
#######################################################
#                                                     #
#                        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   10 (   50),  selected   10 , name T0284TS239_3_2
# Molecule2: number of CA atoms  282 ( 2139),  selected  282 , name T0284.pdb
# PARAMETERS: T0284TS239_3_2.T0284.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      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    W     278      E      69          1.832
LGA    -       -      F      70           -
LGA    A     279      V      71          1.864
LGA    R     280      E      72          3.047
LGA    -       -      Q      73           -
LGA    D     281      A      74          0.226
LGA    Y     282      T      75          0.767
LGA    M     283      R      76          0.839
LGA    E     284      I      77          0.462
LGA    V     285      G      78          0.241
LGA    K     286      R      79          0.741
LGA    E     287      V      80          1.511
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)   10  282    5.0     10    1.43     0.00      3.361     0.652

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.282080 * X  +  -0.954301 * Y  +   0.098694 * Z  + 155.626511
  Y_new =   0.340551 * X  +  -0.003426 * Y  +   0.940220 * Z  +  87.580360
  Z_new =  -0.896914 * X  +   0.298828 * Y  +   0.325955 * Z  + 160.560226 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.742007   -2.399586  [ DEG:    42.5139   -137.4861 ]
  Theta =   1.112742    2.028851  [ DEG:    63.7554    116.2446 ]
  Phi   =   2.262559   -0.879033  [ DEG:   129.6351    -50.3649 ]
 
# 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_2                                
REMARK     2: T0284.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0284TS239_3_2.T0284.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   10  282   5.0   10   1.43    0.00   3.361
REMARK  ---------------------------------------------------------- 
MOLECULE T0284TS239_3_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0284
PARENT 1mum_A
ATOM   1328  N   TRP   278     110.381  60.647  44.382  1.00  9.99
ATOM   1329  CA  TRP   278     110.180  59.207  44.302  1.00  9.99
ATOM   1330  C   TRP   278     111.189  58.529  43.376  1.00  9.99
ATOM   1331  O   TRP   278     110.925  57.456  42.831  1.00  9.99
ATOM   1332  CB  TRP   278     108.742  58.872  43.847  1.00  9.99
ATOM   1333  N   ALA   279     112.347  59.166  43.212  1.00  9.99
ATOM   1334  CA  ALA   279     113.426  58.634  42.381  1.00  9.99
ATOM   1335  C   ALA   279     112.878  58.069  41.082  1.00  9.99
ATOM   1336  O   ALA   279     113.258  56.981  40.650  1.00  9.99
ATOM   1337  CB  ALA   279     114.177  57.543  43.149  1.00  9.99
ATOM   1338  N   ARG   280     111.980  58.829  40.468  1.00  9.99
ATOM   1339  CA  ARG   280     111.331  58.449  39.221  1.00  9.99
ATOM   1340  C   ARG   280     112.319  58.032  38.136  1.00  9.99
ATOM   1341  O   ARG   280     112.069  57.090  37.380  1.00  9.99
ATOM   1342  CB  ARG   280     110.505  59.625  38.707  1.00  9.99
ATOM   1343  N   ASP   281     113.442  58.736  38.065  1.00  9.99
ATOM   1344  CA  ASP   281     114.449  58.471  37.048  1.00  9.99
ATOM   1345  C   ASP   281     115.306  57.233  37.303  1.00  9.99
ATOM   1346  O   ASP   281     115.869  56.667  36.371  1.00  9.99
ATOM   1347  CB  ASP   281     115.314  59.720  36.879  1.00  9.99
ATOM   1348  N   TYR   282     115.405  56.813  38.560  1.00  9.99
ATOM   1349  CA  TYR   282     116.178  55.624  38.901  1.00  9.99
ATOM   1350  C   TYR   282     115.526  54.382  38.296  1.00  9.99
ATOM   1351  O   TYR   282     116.111  53.297  38.305  1.00  9.99
ATOM   1352  CB  TYR   282     116.255  55.449  40.418  1.00  9.99
ATOM   1353  N   MET   283     114.312  54.544  37.777  1.00  9.99
ATOM   1354  CA  MET   283     113.599  53.419  37.187  1.00  9.99
ATOM   1355  C   MET   283     114.003  53.113  35.753  1.00  9.99
ATOM   1356  O   MET   283     114.325  51.967  35.431  1.00  9.99
ATOM   1357  CB  MET   283     112.086  53.633  37.293  1.00  9.99
ATOM   1358  N   GLU   284     113.994  54.118  34.885  1.00  9.99
ATOM   1359  CA  GLU   284     114.390  53.861  33.509  1.00  9.99
ATOM   1360  C   GLU   284     115.889  53.579  33.486  1.00  9.99
ATOM   1361  O   GLU   284     116.395  52.926  32.572  1.00  9.99
ATOM   1362  CB  GLU   284     114.060  55.051  32.604  1.00  9.99
ATOM   1363  N   VAL   285     116.594  54.066  34.503  1.00  9.99
ATOM   1364  CA  VAL   285     118.032  53.849  34.595  1.00  9.99
ATOM   1365  C   VAL   285     118.299  52.374  34.855  1.00  9.99
ATOM   1366  O   VAL   285     119.223  51.797  34.281  1.00  9.99
ATOM   1367  CB  VAL   285     118.642  54.707  35.710  1.00  9.99
ATOM   1368  N   LYS   286     117.480  51.761  35.706  1.00  9.99
ATOM   1369  CA  LYS   286     117.644  50.343  36.005  1.00  9.99
ATOM   1370  C   LYS   286     117.357  49.509  34.761  1.00  9.99
ATOM   1371  O   LYS   286     118.027  48.503  34.510  1.00  9.99
ATOM   1372  CB  LYS   286     116.717  49.911  37.145  1.00  9.99
ATOM   1373  N   GLU   287     116.362  49.932  33.985  1.00  9.99
ATOM   1374  CA  GLU   287     116.002  49.226  32.760  1.00  9.99
ATOM   1375  C   GLU   287     117.179  49.237  31.793  1.00  9.99
ATOM   1376  O   GLU   287     117.495  48.221  31.175  1.00  9.99
ATOM   1377  CB  GLU   287     114.788  49.883  32.096  1.00  9.99
TER
END
