
#######################################################
#                                                     #
#                        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    8 (   51),  selected    8 , name T0298TS268_4_1-D2
# Molecule2: number of CA atoms  186 ( 1394),  selected  186 , name T0298_D2.pdb
# PARAMETERS: T0298TS268_4_1-D2.T0298_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    -       -      C     130           -
LGA    -       -      A     131           -
LGA    -       -      V     132           -
LGA    -       -      A     133           -
LGA    -       -      A     134           -
LGA    -       -      E     135           -
LGA    -       -      L     136           -
LGA    -       -      C     137           -
LGA    -       -      E     138           -
LGA    -       -      V     139           -
LGA    -       -      L     140           -
LGA    -       -      A     141           -
LGA    -       -      P     142           -
LGA    -       -      L     143           -
LGA    -       -      L     144           -
LGA    -       -      A     145           -
LGA    -       -      T     146           -
LGA    -       -      L     147           -
LGA    -       -      D     148           -
LGA    -       -      C     149           -
LGA    -       -      R     150           -
LGA    -       -      Q     151           -
LGA    -       -      L     152           -
LGA    -       -      N     153           -
LGA    -       -      L     154           -
LGA    -       -      T     155           -
LGA    -       -      A     156           -
LGA    -       -      C     157           -
LGA    -       -      L     158           -
LGA    -       -      S     159           -
LGA    -       -      V     160           -
LGA    -       -      S     161           -
LGA    -       -      S     162           -
LGA    -       -      L     163           -
LGA    -       -      G     164           -
LGA    -       -      R     165           -
LGA    -       -      E     166           -
LGA    -       -      G     167           -
LGA    -       -      V     168           -
LGA    -       -      K     169           -
LGA    -       -      E     170           -
LGA    -       -      L     171           -
LGA    -       -      A     172           -
LGA    -       -      R     173           -
LGA    -       -      Q     174           -
LGA    -       -      T     175           -
LGA    -       -      A     176           -
LGA    -       -      E     177           -
LGA    -       -      L     178           -
LGA    -       -      L     179           -
LGA    -       -      N     180           -
LGA    -       -      A     181           -
LGA    -       -      R     182           -
LGA    -       -      P     183           -
LGA    -       -      L     184           -
LGA    -       -      E     185           -
LGA    -       -      P     186           -
LGA    -       -      R     187           -
LGA    -       -      L     188           -
LGA    -       -      F     189           -
LGA    -       -      D     190           -
LGA    -       -      R     191           -
LGA    -       -      Q     192           -
LGA    -       -      I     193           -
LGA    -       -      A     194           -
LGA    -       -      F     195           -
LGA    -       -      N     196           -
LGA    -       -      L     197           -
LGA    -       -      L     198           -
LGA    -       -      A     199           -
LGA    -       -      Q     200           -
LGA    -       -      V     201           -
LGA    -       -      G     202           -
LGA    -       -      A     203           -
LGA    -       -      V     204           -
LGA    -       -      D     205           -
LGA    -       -      A     206           -
LGA    -       -      E     207           -
LGA    -       -      G     208           -
LGA    -       -      H     209           -
LGA    -       -      S     210           -
LGA    -       -      A     211           -
LGA    -       -      I     212           -
LGA    -       -      E     213           -
LGA    -       -      R     214           -
LGA    -       -      R     215           -
LGA    -       -      I     216           -
LGA    -       -      F     217           -
LGA    -       -      A     218           -
LGA    -       -      E     219           -
LGA    -       -      V     220           -
LGA    -       -      Q     221           -
LGA    -       -      A     222           -
LGA    -       -      L     223           -
LGA    -       -      L     224           -
LGA    -       -      G     225           -
LGA    -       -      E     226           -
LGA    -       -      R     227           -
LGA    -       -      I     228           -
LGA    -       -      G     229           -
LGA    -       -      P     230           -
LGA    -       -      L     231           -
LGA    -       -      N     232           -
LGA    -       -      V     233           -
LGA    -       -      T     234           -
LGA    -       -      C     235           -
LGA    -       -      I     236           -
LGA    -       -      Q     237           -
LGA    -       -      A     238           -
LGA    -       -      P     239           -
LGA    -       -      V     240           -
LGA    -       -      F     241           -
LGA    -       -      F     242           -
LGA    -       -      G     243           -
LGA    -       -      D     244           -
LGA    -       -      S     245           -
LGA    -       -      L     246           -
LGA    -       -      S     247           -
LGA    -       -      V     248           -
LGA    -       -      T     249           -
LGA    -       -      L     250           -
LGA    -       -      Q     251           -
LGA    -       -      C     252           -
LGA    -       -      A     253           -
LGA    -       -      E     254           -
LGA    -       -      P     255           -
LGA    C     130      V     256          0.745
LGA    A     131      D     257          1.153
LGA    V     132      L     258          2.061
LGA    -       -      A     259           -
LGA    -       -      A     260           -
LGA    A     133      V     261          0.730
LGA    -       -      T     262           -
LGA    -       -      R     263           -
LGA    A     134      V     264          1.312
LGA    E     135      L     265          1.067
LGA    -       -      D     266           -
LGA    -       -      A     267           -
LGA    L     136      T     268          1.046
LGA    C     137      K     269          2.027
LGA    -       -      G     270           -
LGA    -       -      I     271           -
LGA    -       -      E     272           -
LGA    -       -      W     273           -
LGA    -       -      V     274           -
LGA    -       -      G     275           -
LGA    -       -      E     276           -
LGA    -       -      G     277           -
LGA    -       -      D     278           -
LGA    -       -      Y     279           -
LGA    -       -      P     280           -
LGA    -       -      T     281           -
LGA    -       -      V     282           -
LGA    -       -      V     283           -
LGA    -       -      G     284           -
LGA    -       -      D     285           -
LGA    -       -      A     286           -
LGA    -       -      L     287           -
LGA    -       -      G     288           -
LGA    -       -      Q     289           -
LGA    -       -      D     290           -
LGA    -       -      E     291           -
LGA    -       -      T     292           -
LGA    -       -      Y     293           -
LGA    -       -      V     294           -
LGA    -       -      G     295           -
LGA    -       -      R     296           -
LGA    -       -      V     297           -
LGA    -       -      R     298           -
LGA    -       -      A     299           -
LGA    -       -      G     300           -
LGA    -       -      Q     301           -
LGA    -       -      A     302           -
LGA    -       -      D     303           -
LGA    -       -      P     304           -
LGA    -       -      C     305           -
LGA    -       -      Q     306           -
LGA    -       -      V     307           -
LGA    -       -      N     308           -
LGA    -       -      L     309           -
LGA    -       -      W     310           -
LGA    -       -      I     311           -
LGA    -       -      V     312           -
LGA    -       -      S     313           -
LGA    -       -      D     314           -
LGA    -       -      N     315           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    8  186    5.0      8    1.36     0.00      4.013     0.549

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.236395 * X  +  -0.000354 * Y  +   0.971657 * Z  + -17.112185
  Y_new =  -0.874390 * X  +  -0.436183 * Y  +   0.212572 * Z  +  99.691948
  Z_new =   0.423746 * X  +  -0.899858 * Y  +  -0.103421 * Z  +  17.986351 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.685224    1.456368  [ DEG:   -96.5563     83.4437 ]
  Theta =  -0.437576   -2.704016  [ DEG:   -25.0713   -154.9287 ]
  Phi   =  -1.306755    1.834838  [ DEG:   -74.8715    105.1285 ]
 
# 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: T0298TS268_4_1-D2                             
REMARK     2: T0298_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0298TS268_4_1-D2.T0298_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    8  186   5.0    8   1.36    0.00   4.013
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS268_4_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0298
PARENT 1hdo_A
ATOM    928  N   CYS   130     -11.347  90.005  21.925  1.00  0.00
ATOM    929  CA  CYS   130     -12.710  90.451  21.817  1.00  0.00
ATOM    930  C   CYS   130     -13.513  89.618  22.761  1.00  0.00
ATOM    931  O   CYS   130     -12.984  88.759  23.468  1.00  0.00
ATOM    932  CB  CYS   130     -13.220  90.273  20.386  1.00  0.00
ATOM    933  SG  CYS   130     -13.293  88.555  19.827  1.00  0.00
ATOM    934  N   ALA   131     -14.833  89.869  22.806  1.00  0.00
ATOM    935  CA  ALA   131     -15.694  89.132  23.683  1.00  0.00
ATOM    936  C   ALA   131     -15.866  87.770  23.101  1.00  0.00
ATOM    937  O   ALA   131     -15.526  87.538  21.941  1.00  0.00
ATOM    938  CB  ALA   131     -17.044  89.821  23.804  1.00  0.00
ATOM    939  N   VAL   132     -16.351  86.808  23.908  1.00  0.00
ATOM    940  CA  VAL   132     -16.608  85.543  23.294  1.00  0.00
ATOM    941  C   VAL   132     -17.647  85.843  22.267  1.00  0.00
ATOM    942  O   VAL   132     -18.665  86.469  22.560  1.00  0.00
ATOM    943  CB  VAL   132     -17.119  84.512  24.318  1.00  0.00
ATOM    944  CG1 VAL   132     -17.514  83.219  23.621  1.00  0.00
ATOM    945  CG2 VAL   132     -16.036  84.194  25.339  1.00  0.00
ATOM    946  N   ALA   133     -17.378  85.427  21.017  1.00  0.00
ATOM    947  CA  ALA   133     -18.216  85.758  19.907  1.00  0.00
ATOM    948  C   ALA   133     -19.400  84.860  19.857  1.00  0.00
ATOM    949  O   ALA   133     -19.494  83.864  20.573  1.00  0.00
ATOM    950  CB  ALA   133     -17.448  85.613  18.601  1.00  0.00
ATOM    951  N   ALA   134     -20.382  85.269  19.033  1.00  0.00
ATOM    952  CA  ALA   134     -21.534  84.468  18.799  1.00  0.00
ATOM    953  C   ALA   134     -21.145  83.472  17.754  1.00  0.00
ATOM    954  O   ALA   134     -20.418  83.795  16.817  1.00  0.00
ATOM    955  CB  ALA   134     -22.689  85.329  18.314  1.00  0.00
ATOM    956  N   GLU   135     -21.603  82.219  17.909  1.00  0.00
ATOM    957  CA  GLU   135     -21.365  81.249  16.882  1.00  0.00
ATOM    958  C   GLU   135     -22.715  80.907  16.360  1.00  0.00
ATOM    959  O   GLU   135     -23.669  80.807  17.129  1.00  0.00
ATOM    960  CB  GLU   135     -20.663  80.018  17.459  1.00  0.00
ATOM    961  CG  GLU   135     -19.256  80.286  17.966  1.00  0.00
ATOM    962  CD  GLU   135     -18.572  79.032  18.476  1.00  0.00
ATOM    963  OE1 GLU   135     -19.206  77.958  18.451  1.00  0.00
ATOM    964  OE2 GLU   135     -17.402  79.126  18.903  1.00  0.00
ATOM    965  N   LEU   136     -22.846  80.757  15.030  1.00  0.00
ATOM    966  CA  LEU   136     -24.152  80.477  14.517  1.00  0.00
ATOM    967  C   LEU   136     -24.030  79.254  13.660  1.00  0.00
ATOM    968  O   LEU   136     -23.414  79.284  12.597  1.00  0.00
ATOM    969  CB  LEU   136     -24.666  81.655  13.687  1.00  0.00
ATOM    970  CG  LEU   136     -26.050  81.487  13.056  1.00  0.00
ATOM    971  CD1 LEU   136     -27.114  81.324  14.130  1.00  0.00
ATOM    972  CD2 LEU   136     -26.407  82.703  12.214  1.00  0.00
ATOM    973  N   CYS   137     -24.624  78.133  14.111  1.00  0.00
ATOM    974  CA  CYS   137     -24.526  76.913  13.363  1.00  0.00
ATOM    975  C   CYS   137     -25.679  76.835  12.368  1.00  0.00
ATOM    976  O   CYS   137     -25.639  75.921  11.499  1.00  0.00
ATOM    977  CB  CYS   137     -24.594  75.705  14.299  1.00  0.00
ATOM    978  SG  CYS   137     -23.187  75.552  15.423  1.00  0.00
TER
END
