
#######################################################
#                                                     #
#                        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 (   53),  selected    6 , name T0372TS022_3_1-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected  172 , name T0372_D2.pdb
# PARAMETERS: T0372TS022_3_1-D2.T0372_D2.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    -       -      R     118           -
LGA    -       -      A     119           -
LGA    -       -      Y     120           -
LGA    -       -      A     121           -
LGA    -       -      D     122           -
LGA    -       -      Y     123           -
LGA    -       -      I     124           -
LGA    -       -      Y     125           -
LGA    -       -      L     126           -
LGA    -       -      R     127           -
LGA    -       -      S     128           -
LGA    -       -      D     129           -
LGA    -       -      L     130           -
LGA    -       -      A     131           -
LGA    -       -      T     132           -
LGA    -       -      L     133           -
LGA    -       -      K     134           -
LGA    -       -      G     135           -
LGA    -       -      K     136           -
LGA    -       -      K     137           -
LGA    -       -      F     138           -
LGA    -       -      Q     139           -
LGA    -       -      A     140           -
LGA    -       -      K     141           -
LGA    -       -      R     142           -
LGA    -       -      N     143           -
LGA    -       -      H     144           -
LGA    -       -      I     145           -
LGA    -       -      N     146           -
LGA    -       -      R     147           -
LGA    -       -      F     148           -
LGA    -       -      R     149           -
LGA    -       -      N     150           -
LGA    -       -      T     151           -
LGA    -       -      Y     152           -
LGA    -       -      P     153           -
LGA    -       -      D     154           -
LGA    -       -      Y     155           -
LGA    -       -      E     156           -
LGA    -       -      Y     157           -
LGA    -       -      T     158           -
LGA    -       -      P     159           -
LGA    -       -      I     160           -
LGA    -       -      T     161           -
LGA    -       -      P     162           -
LGA    -       -      D     163           -
LGA    R     118      R     164          0.899
LGA    A     119      I     165          1.062
LGA    Y     120      Q     166          1.035
LGA    A     121      E     167          1.036
LGA    D     122      C     168          2.098
LGA    -       -      L     169           -
LGA    -       -      D     170           -
LGA    -       -      L     171           -
LGA    -       -      E     172           -
LGA    -       -      A     173           -
LGA    -       -      E     174           -
LGA    -       -      W     175           -
LGA    -       -      C     176           -
LGA    -       -      K     177           -
LGA    -       -      V     178           -
LGA    -       -      N     179           -
LGA    -       -      N     180           -
LGA    -       -      C     181           -
LGA    -       -      D     182           -
LGA    -       -      Q     183           -
LGA    -       -      Q     184           -
LGA    -       -      E     185           -
LGA    -       -      G     186           -
LGA    -       -      T     187           -
LGA    -       -      G     188           -
LGA    -       -      N     189           -
LGA    -       -      E     190           -
LGA    -       -      R     191           -
LGA    -       -      R     192           -
LGA    -       -      A     193           -
LGA    -       -      L     194           -
LGA    -       -      I     195           -
LGA    -       -      Y     196           -
LGA    -       -      A     197           -
LGA    -       -      L     198           -
LGA    -       -      H     199           -
LGA    -       -      N     200           -
LGA    -       -      F     201           -
LGA    -       -      E     202           -
LGA    -       -      A     203           -
LGA    -       -      L     204           -
LGA    -       -      G     205           -
LGA    -       -      L     206           -
LGA    -       -      T     207           -
LGA    -       -      G     208           -
LGA    -       -      G     209           -
LGA    Y     123      I     210          3.591
LGA    -       -      L     211           -
LGA    -       -      H     212           -
LGA    -       -      V     213           -
LGA    -       -      N     214           -
LGA    -       -      G     215           -
LGA    -       -      K     216           -
LGA    -       -      I     217           -
LGA    -       -      V     218           -
LGA    -       -      A     219           -
LGA    -       -      F     220           -
LGA    -       -      T     221           -
LGA    -       -      F     222           -
LGA    -       -      G     223           -
LGA    -       -      M     224           -
LGA    -       -      P     225           -
LGA    -       -      I     226           -
LGA    -       -      N     227           -
LGA    -       -      H     228           -
LGA    -       -      E     229           -
LGA    -       -      T     230           -
LGA    -       -      F     231           -
LGA    -       -      G     232           -
LGA    -       -      V     233           -
LGA    -       -      H     234           -
LGA    -       -      V     235           -
LGA    -       -      E     236           -
LGA    -       -      K     237           -
LGA    -       -      A     238           -
LGA    -       -      D     239           -
LGA    -       -      T     240           -
LGA    -       -      S     241           -
LGA    -       -      I     242           -
LGA    -       -      D     243           -
LGA    -       -      G     244           -
LGA    -       -      A     245           -
LGA    -       -      Y     246           -
LGA    -       -      A     247           -
LGA    -       -      M     248           -
LGA    -       -      I     249           -
LGA    -       -      N     250           -
LGA    -       -      Y     251           -
LGA    -       -      E     252           -
LGA    -       -      F     253           -
LGA    -       -      A     254           -
LGA    -       -      N     255           -
LGA    -       -      R     256           -
LGA    -       -      I     257           -
LGA    -       -      P     258           -
LGA    -       -      E     259           -
LGA    -       -      Q     260           -
LGA    -       -      Y     261           -
LGA    -       -      I     262           -
LGA    -       -      Y     263           -
LGA    -       -      I     264           -
LGA    -       -      N     265           -
LGA    -       -      R     266           -
LGA    -       -      E     267           -
LGA    -       -      E     268           -
LGA    -       -      D     269           -
LGA    -       -      L     270           -
LGA    -       -      G     271           -
LGA    -       -      I     272           -
LGA    -       -      E     273           -
LGA    -       -      G     274           -
LGA    -       -      L     275           -
LGA    -       -      R     276           -
LGA    -       -      K     277           -
LGA    -       -      A     278           -
LGA    -       -      K     279           -
LGA    -       -      L     280           -
LGA    -       -      S     281           -
LGA    -       -      Y     282           -
LGA    -       -      Q     283           -
LGA    -       -      P     284           -
LGA    -       -      V     285           -
LGA    -       -      T     286           -
LGA    -       -      I     287           -
LGA    -       -      L     288           -
LGA    -       -      E     289           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    6  172    5.0      6    1.89    16.67      3.238     0.302

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.894368 * X  +  -0.235997 * Y  +   0.380015 * Z  + 161.272705
  Y_new =   0.280254 * X  +  -0.957736 * Y  +   0.064806 * Z  + 142.249603
  Z_new =   0.348660 * X  +   0.164461 * Y  +   0.922707 * Z  + -47.809727 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.176385   -2.965207  [ DEG:    10.1061   -169.8939 ]
  Theta =  -0.356141   -2.785451  [ DEG:   -20.4054   -159.5946 ]
  Phi   =   2.837930   -0.303663  [ DEG:   162.6014    -17.3986 ]
 
# 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: T0372TS022_3_1-D2                             
REMARK     2: T0372_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS022_3_1-D2.T0372_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    6  172   5.0    6   1.89   16.67   3.238
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS022_3_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0372
PARENT 1qso_A
ATOM    953  N   ARG   118      52.167  40.415  31.727  1.00  0.00
ATOM    954  CA  ARG   118      52.761  39.837  30.560  1.00  0.00
ATOM    955  C   ARG   118      51.760  39.875  29.455  1.00  0.00
ATOM    956  O   ARG   118      50.624  39.426  29.607  1.00  0.00
ATOM    957  CB  ARG   118      53.172  38.388  30.828  1.00  0.00
ATOM    958  CG  ARG   118      54.290  38.239  31.848  1.00  0.00
ATOM    959  CD  ARG   118      54.580  36.775  32.138  1.00  0.00
ATOM    960  NE  ARG   118      53.492  36.139  32.878  1.00  0.00
ATOM    961  CZ  ARG   118      53.382  34.827  33.061  1.00  0.00
ATOM    962  NH1 ARG   118      52.358  34.337  33.748  1.00  0.00
ATOM    963  NH2 ARG   118      54.294  34.008  32.557  1.00  0.00
ATOM    964  N   ALA   119      52.178  40.449  28.314  1.00  0.00
ATOM    965  CA  ALA   119      51.397  40.500  27.117  1.00  0.00
ATOM    966  C   ALA   119      51.282  39.095  26.639  1.00  0.00
ATOM    967  O   ALA   119      50.244  38.670  26.137  1.00  0.00
ATOM    968  CB  ALA   119      52.083  41.368  26.073  1.00  0.00
ATOM    969  N   TYR   120      52.377  38.337  26.823  1.00  0.00
ATOM    970  CA  TYR   120      52.497  36.985  26.368  1.00  0.00
ATOM    971  C   TYR   120      51.397  36.196  26.985  1.00  0.00
ATOM    972  O   TYR   120      50.757  35.383  26.320  1.00  0.00
ATOM    973  CB  TYR   120      53.849  36.398  26.781  1.00  0.00
ATOM    974  CG  TYR   120      54.045  34.959  26.362  1.00  0.00
ATOM    975  CD1 TYR   120      54.380  34.638  25.053  1.00  0.00
ATOM    976  CD2 TYR   120      53.896  33.925  27.278  1.00  0.00
ATOM    977  CE1 TYR   120      54.562  33.325  24.661  1.00  0.00
ATOM    978  CE2 TYR   120      54.074  32.607  26.905  1.00  0.00
ATOM    979  CZ  TYR   120      54.409  32.312  25.583  1.00  0.00
ATOM    980  OH  TYR   120      54.590  31.004  25.197  1.00  0.00
ATOM    981  N   ALA   121      51.119  36.447  28.274  1.00  0.00
ATOM    982  CA  ALA   121      50.071  35.736  28.935  1.00  0.00
ATOM    983  C   ALA   121      48.814  36.001  28.175  1.00  0.00
ATOM    984  O   ALA   121      48.772  36.875  27.308  1.00  0.00
ATOM    985  CB  ALA   121      49.928  36.216  30.371  1.00  0.00
ATOM    986  N   ASP   122      47.754  35.227  28.482  1.00  0.00
ATOM    987  CA  ASP   122      46.519  35.341  27.764  1.00  0.00
ATOM    988  C   ASP   122      46.105  36.768  27.867  1.00  0.00
ATOM    989  O   ASP   122      45.625  37.338  26.888  1.00  0.00
ATOM    990  CB  ASP   122      45.456  34.428  28.378  1.00  0.00
ATOM    991  CG  ASP   122      45.707  32.961  28.085  1.00  0.00
ATOM    992  OD1 ASP   122      46.556  32.666  27.218  1.00  0.00
ATOM    993  OD2 ASP   122      45.054  32.108  28.720  1.00  0.00
ATOM    994  N   TYR   123      46.315  37.352  29.067  1.00  0.00
ATOM    995  CA  TYR   123      46.111  38.736  29.401  1.00  0.00
ATOM    996  C   TYR   123      45.296  38.761  30.683  1.00  0.00
ATOM    997  O   TYR   123      44.135  38.274  30.651  1.00  0.00
ATOM    998  CB  TYR   123      45.358  39.452  28.278  1.00  0.00
ATOM    999  CG  TYR   123      45.109  40.920  28.546  1.00  0.00
ATOM   1000  CD1 TYR   123      46.126  41.853  28.392  1.00  0.00
ATOM   1001  CD2 TYR   123      43.859  41.366  28.952  1.00  0.00
ATOM   1002  CE1 TYR   123      45.908  43.196  28.634  1.00  0.00
ATOM   1003  CE2 TYR   123      43.623  42.705  29.201  1.00  0.00
ATOM   1004  CZ  TYR   123      44.661  43.620  29.037  1.00  0.00
ATOM   1005  OH  TYR   123      44.441  44.958  29.280  1.00  0.00
TER
END
