
#######################################################
#                                                     #
#                        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_1_1-D2
# Molecule2: number of CA atoms  186 ( 1394),  selected  186 , name T0298_D2.pdb
# PARAMETERS: T0298TS268_1_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    C     130      I     216          0.912
LGA    A     131      F     217          0.587
LGA    V     132      A     218          0.245
LGA    A     133      E     219          0.873
LGA    -       -      V     220           -
LGA    -       -      Q     221           -
LGA    A     134      A     222          1.925
LGA    E     135      L     223          0.377
LGA    L     136      L     224          0.637
LGA    C     137      G     225          1.828
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    -       -      V     256           -
LGA    -       -      D     257           -
LGA    -       -      L     258           -
LGA    -       -      A     259           -
LGA    -       -      A     260           -
LGA    -       -      V     261           -
LGA    -       -      T     262           -
LGA    -       -      R     263           -
LGA    -       -      V     264           -
LGA    -       -      L     265           -
LGA    -       -      D     266           -
LGA    -       -      A     267           -
LGA    -       -      T     268           -
LGA    -       -      K     269           -
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    1.10    25.00      4.176     0.669

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.391761 * X  +  -0.198249 * Y  +  -0.898455 * Z  +  23.408255
  Y_new =   0.484715 * X  +  -0.874478 * Y  +  -0.018395 * Z  +  85.297371
  Z_new =  -0.782032 * X  +  -0.442701 * Y  +   0.438681 * Z  +  33.119213 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.789960    2.351633  [ DEG:   -45.2614    134.7386 ]
  Theta =   0.897920    2.243672  [ DEG:    51.4470    128.5530 ]
  Phi   =   2.250534   -0.891059  [ DEG:   128.9461    -51.0539 ]
 
# 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_1_1-D2                             
REMARK     2: T0298_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0298TS268_1_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   1.10   25.00   4.176
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS268_1_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0298
PARENT 1oi4_B
ATOM    928  N   CYS   130      -8.013  79.457   1.508  1.00  0.00
ATOM    929  CA  CYS   130      -6.588  79.447   1.311  1.00  0.00
ATOM    930  C   CYS   130      -6.057  80.845   1.236  1.00  0.00
ATOM    931  O   CYS   130      -6.705  81.812   1.629  1.00  0.00
ATOM    932  CB  CYS   130      -6.231  78.725   0.009  1.00  0.00
ATOM    933  SG  CYS   130      -6.844  79.537  -1.486  1.00  0.00
ATOM    934  N   ALA   131      -4.809  80.957   0.730  1.00  0.00
ATOM    935  CA  ALA   131      -4.146  82.219   0.588  1.00  0.00
ATOM    936  C   ALA   131      -4.935  83.044  -0.371  1.00  0.00
ATOM    937  O   ALA   131      -5.179  84.226  -0.134  1.00  0.00
ATOM    938  CB  ALA   131      -2.734  82.020   0.058  1.00  0.00
ATOM    939  N   VAL   132      -5.362  82.441  -1.497  1.00  0.00
ATOM    940  CA  VAL   132      -6.169  83.199  -2.402  1.00  0.00
ATOM    941  C   VAL   132      -7.527  82.579  -2.428  1.00  0.00
ATOM    942  O   VAL   132      -7.813  81.664  -3.200  1.00  0.00
ATOM    943  CB  VAL   132      -5.578  83.195  -3.825  1.00  0.00
ATOM    944  CG1 VAL   132      -6.442  84.022  -4.762  1.00  0.00
ATOM    945  CG2 VAL   132      -4.175  83.782  -3.820  1.00  0.00
ATOM    946  N   ALA   133      -8.431  83.085  -1.577  1.00  0.00
ATOM    947  CA  ALA   133      -9.744  82.528  -1.601  1.00  0.00
ATOM    948  C   ALA   133     -10.655  83.642  -1.969  1.00  0.00
ATOM    949  O   ALA   133     -10.606  84.714  -1.367  1.00  0.00
ATOM    950  CB  ALA   133     -10.107  81.965  -0.236  1.00  0.00
ATOM    951  N   ALA   134     -11.515  83.426  -2.979  1.00  0.00
ATOM    952  CA  ALA   134     -12.410  84.487  -3.310  1.00  0.00
ATOM    953  C   ALA   134     -13.477  84.405  -2.282  1.00  0.00
ATOM    954  O   ALA   134     -14.394  83.595  -2.383  1.00  0.00
ATOM    955  CB  ALA   134     -12.969  84.291  -4.711  1.00  0.00
ATOM    956  N   GLU   135     -13.372  85.266  -1.258  1.00  0.00
ATOM    957  CA  GLU   135     -14.302  85.251  -0.173  1.00  0.00
ATOM    958  C   GLU   135     -14.056  86.471   0.634  1.00  0.00
ATOM    959  O   GLU   135     -13.657  87.506   0.103  1.00  0.00
ATOM    960  CB  GLU   135     -14.101  84.003   0.687  1.00  0.00
ATOM    961  CG  GLU   135     -14.467  82.703  -0.009  1.00  0.00
ATOM    962  CD  GLU   135     -14.205  81.485   0.854  1.00  0.00
ATOM    963  OE1 GLU   135     -13.699  81.655   1.983  1.00  0.00
ATOM    964  OE2 GLU   135     -14.507  80.360   0.403  1.00  0.00
ATOM    965  N   LEU   136     -14.312  86.403   1.949  1.00  0.00
ATOM    966  CA  LEU   136     -14.169  87.624   2.668  1.00  0.00
ATOM    967  C   LEU   136     -12.714  87.900   2.815  1.00  0.00
ATOM    968  O   LEU   136     -12.002  87.198   3.530  1.00  0.00
ATOM    969  CB  LEU   136     -14.816  87.512   4.049  1.00  0.00
ATOM    970  CG  LEU   136     -14.814  88.781   4.904  1.00  0.00
ATOM    971  CD1 LEU   136     -15.649  89.871   4.251  1.00  0.00
ATOM    972  CD2 LEU   136     -15.392  88.501   6.283  1.00  0.00
ATOM    973  N   CYS   137     -12.238  88.956   2.130  1.00  0.00
ATOM    974  CA  CYS   137     -10.855  89.309   2.194  1.00  0.00
ATOM    975  C   CYS   137     -10.809  90.823   2.325  1.00  0.00
ATOM    976  O   CYS   137     -11.898  91.450   2.224  1.00  0.00
ATOM    977  CB  CYS   137     -10.126  88.855   0.928  1.00  0.00
ATOM    978  SG  CYS   137     -10.161  87.071   0.645  1.00  0.00
TER
END
