
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected  214 , name T0320_D1.pdb
# PARAMETERS: T0320TS074_4-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          1.607
LGA    S     223      P      51          1.393
LGA    I     224      L      52          1.491
LGA    G     225      N      53          0.746
LGA    G     226      G      54          2.447
LGA    -       -      E      55           -
LGA    I     227      I      56          3.329
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    2.02    33.33      2.486     0.284

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.572502 * X  +  -0.662172 * Y  +   0.483497 * Z  +  18.511660
  Y_new =   0.617204 * X  +  -0.040127 * Y  +  -0.785779 * Z  +  30.962328
  Z_new =   0.539722 * X  +   0.748277 * Y  +   0.385722 * Z  +  27.063250 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.094841   -2.046752  [ DEG:    62.7298   -117.2702 ]
  Theta =  -0.570107   -2.571486  [ DEG:   -32.6647   -147.3353 ]
  Phi   =   0.822955   -2.318638  [ DEG:    47.1518   -132.8482 ]
 
# 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_4-D1                               
REMARK     2: T0320_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS074_4-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   2.02   33.33   2.486
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS074_4-D1
PFRMAT TS
TARGET T0320
MODEL  4
PARENT N/A
ATOM      1  N   THR   222      12.840  32.851  39.951  1.00  1.00
ATOM      2  CA  THR   222      14.193  33.386  39.838  1.00  1.00
ATOM      3  C   THR   222      14.930  33.117  38.520  1.00  1.00
ATOM      4  O   THR   222      16.071  33.560  38.354  1.00  1.00
ATOM      5  CB  THR   222      14.924  32.638  40.966  1.00  1.00
ATOM      6  OG1 THR   222      14.806  31.194  40.541  1.00  1.00
ATOM      7  CG2 THR   222      14.128  33.016  42.191  1.00  1.00
ATOM      8  N   SER   223      14.299  32.380  37.600  1.00  1.00
ATOM      9  CA  SER   223      15.053  31.888  36.442  1.00  1.00
ATOM     10  C   SER   223      15.525  32.967  35.480  1.00  1.00
ATOM     11  O   SER   223      16.592  32.802  34.841  1.00  1.00
ATOM     12  HN  SER   223      13.335  32.110  37.602  1.00  1.00
ATOM     13  CB  SER   223      14.325  30.771  35.703  1.00  1.00
ATOM     14  OG  SER   223      13.104  31.237  35.194  1.00  1.00
ATOM     15  N   ILE   224      14.763  34.052  35.344  1.00  1.00
ATOM     16  CA  ILE   224      15.195  35.064  34.362  1.00  1.00
ATOM     17  C   ILE   224      16.412  35.889  34.821  1.00  1.00
ATOM     18  O   ILE   224      17.346  36.084  34.032  1.00  1.00
ATOM     19  HN  ILE   224      13.917  34.286  35.825  1.00  1.00
ATOM     20  CB  ILE   224      14.045  35.911  33.800  1.00  1.00
ATOM     21  CG1 ILE   224      13.333  36.729  34.900  1.00  1.00
ATOM     22  CG2 ILE   224      13.138  34.970  33.000  1.00  1.00
ATOM     23  CD1 ILE   224      12.352  37.753  34.263  1.00  1.00
ATOM     24  N   GLY   225      16.435  36.368  36.083  1.00  1.00
ATOM     25  CA  GLY   225      17.690  36.947  36.575  1.00  1.00
ATOM     26  C   GLY   225      18.873  35.953  36.457  1.00  1.00
ATOM     27  O   GLY   225      19.980  36.360  36.114  1.00  1.00
ATOM     28  HN  GLY   225      15.690  36.384  36.751  1.00  1.00
ATOM     29  N   GLY   226      18.638  34.673  36.726  1.00  1.00
ATOM     30  CA  GLY   226      19.697  33.679  36.586  1.00  1.00
ATOM     31  C   GLY   226      20.133  33.560  35.132  1.00  1.00
ATOM     32  O   GLY   226      21.326  33.443  34.845  1.00  1.00
ATOM     33  HN  GLY   226      17.764  34.295  37.033  1.00  1.00
ATOM     34  N   ILE   227      19.165  33.599  34.219  1.00  1.00
ATOM     35  CA  ILE   227      19.470  33.496  32.794  1.00  1.00
ATOM     36  C   ILE   227      20.371  34.639  32.350  1.00  1.00
ATOM     37  O   ILE   227      21.429  34.411  31.775  1.00  1.00
ATOM     38  HN  ILE   227      18.190  33.699  34.420  1.00  1.00
ATOM     39  CB  ILE   227      18.182  33.514  31.928  1.00  1.00
ATOM     40  CG1 ILE   227      17.255  32.394  32.351  1.00  1.00
ATOM     41  CG2 ILE   227      18.637  33.507  30.470  1.00  1.00
ATOM     42  CD1 ILE   227      18.011  31.000  32.155  1.00  1.00
TER
END
