
#######################################################
#                                                     #
#                        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 (   51),  selected    6 , name T0321TS074_4-D2
# Molecule2: number of CA atoms  148 ( 1130),  selected  148 , name T0321_D2.pdb
# PARAMETERS: T0321TS074_4-D2.T0321_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    -       -      V      97           -
LGA    -       -      I      98           -
LGA    -       -      F      99           -
LGA    -       -      S     100           -
LGA    -       -      D     101           -
LGA    -       -      A     102           -
LGA    -       -      N     110           -
LGA    -       -      D     111           -
LGA    -       -      P     112           -
LGA    -       -      F     113           -
LGA    -       -      I     114           -
LGA    -       -      M     115           -
LGA    -       -      S     116           -
LGA    -       -      Q     117           -
LGA    -       -      N     118           -
LGA    -       -      E     119           -
LGA    -       -      V     120           -
LGA    -       -      K     121           -
LGA    -       -      G     122           -
LGA    -       -      K     123           -
LGA    -       -      K     124           -
LGA    -       -      V     125           -
LGA    -       -      G     126           -
LGA    -       -      V     127           -
LGA    -       -      V     128           -
LGA    -       -      G     129           -
LGA    -       -      H     130           -
LGA    -       -      F     131           -
LGA    -       -      P     132           -
LGA    -       -      H     133           -
LGA    -       -      L     134           -
LGA    -       -      E     135           -
LGA    -       -      S     136           -
LGA    -       -      L     137           -
LGA    -       -      L     138           -
LGA    -       -      E     139           -
LGA    -       -      P     140           -
LGA    -       -      I     141           -
LGA    -       -      C     142           -
LGA    -       -      D     143           -
LGA    -       -      L     144           -
LGA    -       -      S     145           -
LGA    -       -      I     146           -
LGA    -       -      L     147           -
LGA    -       -      E     148           -
LGA    -       -      W     149           -
LGA    -       -      S     150           -
LGA    -       -      P     151           -
LGA    -       -      E     152           -
LGA    -       -      E     153           -
LGA    -       -      G     154           -
LGA    -       -      D     155           -
LGA    -       -      Y     156           -
LGA    -       -      P     157           -
LGA    -       -      L     158           -
LGA    -       -      P     159           -
LGA    -       -      A     160           -
LGA    -       -      S     161           -
LGA    -       -      E     162           -
LGA    -       -      F     163           -
LGA    -       -      I     164           -
LGA    -       -      L     165           -
LGA    -       -      P     166           -
LGA    -       -      E     167           -
LGA    -       -      C     168           -
LGA    -       -      D     169           -
LGA    V      97      Y     170          0.587
LGA    I      98      V     171          0.635
LGA    F      99      Y     172          0.461
LGA    S     100      I     173          0.272
LGA    D     101      T     174          0.735
LGA    -       -      C     175           -
LGA    -       -      A     176           -
LGA    -       -      S     177           -
LGA    -       -      V     178           -
LGA    -       -      V     179           -
LGA    -       -      D     180           -
LGA    -       -      K     181           -
LGA    -       -      T     182           -
LGA    -       -      L     183           -
LGA    -       -      P     184           -
LGA    -       -      R     185           -
LGA    -       -      L     186           -
LGA    -       -      L     187           -
LGA    -       -      E     188           -
LGA    -       -      L     189           -
LGA    -       -      S     190           -
LGA    -       -      R     191           -
LGA    -       -      N     192           -
LGA    -       -      A     193           -
LGA    -       -      R     194           -
LGA    -       -      R     195           -
LGA    -       -      I     196           -
LGA    -       -      T     197           -
LGA    -       -      L     198           -
LGA    A     102      V     199          1.023
LGA    -       -      G     200           -
LGA    -       -      P     201           -
LGA    -       -      G     202           -
LGA    -       -      T     203           -
LGA    -       -      P     204           -
LGA    -       -      L     205           -
LGA    -       -      A     206           -
LGA    -       -      P     207           -
LGA    -       -      V     208           -
LGA    -       -      L     209           -
LGA    -       -      F     210           -
LGA    -       -      E     211           -
LGA    -       -      H     212           -
LGA    -       -      G     213           -
LGA    -       -      L     214           -
LGA    -       -      Q     215           -
LGA    -       -      E     216           -
LGA    -       -      L     217           -
LGA    -       -      S     218           -
LGA    -       -      G     219           -
LGA    -       -      F     220           -
LGA    -       -      M     221           -
LGA    -       -      V     222           -
LGA    -       -      K     223           -
LGA    -       -      D     224           -
LGA    -       -      N     225           -
LGA    -       -      A     226           -
LGA    -       -      R     227           -
LGA    -       -      A     228           -
LGA    -       -      F     229           -
LGA    -       -      R     230           -
LGA    -       -      I     231           -
LGA    -       -      V     232           -
LGA    -       -      A     233           -
LGA    -       -      G     234           -
LGA    -       -      A     235           -
LGA    -       -      E     236           -
LGA    -       -      K     237           -
LGA    -       -      V     238           -
LGA    -       -      K     239           -
LGA    -       -      I     240           -
LGA    -       -      Y     241           -
LGA    -       -      S     242           -
LGA    -       -      A     243           -
LGA    -       -      G     244           -
LGA    -       -      Q     245           -
LGA    -       -      K     246           -
LGA    -       -      V     247           -
LGA    -       -      T     248           -
LGA    -       -      I     249           -
LGA    -       -      K     250           -
LGA    -       -      K     251           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    6  148    5.0      6    0.66     0.00      4.001     0.788

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.672218 * X  +   0.413658 * Y  +   0.614011 * Z  +  13.934708
  Y_new =  -0.614305 * X  +   0.151251 * Y  +  -0.774437 * Z  +  32.072605
  Z_new =  -0.413222 * X  +  -0.897781 * Y  +   0.152438 * Z  +  74.595772 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.402606    1.738987  [ DEG:   -80.3634     99.6366 ]
  Theta =   0.425989    2.715604  [ DEG:    24.4074    155.5926 ]
  Phi   =  -2.401179    0.740413  [ DEG:  -137.5774     42.4226 ]
 
# 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: T0321TS074_4-D2                               
REMARK     2: T0321_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0321TS074_4-D2.T0321_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    6  148   5.0    6   0.66    0.00   4.001
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS074_4-D2
PFRMAT TS
TARGET T0321
MODEL  4
PARENT N/A
ATOM    817  N   VAL    97      15.228  35.138  69.077  1.00  1.00
ATOM    818  CA  VAL    97      13.897  35.723  69.095  1.00  1.00
ATOM    819  C   VAL    97      13.974  37.012  68.295  1.00  1.00
ATOM    820  O   VAL    97      14.843  37.846  68.541  1.00  1.00
ATOM    821  HN  VAL    97      15.954  35.769  69.354  1.00  1.00
ATOM    822  CB  VAL    97      13.427  36.061  70.527  1.00  1.00
ATOM    823  CG1 VAL    97      12.091  36.780  70.484  1.00  1.00
ATOM    824  CG2 VAL    97      14.464  36.931  71.219  1.00  1.00
ATOM    825  N   ILE    98      13.088  37.163  67.321  1.00  1.00
ATOM    826  CA  ILE    98      13.067  38.378  66.517  1.00  1.00
ATOM    827  C   ILE    98      11.759  39.105  66.784  1.00  1.00
ATOM    828  O   ILE    98      10.708  38.485  66.975  1.00  1.00
ATOM    829  HN  ILE    98      12.392  36.493  67.063  1.00  1.00
ATOM    830  CB  ILE    98      13.175  38.067  65.024  1.00  1.00
ATOM    831  CG1 ILE    98      14.631  37.112  64.479  1.00  1.00
ATOM    832  CG2 ILE    98      13.037  39.396  64.269  1.00  1.00
ATOM    833  CD1 ILE    98      15.705  37.836  64.817  1.00  1.00
ATOM    834  N   PHE    99      11.836  40.428  66.805  1.00  1.00
ATOM    835  CA  PHE    99      10.673  41.259  67.048  1.00  1.00
ATOM    836  C   PHE    99      10.456  42.231  65.901  1.00  1.00
ATOM    837  O   PHE    99      11.383  42.932  65.490  1.00  1.00
ATOM    838  HN  PHE    99      12.680  40.942  66.658  1.00  1.00
ATOM    839  CB  PHE    99      10.848  42.032  68.357  1.00  1.00
ATOM    840  CG  PHE    99      10.898  41.126  69.569  1.00  1.00
ATOM    841  CD1 PHE    99       9.687  40.717  70.165  1.00  1.00
ATOM    842  CD2 PHE    99      12.056  40.966  70.311  1.00  1.00
ATOM    843  CE1 PHE    99       9.706  40.057  71.378  1.00  1.00
ATOM    844  CE2 PHE    99      12.111  40.297  71.504  1.00  1.00
ATOM    845  CZ  PHE    99      10.891  39.811  72.047  1.00  1.00
ATOM    846  N   SER   100       9.230  42.249  65.381  1.00  1.00
ATOM    847  CA  SER   100       8.868  43.141  64.293  1.00  1.00
ATOM    848  C   SER   100       7.842  44.153  64.786  1.00  1.00
ATOM    849  O   SER   100       6.806  43.775  65.332  1.00  1.00
ATOM    850  HN  SER   100       8.482  41.663  65.693  1.00  1.00
ATOM    851  CB  SER   100       8.267  42.363  63.123  1.00  1.00
ATOM    852  OG  SER   100       7.001  41.643  63.480  1.00  1.00
ATOM    853  N   ASP   101       8.132  45.435  64.586  1.00  1.00
ATOM    854  CA  ASP   101       7.235  46.514  65.010  1.00  1.00
ATOM    855  C   ASP   101       6.773  46.388  66.478  1.00  1.00
ATOM    856  O   ASP   101       5.753  46.949  66.871  1.00  1.00
ATOM    857  HN  ASP   101       8.970  45.753  64.140  1.00  1.00
ATOM    858  CB  ASP   101       6.052  46.656  64.036  1.00  1.00
ATOM    859  CG  ASP   101       5.118  47.817  64.387  1.00  1.00
ATOM    860  OD1 ASP   101       5.323  48.511  65.321  1.00  1.00
ATOM    861  OD2 ASP   101       4.136  47.877  63.589  1.00  1.00
ATOM    862  N   ALA   102       7.566  45.696  67.306  1.00  1.00
ATOM    863  CA  ALA   102       7.247  45.574  68.731  1.00  1.00
ATOM    864  C   ALA   102       7.180  46.948  69.402  1.00  1.00
ATOM    865  O   ALA   102       6.407  47.156  70.339  1.00  1.00
ATOM    866  HN  ALA   102       8.405  45.225  67.035  1.00  1.00
ATOM    867  CB  ALA   102       8.294  44.713  69.450  1.00  1.00
TER
END
