722  1.00  0.00
ATOM     56  CA  ALA   140      22.536  33.656   8.831  1.00  0.00
ATOM     57  CA  SER   141      21.674  36.968  10.541  1.00  0.00
ATOM     58  CA  VAL   142      18.123  37.193   9.214  1.00  0.00
ATOM     59  CA  ASN   143      17.242  33.517   9.705  1.00  0.00
ATOM     60  CA  MET   144      18.402  34.102  13.313  1.00  0.00
ATOM     61  CA  ALA   145      16.171  37.151  13.767  1.00  0.00
ATOM     62  CA  ASP   146      12.852  35.917  12.494  1.00  0.00
ATOM     63  CA  ALA   147      12.957  33.019  14.957  1.00  0.00
ATOM     64  CA  PHE   148      12.996  35.585  17.782  1.00  0.00
ATOM     65  CA  ARG   149       9.714  36.940  16.361  1.00  0.00
ATOM     66  CA  ASP   150       8.155  33.469  16.166  1.00  0.00
ATOM     67  CA  PHE   151       9.362  32.531  19.647  1.00  0.00
ATOM     68  CA  ILE   152      10.177  33.478  23.072  1.00  0.00
ATOM     69  CA  LYS   153       6.554  32.335  22.672  1.00  0.00
ATOM     70  CA  ILE   154       7.368  28.677  23.076  1.00  0.00
ATOM     71  CA  TYR   155      10.057  28.687  25.751  1.00  0.00
ATOM     72  CA  PRO   156       9.912  32.070  27.487  1.00  0.00
ATOM     73  CA  GLU   157       6.398  31.637  28.927  1.00  0.00
ATOM     74  CA  THR   158       4.882  29.950  31.933  1.00  0.00
ATOM     75  CA  GLU   159       5.241  26.421  30.582  1.00  0.00
ATOM     76  CA  SER   223      18.375  15.388  15.664  1.00  0.00
ATOM     77  CA  ILE   224      16.829  18.713  14.635  1.00  0.00
ATOM     78  CA  GLY   225      19.470  19.364  11.988  1.00  0.00
ATOM     79  CA  GLY   226      23.081  20.378  11.420  1.00  0.00
ATOM     80  CA  ILE   227      24.500  22.282  14.358  1.00  0.00
TER
END
