
#######################################################
#                                                     #
#                        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   25 (  100),  selected   25 , name T0320TS550_2_2
# Molecule2: number of CA atoms  287 ( 2364),  selected  287 , name T0320.pdb
# PARAMETERS: T0320TS550_2_2.T0320.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           -
LGA    -       -      C      10           -
LGA    -       -      Y      11           -
LGA    -       -      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    -       -      P      51           -
LGA    -       -      L      52           -
LGA    -       -      N      53           -
LGA    -       -      G      54           -
LGA    -       -      E      55           -
LGA    -       -      I      56           -
LGA    -       -      S      57           -
LGA    -       -      F      58           -
LGA    -       -      S      59           -
LGA    -       -      Y      60           -
LGA    E     248      N      61          2.094
LGA    W     249      G      62          4.457
LGA    E     250      G      63           -
LGA    -       -      K      64           -
LGA    -       -      D      65           -
LGA    I     251      C      66          3.648
LGA    -       -      Q      67           -
LGA    -       -      V      68           -
LGA    -       -      L      69           -
LGA    I     252      L      70          1.973
LGA    -       -      L      71           -
LGA    -       -      L      72           -
LGA    H     253      Y      73          3.092
LGA    A     254      L      74          1.612
LGA    F     255      S      75          3.152
LGA    -       -      C      76           -
LGA    G     256      L      77          2.603
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    K     257      F      97           #
LGA    D     258      P      98           -
LGA    -       -      M      99           -
LGA    A     259      Q     100          3.744
LGA    E     260      R     101          3.784
LGA    G     261      L     102          1.490
LGA    E     262      P     103          1.709
LGA    R     263      T     104          2.393
LGA    S     264      V     105          1.561
LGA    S     265      F     106          2.056
LGA    A     266      I     107          2.034
LGA    I     267      D     108          2.529
LGA    N     268      Q     109           -
LGA    T     269      E     110           -
LGA    S     270      E     111           -
LGA    P     271      T     112           -
LGA    -       -      F     113           -
LGA    -       -      P     114           -
LGA    -       -      T     115           -
LGA    -       -      L     116           -
LGA    -       -      E     117           -
LGA    -       -      N     118           -
LGA    -       -      F     119           -
LGA    I     272      V     120           #
LGA    -       -      L     121           -
LGA    -       -      E     122           -
LGA    -       -      T     123           -
LGA    -       -      S     124           -
LGA    -       -      E     125           -
LGA    -       -      R     126           -
LGA    -       -      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    -       -      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)   25  287    5.0     17    2.73     0.00      4.067     0.601

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.609181 * X  +  -0.619903 * Y  +  -0.494590 * Z  +  18.079199
  Y_new =  -0.645655 * X  +   0.025567 * Y  +   0.763201 * Z  +  30.515553
  Z_new =  -0.460466 * X  +   0.784262 * Y  +  -0.415818 * Z  +  47.764851 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.058313   -1.083279  [ DEG:   117.9327    -62.0673 ]
  Theta =   0.478520    2.663073  [ DEG:    27.4172    152.5828 ]
  Phi   =  -2.327136    0.814457  [ DEG:  -133.3351     46.6649 ]
 
# 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: T0320TS550_2_2                                
REMARK     2: T0320.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS550_2_2.T0320.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   25  287   5.0   17   2.73    0.00   4.067
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS550_2_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0320
PARENT 1mkn_A
ATOM      1  N   GLU   248      22.524  28.682  16.353  1.00  0.00
ATOM      2  CA  GLU   248      22.146  27.615  17.325  1.00  0.00
ATOM      3  C   GLU   248      21.772  28.324  18.627  1.00  0.00
ATOM      4  O   GLU   248      22.615  28.589  19.448  1.00  0.00
ATOM      5  N   TRP   249      20.533  28.701  18.797  1.00  0.00
ATOM      6  CA  TRP   249      20.156  29.473  20.023  1.00  0.00
ATOM      7  C   TRP   249      19.482  28.573  21.062  1.00  0.00
ATOM      8  O   TRP   249      18.310  28.270  20.969  1.00  0.00
ATOM      9  N   GLU   250      20.211  28.172  22.075  1.00  0.00
ATOM     10  CA  GLU   250      19.598  27.327  23.141  1.00  0.00
ATOM     11  C   GLU   250      18.441  28.119  23.742  1.00  0.00
ATOM     12  O   GLU   250      18.333  29.299  23.497  1.00  0.00
ATOM     13  N   ILE   251      17.299  27.716  24.008  1.00  0.00
ATOM     14  CA  ILE   251      15.948  27.183  24.010  1.00  0.00
ATOM     15  C   ILE   251      15.032  28.327  24.385  1.00  0.00
ATOM     16  O   ILE   251      15.351  29.094  25.284  1.00  0.00
ATOM     17  N   ILE   252      13.896  28.438  23.703  1.00  0.00
ATOM     18  CA  ILE   252      12.952  29.522  23.958  1.00  0.00
ATOM     19  C   ILE   252      11.988  29.267  25.132  1.00  0.00
ATOM     20  O   ILE   252      11.169  28.346  25.091  1.00  0.00
ATOM     21  N   HIS   253      12.091  30.104  26.168  1.00  0.00
ATOM     22  CA  HIS   253      11.248  29.994  27.360  1.00  0.00
ATOM     23  C   HIS   253       9.817  30.423  27.038  1.00  0.00
ATOM     24  O   HIS   253       9.582  31.510  26.510  1.00  0.00
ATOM     25  N   ALA   254       8.863  29.569  27.383  1.00  0.00
ATOM     26  CA  ALA   254       7.464  29.831  27.098  1.00  0.00
ATOM     27  C   ALA   254       6.649  30.339  28.284  1.00  0.00
ATOM     28  O   ALA   254       5.442  30.551  28.166  1.00  0.00
ATOM     29  N   PHE   255       7.298  30.520  29.429  1.00  0.00
ATOM     30  CA  PHE   255       6.604  31.027  30.609  1.00  0.00
ATOM     31  C   PHE   255       7.335  32.259  31.129  1.00  0.00
ATOM     32  O   PHE   255       8.531  32.432  30.887  1.00  0.00
ATOM     33  N   GLY   256       6.611  33.110  31.842  1.00  0.00
ATOM     34  CA  GLY   256       7.212  34.315  32.378  1.00  0.00
ATOM     35  C   GLY   256       7.300  35.448  31.370  1.00  0.00
ATOM     36  O   GLY   256       6.665  35.411  30.314  1.00  0.00
ATOM     37  N   LYS   257       8.095  36.461  31.704  1.00  0.00
ATOM     38  CA  LYS   257       8.273  37.607  30.835  1.00  0.00
ATOM     39  C   LYS   257       9.447  37.341  29.902  1.00  0.00
ATOM     40  O   LYS   257      10.570  37.089  30.346  1.00  0.00
ATOM     41  N   ASP   258       9.196  37.392  28.585  1.00  0.00
ATOM     42  CA  ASP   258      10.199  37.158  27.542  1.00  0.00
ATOM     43  C   ASP   258      11.390  38.090  27.675  1.00  0.00
ATOM     44  O   ASP   258      12.493  37.765  27.245  1.00  0.00
ATOM     45  N   ALA   259      11.155  39.260  28.255  1.00  0.00
ATOM     46  CA  ALA   259      12.213  40.242  28.427  1.00  0.00
ATOM     47  C   ALA   259      13.230  39.757  29.447  1.00  0.00
ATOM     48  O   ALA   259      14.431  40.020  29.322  1.00  0.00
ATOM     49  N   GLU   260      12.740  39.035  30.449  1.00  0.00
ATOM     50  CA  GLU   260      13.597  38.507  31.498  1.00  0.00
ATOM     51  C   GLU   260      14.264  37.179  31.098  1.00  0.00
ATOM     52  O   GLU   260      15.051  36.607  31.855  1.00  0.00
ATOM     53  N   GLY   261      13.955  36.707  29.895  1.00  0.00
ATOM     54  CA  GLY   261      14.528  35.472  29.380  1.00  0.00
ATOM     55  C   GLY   261      15.859  35.805  28.697  1.00  0.00
ATOM     56  O   GLY   261      16.020  36.892  28.143  1.00  0.00
ATOM     57  N   GLU   262      16.813  34.877  28.752  1.00  0.00
ATOM     58  CA  GLU   262      18.137  35.065  28.149  1.00  0.00
ATOM     59  C   GLU   262      18.656  33.733  27.596  1.00  0.00
ATOM     60  O   GLU   262      19.296  32.963  28.312  1.00  0.00
ATOM     61  N   ARG   263      18.343  33.246  26.146  1.00  0.00
ATOM     62  CA  ARG   263      18.753  31.953  25.545  1.00  0.00
ATOM     63  C   ARG   263      20.260  32.028  25.357  1.00  0.00
ATOM     64  O   ARG   263      20.876  33.010  25.720  1.00  0.00
ATOM     65  N   SER   264      20.885  31.022  24.824  1.00  0.00
ATOM     66  CA  SER   264      22.362  31.125  24.678  1.00  0.00
ATOM     67  C   SER   264      22.884  30.118  23.663  1.00  0.00
ATOM     68  O   SER   264      22.519  28.959  23.697  1.00  0.00
ATOM     69  N   SER   265      23.746  30.521  22.758  1.00  0.00
ATOM     70  CA  SER   265      24.249  29.510  21.795  1.00  0.00
ATOM     71  C   SER   265      25.363  30.036  20.898  1.00  0.00
ATOM     72  O   SER   265      26.253  30.738  21.327  1.00  0.00
ATOM     73  N   ALA   266      25.342  29.637  19.652  1.00  0.00
ATOM     74  CA  ALA   266      26.418  30.038  18.711  1.00  0.00
ATOM     75  C   ALA   266      25.847  30.318  17.319  1.00  0.00
ATOM     76  O   ALA   266      24.799  29.831  16.955  1.00  0.00
ATOM     77  N   ILE   267      26.470  31.509  17.136  1.00  0.00
ATOM     78  CA  ILE   267      26.116  32.920  17.333  1.00  0.00
ATOM     79  C   ILE   267      25.392  33.377  18.609  1.00  0.00
ATOM     80  O   ILE   267      25.973  34.101  19.421  1.00  0.00
ATOM     81  N   ASN   268      24.130  32.975  18.773  1.00  0.00
ATOM     82  CA  ASN   268      23.319  33.378  19.929  1.00  0.00
ATOM     83  C   ASN   268      23.947  33.129  21.297  1.00  0.00
ATOM     84  O   ASN   268      23.603  33.808  22.266  1.00  0.00
ATOM     85  N   THR   269      24.865  32.163  21.356  1.00  0.00
ATOM     86  CA  THR   269      25.580  31.770  22.580  1.00  0.00
ATOM     87  C   THR   269      25.776  32.887  23.607  1.00  0.00
ATOM     88  O   THR   269      25.295  32.794  24.736  1.00  0.00
ATOM     89  N   SER   270      26.902  33.637  22.611  1.00  0.00
ATOM     90  CA  SER   270      26.563  34.542  23.751  1.00  0.00
ATOM     91  C   SER   270      25.116  34.334  24.178  1.00  0.00
ATOM     92  O   SER   270      24.476  33.371  23.803  1.00  0.00
ATOM     93  N   PRO   271      24.599  35.222  24.980  1.00  0.00
ATOM     94  CA  PRO   271      23.204  35.065  25.450  1.00  0.00
ATOM     95  C   PRO   271      22.395  36.319  25.137  1.00  0.00
ATOM     96  O   PRO   271      22.923  37.384  24.886  1.00  0.00
ATOM     97  N   ILE   272      21.108  36.173  25.173  1.00  0.00
ATOM     98  CA  ILE   272      20.170  37.301  24.903  1.00  0.00
ATOM     99  C   ILE   272      18.925  37.015  25.682  1.00  0.00
ATOM    100  O   ILE   272      18.489  35.902  25.749  1.00  0.00
TER
END
