
#######################################################
#                                                     #
#                        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    5 (   25),  selected    5 , name T0284TS239_3_3
# Molecule2: number of CA atoms  282 ( 2139),  selected  282 , name T0284.pdb
# PARAMETERS: T0284TS239_3_3.T0284.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    -       -      A       4           -
LGA    -       -      S       5           -
LGA    -       -      H       6           -
LGA    -       -      H       7           -
LGA    -       -      E       8           -
LGA    -       -      L       9           -
LGA    -       -      R      10           -
LGA    -       -      A      11           -
LGA    -       -      M      12           -
LGA    -       -      F      13           -
LGA    -       -      R      14           -
LGA    -       -      A      15           -
LGA    -       -      L      16           -
LGA    -       -      L      17           -
LGA    -       -      D      18           -
LGA    -       -      S      19           -
LGA    -       -      S      20           -
LGA    -       -      R      21           -
LGA    -       -      C      22           -
LGA    -       -      Y      23           -
LGA    -       -      H      24           -
LGA    -       -      T      25           -
LGA    -       -      A      26           -
LGA    -       -      S      27           -
LGA    -       -      V      28           -
LGA    -       -      F      29           -
LGA    -       -      D      30           -
LGA    -       -      P      31           -
LGA    -       -      M      32           -
LGA    -       -      S      33           -
LGA    -       -      A      34           -
LGA    -       -      R      35           -
LGA    -       -      I      36           -
LGA    -       -      A      37           -
LGA    -       -      A      38           -
LGA    -       -      D      39           -
LGA    -       -      L      40           -
LGA    -       -      G      41           -
LGA    -       -      F      42           -
LGA    -       -      E      43           -
LGA    -       -      C      44           -
LGA    -       -      G      45           -
LGA    -       -      I      46           -
LGA    -       -      L      47           -
LGA    -       -      G      48           -
LGA    -       -      G      49           -
LGA    -       -      S      50           -
LGA    -       -      V      51           -
LGA    -       -      A      52           -
LGA    -       -      S      53           -
LGA    -       -      L      54           -
LGA    -       -      Q      55           -
LGA    -       -      V      56           -
LGA    -       -      L      57           -
LGA    -       -      A      58           -
LGA    -       -      A      59           -
LGA    -       -      P      60           -
LGA    -       -      D      61           -
LGA    -       -      F      62           -
LGA    -       -      A      63           -
LGA    -       -      L      64           -
LGA    -       -      I      65           -
LGA    -       -      T      66           -
LGA    -       -      L      67           -
LGA    -       -      S      68           -
LGA    -       -      E      69           -
LGA    -       -      F      70           -
LGA    -       -      V      71           -
LGA    -       -      E      72           -
LGA    -       -      Q      73           -
LGA    M       1      A      74          0.969
LGA    H       2      T      75          0.898
LGA    -       -      R      76           -
LGA    -       -      I      77           -
LGA    R       3      G      78          0.914
LGA    A       4      R      79          0.608
LGA    S       5      V      80          1.132
LGA    -       -      A      81           -
LGA    -       -      R      82           -
LGA    -       -      L      83           -
LGA    -       -      P      84           -
LGA    -       -      V      85           -
LGA    -       -      I      86           -
LGA    -       -      A      87           -
LGA    -       -      D      88           -
LGA    -       -      A      89           -
LGA    -       -      D      90           -
LGA    -       -      H      91           -
LGA    -       -      G      92           -
LGA    -       -      Y      93           -
LGA    -       -      G      94           -
LGA    -       -      N      95           -
LGA    -       -      A      96           -
LGA    -       -      L      97           -
LGA    -       -      N      98           -
LGA    -       -      V      99           -
LGA    -       -      M     100           -
LGA    -       -      R     101           -
LGA    -       -      T     102           -
LGA    -       -      V     103           -
LGA    -       -      V     104           -
LGA    -       -      E     105           -
LGA    -       -      L     106           -
LGA    -       -      E     107           -
LGA    -       -      R     108           -
LGA    -       -      A     109           -
LGA    -       -      G     110           -
LGA    -       -      I     111           -
LGA    -       -      A     112           -
LGA    -       -      A     113           -
LGA    -       -      L     114           -
LGA    -       -      T     115           -
LGA    -       -      I     116           -
LGA    -       -      E     117           -
LGA    -       -      D     118           -
LGA    -       -      T     119           -
LGA    -       -      L     120           -
LGA    -       -      L     121           -
LGA    -       -      P     122           -
LGA    -       -      A     123           -
LGA    -       -      Q     124           -
LGA    -       -      F     125           -
LGA    -       -      G     126           -
LGA    -       -      R     127           -
LGA    -       -      K     128           -
LGA    -       -      S     129           -
LGA    -       -      T     130           -
LGA    -       -      D     131           -
LGA    -       -      L     132           -
LGA    -       -      I     133           -
LGA    -       -      C     134           -
LGA    -       -      V     135           -
LGA    -       -      E     136           -
LGA    -       -      E     137           -
LGA    -       -      G     138           -
LGA    -       -      V     139           -
LGA    -       -      G     140           -
LGA    -       -      K     141           -
LGA    -       -      I     142           -
LGA    -       -      R     143           -
LGA    -       -      A     144           -
LGA    -       -      A     145           -
LGA    -       -      L     146           -
LGA    -       -      E     147           -
LGA    -       -      A     148           -
LGA    -       -      R     149           -
LGA    -       -      V     150           -
LGA    -       -      D     151           -
LGA    -       -      P     152           -
LGA    -       -      A     153           -
LGA    -       -      L     154           -
LGA    -       -      T     155           -
LGA    -       -      I     156           -
LGA    -       -      I     157           -
LGA    -       -      A     158           -
LGA    -       -      R     159           -
LGA    -       -      T     160           -
LGA    -       -      N     161           -
LGA    -       -      A     162           -
LGA    -       -      E     163           -
LGA    -       -      L     164           -
LGA    -       -      I     165           -
LGA    -       -      D     166           -
LGA    -       -      V     167           -
LGA    -       -      D     168           -
LGA    -       -      A     169           -
LGA    -       -      V     170           -
LGA    -       -      I     171           -
LGA    -       -      Q     172           -
LGA    -       -      R     173           -
LGA    -       -      T     174           -
LGA    -       -      L     175           -
LGA    -       -      A     176           -
LGA    -       -      Y     177           -
LGA    -       -      Q     178           -
LGA    -       -      E     179           -
LGA    -       -      A     180           -
LGA    -       -      G     181           -
LGA    -       -      A     182           -
LGA    -       -      D     183           -
LGA    -       -      G     184           -
LGA    -       -      I     185           -
LGA    -       -      C     186           -
LGA    -       -      L     187           -
LGA    -       -      V     188           -
LGA    -       -      G     189           -
LGA    -       -      V     190           -
LGA    -       -      R     191           -
LGA    -       -      D     192           -
LGA    -       -      F     193           -
LGA    -       -      A     194           -
LGA    -       -      H     195           -
LGA    -       -      L     196           -
LGA    -       -      E     197           -
LGA    -       -      A     198           -
LGA    -       -      I     199           -
LGA    -       -      A     200           -
LGA    -       -      E     201           -
LGA    -       -      H     202           -
LGA    -       -      L     203           -
LGA    -       -      H     204           -
LGA    -       -      I     205           -
LGA    -       -      P     206           -
LGA    -       -      L     207           -
LGA    -       -      M     208           -
LGA    -       -      L     209           -
LGA    -       -      V     210           -
LGA    -       -      T     211           -
LGA    -       -      Y     212           -
LGA    -       -      G     213           -
LGA    -       -      N     214           -
LGA    -       -      P     215           -
LGA    -       -      Q     216           -
LGA    -       -      L     217           -
LGA    -       -      R     218           -
LGA    -       -      D     219           -
LGA    -       -      D     220           -
LGA    -       -      A     221           -
LGA    -       -      R     222           -
LGA    -       -      L     223           -
LGA    -       -      A     224           -
LGA    -       -      R     225           -
LGA    -       -      L     226           -
LGA    -       -      G     227           -
LGA    -       -      V     228           -
LGA    -       -      R     229           -
LGA    -       -      V     230           -
LGA    -       -      V     231           -
LGA    -       -      V     232           -
LGA    -       -      N     233           -
LGA    -       -      G     234           -
LGA    -       -      H     235           -
LGA    -       -      A     236           -
LGA    -       -      A     237           -
LGA    -       -      Y     238           -
LGA    -       -      F     239           -
LGA    -       -      A     240           -
LGA    -       -      A     241           -
LGA    -       -      I     242           -
LGA    -       -      K     243           -
LGA    -       -      A     244           -
LGA    -       -      T     245           -
LGA    -       -      Y     246           -
LGA    -       -      D     247           -
LGA    -       -      C     248           -
LGA    -       -      L     249           -
LGA    -       -      R     250           -
LGA    -       -      E     251           -
LGA    -       -      E     252           -
LGA    -       -      R     253           -
LGA    -       -      G     254           -
LGA    -       -      A     255           -
LGA    -       -      V     256           -
LGA    -       -      A     257           -
LGA    -       -      S     258           -
LGA    -       -      D     259           -
LGA    -       -      L     260           -
LGA    -       -      T     261           -
LGA    -       -      A     262           -
LGA    -       -      S     263           -
LGA    -       -      E     264           -
LGA    -       -      L     265           -
LGA    -       -      S     266           -
LGA    -       -      K     267           -
LGA    -       -      K     268           -
LGA    -       -      Y     269           -
LGA    -       -      T     270           -
LGA    -       -      F     271           -
LGA    -       -      P     272           -
LGA    -       -      E     273           -
LGA    -       -      E     274           -
LGA    -       -      Y     275           -
LGA    -       -      Q     276           -
LGA    -       -      A     277           -
LGA    -       -      W     278           -
LGA    -       -      A     279           -
LGA    -       -      R     280           -
LGA    -       -      D     281           -
LGA    -       -      Y     282           -
LGA    -       -      M     283           -
LGA    -       -      E     284           -
LGA    -       -      V     285           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5  282    5.0      5    0.92     0.00      1.745     0.490

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.508485 * X  +   0.840890 * Y  +  -0.185332 * Z  +  98.149666
  Y_new =  -0.781014 * X  +  -0.359770 * Y  +   0.510473 * Z  + 104.182938
  Z_new =   0.362574 * X  +   0.404315 * Y  +   0.839684 * Z  + -40.259502 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.448745   -2.692848  [ DEG:    25.7112   -154.2888 ]
  Theta =  -0.371029   -2.770564  [ DEG:   -21.2584   -158.7416 ]
  Phi   =  -2.147914    0.993679  [ DEG:  -123.0664     56.9336 ]
 
# 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: T0284TS239_3_3                                
REMARK     2: T0284.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0284TS239_3_3.T0284.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5  282   5.0    5   0.92    0.00   1.745
REMARK  ---------------------------------------------------------- 
MOLECULE T0284TS239_3_3
REMARK PARENT number 3
PFRMAT TS
TARGET T0284
PARENT 1f61_A
ATOM      1  N   MET     1     115.178  59.801  38.589  1.00  9.99
ATOM      2  CA  MET     1     114.532  58.633  38.039  1.00  9.99
ATOM      3  C   MET     1     115.591  57.510  37.916  1.00  9.99
ATOM      4  O   MET     1     116.744  57.747  37.464  1.00  9.99
ATOM      5  CB  MET     1     113.982  58.926  36.626  1.00  9.99
ATOM      6  N   HIS     2     115.195  56.308  38.308  1.00  9.99
ATOM      7  CA  HIS     2     116.028  55.118  38.160  1.00  9.99
ATOM      8  C   HIS     2     115.928  54.664  36.682  1.00  9.99
ATOM      9  O   HIS     2     114.848  54.674  36.097  1.00  9.99
ATOM     10  CB  HIS     2     115.488  53.998  39.063  1.00  9.99
ATOM     11  N   ARG     3     117.045  54.294  36.074  1.00  9.99
ATOM     12  CA  ARG     3     117.060  53.819  34.685  1.00  9.99
ATOM     13  C   ARG     3     117.570  52.381  34.766  1.00  9.99
ATOM     14  O   ARG     3     118.765  52.115  34.587  1.00  9.99
ATOM     15  CB  ARG     3     118.012  54.709  33.855  1.00  9.99
ATOM     16  N   ALA     4     116.647  51.458  35.045  1.00  9.99
ATOM     17  CA  ALA     4     117.003  50.055  35.251  1.00  9.99
ATOM     18  C   ALA     4     117.787  49.427  34.122  1.00  9.99
ATOM     19  O   ALA     4     118.885  48.857  34.341  1.00  9.99
ATOM     20  CB  ALA     4     115.731  49.233  35.516  1.00  9.99
ATOM     21  N   SER     5     117.253  49.539  32.907  1.00  9.99
ATOM     22  CA  SER     5     117.935  48.909  31.795  1.00  9.99
ATOM     23  C   SER     5     119.273  49.535  31.503  1.00  9.99
ATOM     24  O   SER     5     120.206  48.840  31.110  1.00  9.99
ATOM     25  CB  SER     5     117.041  48.894  30.544  1.00  9.99
TER
END
