
#######################################################
#                                                     #
#                        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    7 (   28),  selected    7 , name T0356AL044_3-D2
# Molecule2: number of CA atoms  192 ( 1487),  selected  192 , name T0356_D2.pdb
# PARAMETERS: T0356AL044_3-D2.T0356_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    -       -      T     122           -
LGA    -       -      K     123           -
LGA    -       -      R     124           -
LGA    -       -      L     125           -
LGA    -       -      R     126           -
LGA    -       -      G     127           -
LGA    -       -      A     128           -
LGA    -       -      P     129           -
LGA    -       -      C     130           -
LGA    -       -      Q     131           -
LGA    -       -      Q     132           -
LGA    -       -      K     133           -
LGA    -       -      I     134           -
LGA    -       -      V     135           -
LGA    -       -      S     136           -
LGA    -       -      G     137           -
LGA    -       -      D     138           -
LGA    -       -      D     139           -
LGA    -       -      V     140           -
LGA    -       -      D     141           -
LGA    -       -      L     142           -
LGA    -       -      N     143           -
LGA    -       -      R     144           -
LGA    -       -      I     145           -
LGA    -       -      P     146           -
LGA    -       -      I     147           -
LGA    -       -      M     148           -
LGA    -       -      T     149           -
LGA    -       -      C     150           -
LGA    -       -      W     151           -
LGA    -       -      P     152           -
LGA    -       -      E     153           -
LGA    -       -      D     154           -
LGA    -       -      A     155           -
LGA    -       -      A     156           -
LGA    -       -      P     157           -
LGA    -       -      L     158           -
LGA    -       -      I     159           -
LGA    -       -      T     160           -
LGA    -       -      W     161           -
LGA    T     305      G     162          1.147
LGA    V     306      L     163          0.400
LGA    H     308      T     164          0.601
LGA    I     309      V     165          1.510
LGA    -       -      T     166           -
LGA    -       -      R     167           -
LGA    T     310      G     168          1.099
LGA    R     312      P     169          1.673
LGA    -       -      H     170           -
LGA    -       -      K     171           -
LGA    -       -      E     172           -
LGA    E     313      R     173          1.755
LGA    -       -      Q     174           -
LGA    -       -      N     175           -
LGA    -       -      L     176           -
LGA    -       -      G     177           -
LGA    -       -      I     178           -
LGA    -       -      Y     179           -
LGA    -       -      R     180           -
LGA    -       -      Q     181           -
LGA    -       -      Q     182           -
LGA    -       -      L     183           -
LGA    -       -      I     184           -
LGA    -       -      G     185           -
LGA    -       -      K     186           -
LGA    -       -      N     187           -
LGA    -       -      K     188           -
LGA    -       -      L     189           -
LGA    -       -      I     190           -
LGA    -       -      M     191           -
LGA    -       -      R     192           -
LGA    -       -      W     193           -
LGA    -       -      L     194           -
LGA    -       -      S     195           -
LGA    -       -      H     196           -
LGA    -       -      R     197           -
LGA    -       -      G     198           -
LGA    -       -      G     199           -
LGA    -       -      A     200           -
LGA    -       -      L     201           -
LGA    -       -      D     202           -
LGA    -       -      Y     203           -
LGA    -       -      Q     204           -
LGA    -       -      E     205           -
LGA    -       -      W     206           -
LGA    -       -      C     207           -
LGA    -       -      A     208           -
LGA    -       -      A     209           -
LGA    -       -      H     210           -
LGA    -       -      P     211           -
LGA    -       -      G     212           -
LGA    -       -      E     213           -
LGA    -       -      R     214           -
LGA    -       -      F     215           -
LGA    -       -      P     216           -
LGA    -       -      V     217           -
LGA    -       -      S     218           -
LGA    -       -      V     219           -
LGA    -       -      A     220           -
LGA    -       -      L     221           -
LGA    -       -      G     222           -
LGA    -       -      A     223           -
LGA    -       -      D     224           -
LGA    -       -      P     225           -
LGA    -       -      A     226           -
LGA    -       -      T     227           -
LGA    -       -      I     228           -
LGA    -       -      L     229           -
LGA    -       -      G     230           -
LGA    -       -      A     231           -
LGA    -       -      V     232           -
LGA    -       -      T     233           -
LGA    -       -      P     234           -
LGA    -       -      V     235           -
LGA    -       -      P     236           -
LGA    -       -      D     237           -
LGA    -       -      T     238           -
LGA    -       -      L     239           -
LGA    -       -      S     240           -
LGA    -       -      E     241           -
LGA    -       -      Y     242           -
LGA    -       -      A     243           -
LGA    -       -      F     244           -
LGA    -       -      A     245           -
LGA    -       -      G     246           -
LGA    -       -      L     247           -
LGA    -       -      L     248           -
LGA    -       -      R     249           -
LGA    -       -      G     250           -
LGA    -       -      T     251           -
LGA    -       -      K     252           -
LGA    -       -      T     253           -
LGA    -       -      E     254           -
LGA    -       -      V     255           -
LGA    -       -      V     256           -
LGA    -       -      K     257           -
LGA    -       -      C     258           -
LGA    -       -      I     259           -
LGA    -       -      S     260           -
LGA    -       -      N     261           -
LGA    -       -      D     262           -
LGA    -       -      L     263           -
LGA    -       -      E     264           -
LGA    -       -      V     265           -
LGA    -       -      P     266           -
LGA    -       -      A     267           -
LGA    -       -      S     268           -
LGA    -       -      A     269           -
LGA    -       -      E     270           -
LGA    -       -      I     271           -
LGA    -       -      V     272           -
LGA    -       -      L     273           -
LGA    -       -      E     274           -
LGA    -       -      G     275           -
LGA    -       -      Y     276           -
LGA    -       -      I     277           -
LGA    -       -      E     278           -
LGA    -       -      Q     279           -
LGA    -       -      G     280           -
LGA    -       -      E     281           -
LGA    -       -      T     282           -
LGA    -       -      A     283           -
LGA    -       -      P     284           -
LGA    -       -      E     285           -
LGA    -       -      G     286           -
LGA    -       -      P     287           -
LGA    -       -      Y     288           -
LGA    -       -      G     289           -
LGA    -       -      D     290           -
LGA    -       -      H     291           -
LGA    -       -      T     292           -
LGA    -       -      G     293           -
LGA    -       -      Y     294           -
LGA    -       -      Y     295           -
LGA    -       -      N     296           -
LGA    -       -      E     297           -
LGA    -       -      V     298           -
LGA    -       -      D     299           -
LGA    -       -      S     300           -
LGA    -       -      F     301           -
LGA    -       -      P     302           -
LGA    -       -      V     303           -
LGA    -       -      F     304           -
LGA    -       -      T     305           -
LGA    -       -      V     306           -
LGA    -       -      T     307           -
LGA    -       -      H     308           -
LGA    -       -      I     309           -
LGA    -       -      T     310           -
LGA    -       -      Q     311           -
LGA    -       -      R     312           -
LGA    -       -      E     313           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    7  192    5.0      7    1.27     0.00      3.484     0.513

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.090676 * X  +   0.973546 * Y  +   0.209731 * Z  +  37.250370
  Y_new =   0.108284 * X  +   0.218988 * Y  +  -0.969700 * Z  +  63.360886
  Z_new =  -0.989976 * X  +  -0.065218 * Y  +  -0.125276 * Z  +  84.214539 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.661608    0.479984  [ DEG:  -152.4989     27.5011 ]
  Theta =   1.429087    1.712506  [ DEG:    81.8806     98.1194 ]
  Phi   =   2.267922   -0.873671  [ DEG:   129.9423    -50.0577 ]
 
# 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: T0356AL044_3-D2                               
REMARK     2: T0356_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356AL044_3-D2.T0356_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    7  192   5.0    7   1.27    0.00   3.484
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL044_3-D2
REMARK Aligment from pdb entry: 2bco_A
ATOM      1  N   THR   305      72.589  66.655  83.572  1.00  0.00              
ATOM      2  CA  THR   305      73.914  66.077  83.415  1.00  0.00              
ATOM      3  C   THR   305      73.979  65.400  82.060  1.00  0.00              
ATOM      4  O   THR   305      72.950  65.188  81.426  1.00  0.00              
ATOM      5  N   VAL   306      75.185  65.080  81.604  1.00  0.00              
ATOM      6  CA  VAL   306      75.348  64.462  80.299  1.00  0.00              
ATOM      7  C   VAL   306      76.346  63.324  80.332  1.00  0.00              
ATOM      8  O   VAL   306      77.164  63.214  81.251  1.00  0.00              
ATOM      9  N   HIS   308      76.274  62.483  79.310  1.00  0.00              
ATOM     10  CA  HIS   308      77.162  61.346  79.184  1.00  0.00              
ATOM     11  C   HIS   308      77.873  61.401  77.837  1.00  0.00              
ATOM     12  O   HIS   308      77.227  61.446  76.790  1.00  0.00              
ATOM     13  N   ILE   309      79.203  61.416  77.877  1.00  0.00              
ATOM     14  CA  ILE   309      80.018  61.458  76.667  1.00  0.00              
ATOM     15  C   ILE   309      80.499  60.040  76.334  1.00  0.00              
ATOM     16  O   ILE   309      81.229  59.429  77.118  1.00  0.00              
ATOM     17  N   THR   310      84.925  56.308  72.518  1.00  0.00              
ATOM     18  CA  THR   310      85.336  55.943  71.166  1.00  0.00              
ATOM     19  C   THR   310      86.775  56.403  70.982  1.00  0.00              
ATOM     20  O   THR   310      87.244  57.278  71.710  1.00  0.00              
ATOM     21  N   ARG   312      87.481  55.806  70.028  1.00  0.00              
ATOM     22  CA  ARG   312      88.870  56.173  69.761  1.00  0.00              
ATOM     23  C   ARG   312      88.915  57.531  69.055  1.00  0.00              
ATOM     24  O   ARG   312      89.949  58.196  69.017  1.00  0.00              
ATOM     25  N   GLU   313      85.937  63.003  70.233  1.00  0.00              
ATOM     26  CA  GLU   313      84.586  63.556  70.218  1.00  0.00              
ATOM     27  C   GLU   313      84.289  64.376  71.470  1.00  0.00              
ATOM     28  O   GLU   313      83.142  64.711  71.750  1.00  0.00              
END
