
#######################################################
#                                                     #
#                        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   34 (   34),  selected   34 , name T0372TS464_5_2
# Molecule2: number of CA atoms  298 ( 2427),  selected  298 , name T0372.pdb
# PARAMETERS: T0372TS464_5_2.T0372.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    S      98      M       1           -
LGA    N      99      I       2           -
LGA    M     100      P       3           -
LGA    -       -      F       4           -
LGA    -       -      K       5           -
LGA    -       -      D       6           -
LGA    -       -      I       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    -       -      D      11           -
LGA    -       -      R      12           -
LGA    -       -      D      13           -
LGA    -       -      T      14           -
LGA    -       -      I      15           -
LGA    -       -      T      16           -
LGA    -       -      A      17           -
LGA    -       -      F      18           -
LGA    -       -      T      19           -
LGA    -       -      M      20           -
LGA    -       -      K      21           -
LGA    -       -      S      22           -
LGA    -       -      D      23           -
LGA    -       -      R      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      S      30           -
LGA    -       -      F      31           -
LGA    -       -      S      32           -
LGA    -       -      N      33           -
LGA    -       -      L      34           -
LGA    -       -      C      35           -
LGA    -       -      S      36           -
LGA    -       -      W      37           -
LGA    -       -      R      38           -
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    -       -      Y      41           -
LGA    -       -      D      42           -
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    -       -      F      45           -
LGA    -       -      A      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    -       -      D      50           -
LGA    -       -      F      51           -
LGA    -       -      L      52           -
LGA    -       -      V      53           -
LGA    -       -      F      54           -
LGA    -       -      K      55           -
LGA    -       -      F      56           -
LGA    -       -      W      57           -
LGA    -       -      A      58           -
LGA    -       -      G      59           -
LGA    -       -      E      60           -
LGA    -       -      Q      61           -
LGA    -       -      L      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      M      65           -
LGA    -       -      M      66           -
LGA    -       -      P      67           -
LGA    -       -      V      68           -
LGA    -       -      G      69           -
LGA    -       -      N      70           -
LGA    -       -      G      71           -
LGA    -       -      D      72           -
LGA    -       -      L      73           -
LGA    -       -      K      74           -
LGA    -       -      A      75           -
LGA    -       -      V      76           -
LGA    -       -      L      77           -
LGA    -       -      R      78           -
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      I      81           -
LGA    -       -      E      82           -
LGA    -       -      D      83           -
LGA    -       -      A      84           -
LGA    -       -      D      85           -
LGA    -       -      K      86           -
LGA    -       -      E      87           -
LGA    -       -      K      88           -
LGA    -       -      H      89           -
LGA    -       -      N      90           -
LGA    -       -      F      91           -
LGA    -       -      C      92           -
LGA    -       -      M      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      V      96           -
LGA    -       -      C      97           -
LGA    -       -      S      98           -
LGA    -       -      N      99           -
LGA    -       -      M     100           -
LGA    -       -      R     101           -
LGA    -       -      A     102           -
LGA    -       -      D     103           -
LGA    -       -      L     104           -
LGA    -       -      E     105           -
LGA    -       -      A     106           -
LGA    -       -      I     107           -
LGA    -       -      L     108           -
LGA    -       -      P     109           -
LGA    -       -      E     110           -
LGA    -       -      R     111           -
LGA    -       -      F     112           -
LGA    -       -      I     113           -
LGA    -       -      F     114           -
LGA    -       -      T     115           -
LGA    -       -      E     116           -
LGA    -       -      D     117           -
LGA    -       -      R     118           -
LGA    -       -      A     119           -
LGA    -       -      Y     120           -
LGA    -       -      A     121           -
LGA    -       -      D     122           -
LGA    -       -      Y     123           -
LGA    -       -      I     124           -
LGA    R     101      Y     125          3.732
LGA    A     102      L     126          2.268
LGA    -       -      R     127           -
LGA    D     103      S     128          3.444
LGA    L     104      D     129          3.579
LGA    -       -      L     130           -
LGA    E     105      A     131          1.240
LGA    A     106      T     132          2.214
LGA    I     107      L     133          3.780
LGA    L     108      K     134           -
LGA    P     109      G     135           -
LGA    E     110      -       -           -
LGA    S     128      -       -           -
LGA    D     129      -       -           -
LGA    L     130      -       -           -
LGA    A     131      -       -           -
LGA    T     132      -       -           -
LGA    A     193      K     136          3.991
LGA    L     194      K     137          3.008
LGA    I     195      F     138          0.970
LGA    Y     196      Q     139          1.327
LGA    A     197      A     140          1.291
LGA    L     198      K     141          0.957
LGA    H     199      R     142          0.983
LGA    N     200      N     143          1.043
LGA    F     201      H     144          1.191
LGA    E     202      I     145          0.977
LGA    A     203      N     146          1.020
LGA    L     204      R     147          1.224
LGA    G     205      F     148          1.111
LGA    -       -      R     149           -
LGA    -       -      N     150           -
LGA    -       -      T     151           -
LGA    -       -      Y     152           -
LGA    -       -      P     153           -
LGA    -       -      D     154           -
LGA    -       -      Y     155           -
LGA    -       -      E     156           -
LGA    -       -      Y     157           -
LGA    -       -      T     158           -
LGA    -       -      P     159           -
LGA    -       -      I     160           -
LGA    -       -      T     161           -
LGA    -       -      P     162           -
LGA    -       -      D     163           -
LGA    -       -      R     164           -
LGA    -       -      I     165           -
LGA    -       -      Q     166           -
LGA    -       -      E     167           -
LGA    -       -      C     168           -
LGA    -       -      L     169           -
LGA    -       -      D     170           -
LGA    -       -      L     171           -
LGA    -       -      E     172           -
LGA    -       -      A     173           -
LGA    -       -      E     174           -
LGA    -       -      W     175           -
LGA    -       -      C     176           -
LGA    -       -      K     177           -
LGA    -       -      V     178           -
LGA    -       -      N     179           -
LGA    -       -      N     180           -
LGA    -       -      C     181           -
LGA    -       -      D     182           -
LGA    -       -      Q     183           -
LGA    -       -      Q     184           -
LGA    -       -      E     185           -
LGA    -       -      G     186           -
LGA    -       -      T     187           -
LGA    -       -      G     188           -
LGA    -       -      N     189           -
LGA    -       -      E     190           -
LGA    -       -      R     191           -
LGA    -       -      R     192           -
LGA    -       -      A     193           -
LGA    -       -      L     194           -
LGA    -       -      I     195           -
LGA    -       -      Y     196           -
LGA    -       -      A     197           -
LGA    -       -      L     198           -
LGA    -       -      H     199           -
LGA    -       -      N     200           -
LGA    -       -      F     201           -
LGA    -       -      E     202           -
LGA    -       -      A     203           -
LGA    -       -      L     204           -
LGA    -       -      G     205           -
LGA    -       -      L     206           -
LGA    -       -      T     207           -
LGA    -       -      G     208           -
LGA    -       -      G     209           -
LGA    -       -      I     210           -
LGA    -       -      L     211           -
LGA    -       -      H     212           -
LGA    -       -      V     213           -
LGA    -       -      N     214           -
LGA    -       -      G     215           -
LGA    -       -      K     216           -
LGA    -       -      I     217           -
LGA    -       -      V     218           -
LGA    -       -      A     219           -
LGA    -       -      F     220           -
LGA    -       -      T     221           -
LGA    -       -      F     222           -
LGA    -       -      G     223           -
LGA    -       -      M     224           -
LGA    -       -      P     225           -
LGA    -       -      I     226           -
LGA    -       -      N     227           -
LGA    -       -      H     228           -
LGA    -       -      E     229           -
LGA    -       -      T     230           -
LGA    -       -      F     231           -
LGA    -       -      G     232           -
LGA    -       -      V     233           -
LGA    -       -      H     234           -
LGA    -       -      V     235           -
LGA    -       -      E     236           -
LGA    -       -      K     237           -
LGA    -       -      A     238           -
LGA    -       -      D     239           -
LGA    -       -      T     240           -
LGA    -       -      S     241           -
LGA    -       -      I     242           -
LGA    -       -      D     243           -
LGA    L     206      G     244          1.501
LGA    T     207      A     245          3.544
LGA    -       -      Y     246           -
LGA    G     208      A     247          2.121
LGA    -       -      M     248           -
LGA    -       -      I     249           -
LGA    -       -      N     250           -
LGA    -       -      Y     251           -
LGA    -       -      E     252           -
LGA    -       -      F     253           -
LGA    -       -      A     254           -
LGA    -       -      N     255           -
LGA    -       -      R     256           -
LGA    -       -      I     257           -
LGA    -       -      P     258           -
LGA    -       -      E     259           -
LGA    -       -      Q     260           -
LGA    -       -      Y     261           -
LGA    -       -      I     262           -
LGA    -       -      Y     263           -
LGA    -       -      I     264           -
LGA    -       -      N     265           -
LGA    -       -      R     266           -
LGA    -       -      E     267           -
LGA    -       -      E     268           -
LGA    -       -      D     269           -
LGA    -       -      L     270           -
LGA    -       -      G     271           -
LGA    -       -      I     272           -
LGA    -       -      E     273           -
LGA    -       -      G     274           -
LGA    -       -      L     275           -
LGA    -       -      R     276           -
LGA    -       -      K     277           -
LGA    -       -      A     278           -
LGA    -       -      K     279           -
LGA    -       -      L     280           -
LGA    -       -      S     281           -
LGA    -       -      Y     282           -
LGA    -       -      Q     283           -
LGA    -       -      P     284           -
LGA    -       -      V     285           -
LGA    -       -      T     286           -
LGA    -       -      I     287           -
LGA    -       -      L     288           -
LGA    -       -      E     289           -
LGA    -       -      K     290           -
LGA    -       -      Y     291           -
LGA    -       -      M     292           -
LGA    -       -      A     293           -
LGA    -       -      C     294           -
LGA    -       -      L     295           -
LGA    -       -      K     296           -
LGA    -       -      D     297           -
LGA    -       -      H     298           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   34  298    5.0     23    2.31     8.70      6.319     0.956

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.928024 * X  +   0.369445 * Y  +   0.047764 * Z  + -102.938438
  Y_new =   0.275873 * X  +  -0.595424 * Y  +  -0.754563 * Z  +  81.931702
  Z_new =  -0.250330 * X  +   0.713429 * Y  +  -0.654487 * Z  +  36.010323 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.313133   -0.828460  [ DEG:   132.5327    -47.4673 ]
  Theta =   0.253021    2.888572  [ DEG:    14.4970    165.5030 ]
  Phi   =   0.288950   -2.852643  [ DEG:    16.5556   -163.4444 ]
 
# 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: T0372TS464_5_2                                
REMARK     2: T0372.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS464_5_2.T0372.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   34  298   5.0   23   2.31    8.70   6.319
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS464_5_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT N/A
ATOM      1  CA  SER    98      21.539  47.545  23.742  1.00  0.00
ATOM      2  CA  ASN    99      21.147  49.572  26.889  1.00  0.00
ATOM      3  CA  MET   100      22.214  46.583  28.983  1.00  0.00
ATOM      4  CA  ARG   101      25.568  46.663  27.159  1.00  0.00
ATOM      5  CA  ALA   102      25.955  50.262  28.394  1.00  0.00
ATOM      6  CA  ASP   103      25.090  49.318  31.983  1.00  0.00
ATOM      7  CA  LEU   104      27.358  46.270  31.923  1.00  0.00
ATOM      8  CA  GLU   105      30.462  48.449  32.145  1.00  0.00
ATOM      9  CA  ALA   106      29.372  48.922  35.756  1.00  0.00
ATOM     10  CA  ILE   107      28.442  45.286  36.270  1.00  0.00
ATOM     11  CA  LEU   108      31.427  43.373  35.003  1.00  0.00
ATOM     12  CA  PRO   109      34.873  43.913  33.411  1.00  0.00
ATOM     13  CA  GLU   110      34.292  40.994  31.058  1.00  0.00
ATOM     14  CA  SER   128      19.657  26.996  35.752  1.00  0.00
ATOM     15  CA  ASP   129      21.776  29.557  33.881  1.00  0.00
ATOM     16  CA  LEU   130      23.886  30.673  36.859  1.00  0.00
ATOM     17  CA  ALA   131      23.967  27.145  38.321  1.00  0.00
ATOM     18  CA  THR   132      24.815  25.569  35.006  1.00  0.00
ATOM     19  CA  ALA   193      15.941  40.257  33.465  1.00  0.00
ATOM     20  CA  LEU   194      18.963  40.383  31.135  1.00  0.00
ATOM     21  CA  ILE   195      20.666  43.072  33.224  1.00  0.00
ATOM     22  CA  TYR   196      19.711  41.330  36.465  1.00  0.00
ATOM     23  CA  ALA   197      20.964  38.027  35.045  1.00  0.00
ATOM     24  CA  LEU   198      24.400  39.572  34.289  1.00  0.00
ATOM     25  CA  HIS   199      24.613  40.813  37.882  1.00  0.00
ATOM     26  CA  ASN   200      23.983  37.282  39.120  1.00  0.00
ATOM     27  CA  PHE   201      26.506  35.886  36.646  1.00  0.00
ATOM     28  CA  GLU   202      29.223  38.230  37.520  1.00  0.00
ATOM     29  CA  ALA   203      28.516  37.766  41.215  1.00  0.00
ATOM     30  CA  LEU   204      29.389  34.125  40.671  1.00  0.00
ATOM     31  CA  GLY   205      32.742  34.190  38.923  1.00  0.00
ATOM     32  CA  LEU   206      31.279  33.722  35.447  1.00  0.00
ATOM     33  CA  THR   207      32.672  36.088  32.808  1.00  0.00
ATOM     34  CA  GLY   208      29.632  37.401  30.968  1.00  0.00
TER
END
