
#######################################################
#                                                     #
#                        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   10 (   40),  selected   10 , name T0356AL044_4-D2
# Molecule2: number of CA atoms  192 ( 1487),  selected  192 , name T0356_D2.pdb
# PARAMETERS: T0356AL044_4-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    V     303      R     173          2.301
LGA    T     305      Q     174          1.753
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    V     306      I     190           #
LGA    T     307      M     191          1.197
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    H     308      P     302          1.843
LGA    I     309      V     303          1.890
LGA    T     310      F     304           -
LGA    Q     311      T     305           -
LGA    -       -      V     306           -
LGA    -       -      T     307           -
LGA    -       -      H     308           -
LGA    R     312      I     309          5.011
LGA    -       -      T     310           -
LGA    E     313      Q     311          4.326
LGA    -       -      R     312           -
LGA    -       -      E     313           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   10  192    5.0      7    2.94     0.00      2.600     0.230

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.461255 * X  +  -0.025824 * Y  +   0.886892 * Z  +  -0.261127
  Y_new =  -0.167155 * X  +   0.979149 * Y  +   0.115445 * Z  + -31.292448
  Z_new =  -0.871380 * X  +  -0.201498 * Y  +   0.447320 * Z  + 159.654419 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.423232    2.718360  [ DEG:   -24.2494    155.7506 ]
  Theta =   1.058008    2.083585  [ DEG:    60.6194    119.3806 ]
  Phi   =  -0.347671    2.793922  [ DEG:   -19.9201    160.0799 ]
 
# 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_4-D2                               
REMARK     2: T0356_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356AL044_4-D2.T0356_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   10  192   5.0    7   2.94    0.00   2.600
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL044_4-D2
REMARK Aligment from pdb entry: 1yw6_A
ATOM      1  N   VAL   303      85.337  62.016  67.955  1.00  0.00              
ATOM      2  CA  VAL   303      85.556  61.942  69.385  1.00  0.00              
ATOM      3  C   VAL   303      84.254  62.151  70.150  1.00  0.00              
ATOM      4  O   VAL   303      83.997  61.425  71.100  1.00  0.00              
ATOM      5  N   THR   305      83.414  63.099  69.733  1.00  0.00              
ATOM      6  CA  THR   305      82.157  63.300  70.451  1.00  0.00              
ATOM      7  C   THR   305      81.423  61.972  70.473  1.00  0.00              
ATOM      8  O   THR   305      80.879  61.580  71.493  1.00  0.00              
ATOM      9  N   VAL   306      79.528  53.065  80.608  1.00  0.00              
ATOM     10  CA  VAL   306      79.617  53.364  82.018  1.00  0.00              
ATOM     11  C   VAL   306      78.272  53.129  82.671  1.00  0.00              
ATOM     12  O   VAL   306      78.201  52.640  83.791  1.00  0.00              
ATOM     13  N   THR   307      77.202  53.475  81.969  1.00  0.00              
ATOM     14  CA  THR   307      75.870  53.302  82.520  1.00  0.00              
ATOM     15  C   THR   307      75.467  51.839  82.531  1.00  0.00              
ATOM     16  O   THR   307      74.794  51.400  83.454  1.00  0.00              
ATOM     17  N   HIS   308      75.873  51.079  81.519  1.00  0.00              
ATOM     18  CA  HIS   308      75.543  49.664  81.527  1.00  0.00              
ATOM     19  C   HIS   308      76.337  49.058  82.669  1.00  0.00              
ATOM     20  O   HIS   308      75.788  48.406  83.549  1.00  0.00              
ATOM     21  N   ILE   309      77.641  49.281  82.659  1.00  0.00              
ATOM     22  CA  ILE   309      78.472  48.717  83.697  1.00  0.00              
ATOM     23  C   ILE   309      77.890  48.948  85.070  1.00  0.00              
ATOM     24  O   ILE   309      77.419  48.026  85.708  1.00  0.00              
ATOM     25  N   THR   310      96.656  63.461  92.233  1.00  0.00              
ATOM     26  CA  THR   310      95.327  63.095  91.783  1.00  0.00              
ATOM     27  C   THR   310      94.369  64.275  91.796  1.00  0.00              
ATOM     28  O   THR   310      94.433  65.152  92.657  1.00  0.00              
ATOM     29  N   GLN   311      93.469  64.294  90.826  1.00  0.00              
ATOM     30  CA  GLN   311      92.492  65.359  90.707  1.00  0.00              
ATOM     31  C   GLN   311      91.117  64.703  90.793  1.00  0.00              
ATOM     32  O   GLN   311      90.821  63.776  90.031  1.00  0.00              
ATOM     33  N   ARG   312      84.071  67.619  91.168  1.00  0.00              
ATOM     34  CA  ARG   312      83.283  68.350  92.142  1.00  0.00              
ATOM     35  C   ARG   312      82.260  67.336  92.623  1.00  0.00              
ATOM     36  O   ARG   312      81.608  66.684  91.809  1.00  0.00              
ATOM     37  N   GLU   313      82.134  67.175  93.933  1.00  0.00              
ATOM     38  CA  GLU   313      81.165  66.216  94.467  1.00  0.00              
ATOM     39  C   GLU   313      80.175  66.910  95.402  1.00  0.00              
ATOM     40  O   GLU   313      80.528  67.853  96.099  1.00  0.00              
END
