
#######################################################
#                                                     #
#                        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    9 (   42),  selected    9 , name T0320TS103_1_2-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected  214 , name T0320_D1.pdb
# PARAMETERS: T0320TS103_1_2-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    -       -      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    -       -      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    G     218      P     103          0.696
LGA    K     219      T     104          0.587
LGA    F     221      V     105          1.123
LGA    T     222      F     106          0.856
LGA    S     223      I     107          1.384
LGA    I     224      D     108          1.943
LGA    G     225      Q     109          2.678
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    G     226      V     142          1.523
LGA    I     227      N     143          1.586
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)    9  214    5.0      9    1.51     0.00      3.992     0.559

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.807511 * X  +  -0.570318 * Y  +  -0.150543 * Z  +  61.118122
  Y_new =  -0.544812 * X  +  -0.623334 * Y  +  -0.560923 * Z  +  81.790810
  Z_new =   0.226066 * X  +   0.534969 * Y  +  -0.814065 * Z  +  12.658937 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.560202   -0.581391  [ DEG:   146.6888    -33.3112 ]
  Theta =  -0.228037   -2.913555  [ DEG:   -13.0656   -166.9344 ]
  Phi   =  -0.593530    2.548063  [ DEG:   -34.0068    145.9932 ]
 
# 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: T0320TS103_1_2-D1                             
REMARK     2: T0320_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS103_1_2-D1.T0320_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    9  214   5.0    9   1.51    0.00   3.992
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS103_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0320
PARENT 1se8_A
ATOM      1  N   GLY   218      17.201  35.675  30.130  1.00  1.00
ATOM      2  CA  GLY   218      18.631  35.464  30.013  1.00  1.00
ATOM      3  C   GLY   218      18.857  34.422  28.935  1.00  1.00
ATOM      4  O   GLY   218      18.561  33.240  29.139  1.00  1.00
ATOM      5  N   LYS   219      19.308  34.874  27.766  1.00  1.00
ATOM      6  CA  LYS   219      19.531  33.985  26.637  1.00  1.00
ATOM      7  C   LYS   219      20.851  34.273  25.938  1.00  1.00
ATOM      8  O   LYS   219      21.193  35.426  25.672  1.00  1.00
ATOM      9  CB  LYS   219      18.394  34.093  25.622  1.00  1.00
ATOM     10  N   PHE   221      21.573  33.204  25.614  1.00  1.00
ATOM     11  CA  PHE   221      22.819  33.295  24.883  1.00  1.00
ATOM     12  C   PHE   221      22.739  32.389  23.667  1.00  1.00
ATOM     13  O   PHE   221      22.207  31.288  23.753  1.00  1.00
ATOM     14  CB  PHE   221      24.021  32.834  25.748  1.00  1.00
ATOM     15  N   THR   222      23.244  32.879  22.542  1.00  1.00
ATOM     16  CA  THR   222      23.429  32.068  21.337  1.00  1.00
ATOM     17  C   THR   222      24.835  32.320  20.847  1.00  1.00
ATOM     18  O   THR   222      25.190  33.449  20.533  1.00  1.00
ATOM     19  CB  THR   222      22.422  32.462  20.234  1.00  1.00
ATOM     20  N   SER   223      25.640  31.270  20.805  1.00  1.00
ATOM     21  CA  SER   223      27.010  31.392  20.303  1.00  1.00
ATOM     22  C   SER   223      27.298  30.262  19.325  1.00  1.00
ATOM     23  O   SER   223      26.752  29.169  19.439  1.00  1.00
ATOM     24  CB  SER   223      28.082  31.391  21.444  1.00  1.00
ATOM     25  N   ILE   224      28.162  30.541  18.373  1.00  1.00
ATOM     26  CA  ILE   224      28.544  29.557  17.380  1.00  1.00
ATOM     27  C   ILE   224      30.015  29.787  17.117  1.00  1.00
ATOM     28  O   ILE   224      30.436  30.916  16.806  1.00  1.00
ATOM     29  CB  ILE   224      27.718  29.734  16.101  1.00  1.00
ATOM     30  N   GLY   225      30.802  28.728  17.279  1.00  1.00
ATOM     31  CA  GLY   225      32.236  28.803  17.085  1.00  1.00
ATOM     32  C   GLY   225      32.819  27.410  16.919  1.00  1.00
ATOM     33  O   GLY   225      32.131  26.500  16.449  1.00  1.00
ATOM     34  N   GLY   226      34.076  27.232  17.305  1.00  1.00
ATOM     35  CA  GLY   226      34.715  25.922  17.187  1.00  1.00
ATOM     36  C   GLY   226      35.335  25.519  18.501  1.00  1.00
ATOM     37  O   GLY   226      35.863  26.360  19.234  1.00  1.00
ATOM     38  N   ILE   227      35.292  24.231  18.798  1.00  1.00
ATOM     39  CA  ILE   227      35.868  23.715  20.031  1.00  1.00
ATOM     40  C   ILE   227      37.391  23.971  20.055  1.00  1.00
ATOM     41  O   ILE   227      38.077  23.709  19.070  1.00  1.00
ATOM     42  CB  ILE   227      35.575  22.217  20.168  1.00  1.00
TER
END
