
#######################################################
#                                                     #
#                        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_5-D2
# Molecule2: number of CA atoms  192 ( 1487),  selected  192 , name T0356_D2.pdb
# PARAMETERS: T0356AL044_5-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    -       -      G     162           -
LGA    -       -      L     163           -
LGA    -       -      T     164           -
LGA    -       -      V     165           -
LGA    -       -      T     166           -
LGA    -       -      R     167           -
LGA    -       -      G     168           -
LGA    -       -      P     169           -
LGA    -       -      H     170           -
LGA    -       -      K     171           -
LGA    -       -      E     172           -
LGA    -       -      R     173           -
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    T     305      H     196          2.757
LGA    V     306      R     197          1.783
LGA    H     308      G     198          1.669
LGA    I     309      G     199          0.995
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    T     310      P     216          2.751
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    Q     311      Y     276          2.810
LGA    E     313      I     277          1.163
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    2.12     0.00      3.150     0.316

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.802592 * X  +  -0.588524 * Y  +  -0.097396 * Z  +  58.419704
  Y_new =  -0.076640 * X  +  -0.263649 * Y  +   0.961569 * Z  + -42.411339
  Z_new =  -0.591585 * X  +  -0.764283 * Y  +  -0.256707 * Z  + 135.097626 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.894836    1.246756  [ DEG:  -108.5661     71.4339 ]
  Theta =   0.633024    2.508569  [ DEG:    36.2696    143.7304 ]
  Phi   =  -0.095202    3.046391  [ DEG:    -5.4547    174.5453 ]
 
# 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_5-D2                               
REMARK     2: T0356_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356AL044_5-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   2.12    0.00   3.150
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL044_5-D2
REMARK Aligment from pdb entry: 1yw4_A
ATOM      1  N   THR   305      70.167  53.062  66.878  1.00  0.00              
ATOM      2  CA  THR   305      71.395  52.748  67.587  1.00  0.00              
ATOM      3  C   THR   305      71.888  53.911  68.434  1.00  0.00              
ATOM      4  O   THR   305      71.438  55.047  68.280  1.00  0.00              
ATOM      5  N   VAL   306      72.796  53.612  69.354  1.00  0.00              
ATOM      6  CA  VAL   306      73.329  54.632  70.234  1.00  0.00              
ATOM      7  C   VAL   306      74.836  54.753  70.099  1.00  0.00              
ATOM      8  O   VAL   306      75.516  53.815  69.683  1.00  0.00              
ATOM      9  N   HIS   308      75.339  55.927  70.457  1.00  0.00              
ATOM     10  CA  HIS   308      76.764  56.206  70.434  1.00  0.00              
ATOM     11  C   HIS   308      77.147  56.462  71.884  1.00  0.00              
ATOM     12  O   HIS   308      76.576  57.344  72.530  1.00  0.00              
ATOM     13  N   ILE   309      78.091  55.679  72.396  1.00  0.00              
ATOM     14  CA  ILE   309      78.553  55.816  73.776  1.00  0.00              
ATOM     15  C   ILE   309      79.847  56.624  73.756  1.00  0.00              
ATOM     16  O   ILE   309      80.864  56.177  73.224  1.00  0.00              
ATOM     17  N   THR   310      87.003  58.217  79.860  1.00  0.00              
ATOM     18  CA  THR   310      88.389  58.221  80.323  1.00  0.00              
ATOM     19  C   THR   310      88.530  57.424  81.619  1.00  0.00              
ATOM     20  O   THR   310      89.218  57.847  82.554  1.00  0.00              
ATOM     21  N   GLN   311      85.010  53.057  86.294  1.00  0.00              
ATOM     22  CA  GLN   311      83.599  52.810  86.021  1.00  0.00              
ATOM     23  C   GLN   311      83.367  52.045  84.726  1.00  0.00              
ATOM     24  O   GLN   311      82.547  51.127  84.681  1.00  0.00              
ATOM     25  N   GLU   313      84.089  52.427  83.676  1.00  0.00              
ATOM     26  CA  GLU   313      83.947  51.783  82.377  1.00  0.00              
ATOM     27  C   GLU   313      82.531  52.069  81.882  1.00  0.00              
ATOM     28  O   GLU   313      81.871  52.981  82.385  1.00  0.00              
END
