
#######################################################
#                                                     #
#                        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    6 (   42),  selected    6 , name T0320TS074_1-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected  214 , name T0320_D1.pdb
# PARAMETERS: T0320TS074_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           -
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    T     222      S      50          1.526
LGA    S     223      P      51          1.324
LGA    I     224      L      52          1.298
LGA    G     225      N      53          0.762
LGA    G     226      G      54          2.125
LGA    -       -      E      55           -
LGA    I     227      I      56          2.996
LGA    -       -      S      57           -
LGA    -       -      F      58           -
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    -       -      V      68           -
LGA    -       -      L      69           -
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    -       -      M      99           -
LGA    -       -      Q     100           -
LGA    -       -      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    -       -      E     117           -
LGA    -       -      N     118           -
LGA    -       -      F     119           -
LGA    -       -      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           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    6  214    5.0      6    1.82    33.33      2.668     0.313

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.809096 * X  +  -0.586010 * Y  +  -0.044230 * Z  +  10.762617
  Y_new =   0.578506 * X  +  -0.780967 * Y  +  -0.235417 * Z  +  34.979443
  Z_new =   0.103414 * X  +  -0.216062 * Y  +   0.970888 * Z  +  26.660875 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.218973    2.922620  [ DEG:   -12.5462    167.4538 ]
  Theta =  -0.103599   -3.037993  [ DEG:    -5.9358   -174.0642 ]
  Phi   =   2.520869   -0.620724  [ DEG:   144.4351    -35.5649 ]
 
# 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: T0320TS074_1-D1                               
REMARK     2: T0320_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS074_1-D1.T0320_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    6  214   5.0    6   1.82   33.33   2.668
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS074_1-D1
PFRMAT TS
TARGET T0320
MODEL  1
PARENT N/A
ATOM      1  N   THR   222      13.086  32.464  39.945  1.00  1.00
ATOM      2  CA  THR   222      14.288  33.337  39.848  1.00  1.00
ATOM      3  C   THR   222      15.008  33.027  38.522  1.00  1.00
ATOM      4  O   THR   222      16.114  33.493  38.289  1.00  1.00
ATOM      5  CB  THR   222      15.291  33.136  41.005  1.00  1.00
ATOM      6  OG1 THR   222      15.873  31.737  41.070  1.00  1.00
ATOM      7  CG2 THR   222      14.694  33.376  42.378  1.00  1.00
ATOM      8  N   SER   223      14.353  32.330  37.614  1.00  1.00
ATOM      9  CA  SER   223      15.054  31.980  36.382  1.00  1.00
ATOM     10  C   SER   223      15.469  33.107  35.473  1.00  1.00
ATOM     11  O   SER   223      16.580  33.068  34.940  1.00  1.00
ATOM     12  HN  SER   223      13.410  31.996  37.654  1.00  1.00
ATOM     13  CB  SER   223      14.280  30.951  35.575  1.00  1.00
ATOM     14  OG  SER   223      14.156  29.710  36.205  1.00  1.00
ATOM     15  N   ILE   224      14.593  34.099  35.269  1.00  1.00
ATOM     16  CA  ILE   224      14.955  35.199  34.355  1.00  1.00
ATOM     17  C   ILE   224      16.263  35.873  34.785  1.00  1.00
ATOM     18  O   ILE   224      17.126  36.102  33.969  1.00  1.00
ATOM     19  HN  ILE   224      13.684  34.191  35.676  1.00  1.00
ATOM     20  CB  ILE   224      13.853  36.277  34.324  1.00  1.00
ATOM     21  CG1 ILE   224      12.446  35.827  33.936  1.00  1.00
ATOM     22  CG2 ILE   224      14.366  37.415  33.439  1.00  1.00
ATOM     23  CD1 ILE   224      12.261  35.236  32.643  1.00  1.00
ATOM     24  N   GLY   225      16.376  36.191  36.066  1.00  1.00
ATOM     25  CA  GLY   225      17.552  36.853  36.613  1.00  1.00
ATOM     26  C   GLY   225      18.870  36.084  36.384  1.00  1.00
ATOM     27  O   GLY   225      19.909  36.628  35.988  1.00  1.00
ATOM     28  HN  GLY   225      15.665  35.999  36.743  1.00  1.00
ATOM     29  N   GLY   226      18.819  34.791  36.665  1.00  1.00
ATOM     30  CA  GLY   226      20.009  33.951  36.537  1.00  1.00
ATOM     31  C   GLY   226      20.291  33.731  35.052  1.00  1.00
ATOM     32  O   GLY   226      21.411  33.922  34.601  1.00  1.00
ATOM     33  HN  GLY   226      18.005  34.298  36.973  1.00  1.00
ATOM     34  N   ILE   227      19.268  33.357  34.288  1.00  1.00
ATOM     35  CA  ILE   227      19.439  33.140  32.863  1.00  1.00
ATOM     36  C   ILE   227      20.065  34.363  32.197  1.00  1.00
ATOM     37  O   ILE   227      21.027  34.248  31.450  1.00  1.00
ATOM     38  HN  ILE   227      18.336  33.199  34.614  1.00  1.00
ATOM     39  CB  ILE   227      18.102  32.818  32.180  1.00  1.00
ATOM     40  CG1 ILE   227      18.324  32.527  30.719  1.00  1.00
ATOM     41  CG2 ILE   227      17.142  33.967  32.503  1.00  1.00
ATOM     42  CD1 ILE   227      17.003  31.816  30.117  1.00  1.00
TER
END
