
#######################################################
#                                                     #
#                        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   24 (   24),  selected   24 , name T0321TS464_3_2-D2
# Molecule2: number of CA atoms  148 ( 1130),  selected  148 , name T0321_D2.pdb
# PARAMETERS: T0321TS464_3_2-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    R     104      K     123          2.661
LGA    V     105      K     124          1.315
LGA    E     106      V     125          0.961
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    D     107      C     142          4.717
LGA    -       -      D     143           -
LGA    R     108      L     144          0.580
LGA    M     109      S     145          2.637
LGA    N     110      I     146          2.679
LGA    D     111      -       -           -
LGA    P     112      -       -           -
LGA    F     113      -       -           -
LGA    I     114      -       -           -
LGA    M     115      -       -           -
LGA    F     220      -       -           -
LGA    M     221      L     147          4.924
LGA    V     222      E     148          3.092
LGA    K     223      W     149          4.503
LGA    D     224      S     150          3.200
LGA    -       -      P     151           -
LGA    -       -      E     152           -
LGA    -       -      E     153           -
LGA    -       -      G     154           -
LGA    -       -      D     155           -
LGA    -       -      Y     156           -
LGA    -       -      P     157           -
LGA    N     225      L     158          3.445
LGA    A     226      P     159          3.399
LGA    R     227      A     160           #
LGA    A     228      S     161          1.776
LGA    F     229      E     162          4.260
LGA    R     230      F     163          2.585
LGA    -       -      I     164           -
LGA    -       -      L     165           -
LGA    -       -      P     166           -
LGA    I     231      E     167          4.415
LGA    -       -      C     168           -
LGA    -       -      D     169           -
LGA    -       -      Y     170           -
LGA    -       -      V     171           -
LGA    -       -      Y     172           -
LGA    -       -      I     173           -
LGA    -       -      T     174           -
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    -       -      V     199           -
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)   24  148    5.0     17    3.27     0.00      6.991     0.505

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.376053 * X  +   0.828825 * Y  +   0.414286 * Z  +  25.755867
  Y_new =  -0.701415 * X  +  -0.546783 * Y  +   0.457214 * Z  +  54.403484
  Z_new =   0.605475 * X  +  -0.118650 * Y  +   0.786970 * Z  +  -0.107408 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.149641    2.991952  [ DEG:    -8.5738    171.4262 ]
  Theta =  -0.650363   -2.491230  [ DEG:   -37.2630   -142.7370 ]
  Phi   =  -2.062932    1.078660  [ DEG:  -118.1973     61.8027 ]
 
# 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: T0321TS464_3_2-D2                             
REMARK     2: T0321_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0321TS464_3_2-D2.T0321_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   24  148   5.0   17   3.27    0.00   6.991
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS464_3_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0321
PARENT N/A
ATOM      8  CA  ARG   104      23.011  36.291  69.957  1.00  0.00
ATOM      9  CA  VAL   105      21.589  35.845  66.470  1.00  0.00
ATOM     10  CA  GLU   106      18.198  37.161  67.600  1.00  0.00
ATOM     11  CA  ASP   107      19.874  40.287  69.035  1.00  0.00
ATOM     12  CA  ARG   108      21.604  41.102  65.738  1.00  0.00
ATOM     13  CA  MET   109      18.502  40.381  63.658  1.00  0.00
ATOM     14  CA  ASN   110      16.319  43.247  62.442  1.00  0.00
ATOM     15  CA  ASP   111      14.345  41.319  59.802  1.00  0.00
ATOM     16  CA  PRO   112      13.539  37.785  60.995  1.00  0.00
ATOM     17  CA  PHE   113      15.324  34.618  62.069  1.00  0.00
ATOM     18  CA  ILE   114      15.452  31.917  59.416  1.00  0.00
ATOM     19  CA  MET   115      15.471  28.339  60.728  1.00  0.00
ATOM     20  CA  PHE   220      20.919  47.617  55.199  1.00  0.00
ATOM     21  CA  MET   221      18.283  44.989  54.462  1.00  0.00
ATOM     22  CA  VAL   222      16.395  45.643  57.686  1.00  0.00
ATOM     23  CA  LYS   223      16.521  49.378  56.968  1.00  0.00
ATOM     24  CA  ASP   224      15.071  49.001  53.513  1.00  0.00
ATOM     25  CA  ASN   225      11.969  47.033  54.296  1.00  0.00
ATOM     26  CA  ALA   226      13.126  43.426  53.969  1.00  0.00
ATOM     27  CA  ARG   227      10.791  41.421  56.211  1.00  0.00
ATOM     28  CA  ALA   228      13.161  38.693  57.327  1.00  0.00
ATOM     29  CA  PHE   229      16.639  37.297  56.742  1.00  0.00
ATOM     30  CA  ARG   230      16.813  33.548  56.363  1.00  0.00
ATOM     31  CA  ILE   231      19.990  31.754  57.438  1.00  0.00
TER
END
