
#######################################################
#                                                     #
#                        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_2_1-D2
# Molecule2: number of CA atoms  186 ( 1394),  selected  186 , name T0298_D2.pdb
# PARAMETERS: T0298TS268_2_1-D2.T0298_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      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    C     130      L     152          1.556
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    A     131      P     230          2.634
LGA    V     132      L     231          1.961
LGA    A     133      N     232          0.179
LGA    A     134      V     233          1.118
LGA    E     135      T     234          0.281
LGA    L     136      C     235          0.520
LGA    C     137      I     236          0.333
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    1.37     0.00      4.096     0.545

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.354981 * X  +   0.334149 * Y  +   0.873117 * Z  + -77.913399
  Y_new =  -0.518008 * X  +   0.847766 * Y  +  -0.113842 * Z  +  73.780495
  Z_new =  -0.778239 * X  +  -0.411870 * Y  +   0.474033 * Z  +  99.091446 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.715344    2.426249  [ DEG:   -40.9862    139.0138 ]
  Theta =   0.891857    2.249736  [ DEG:    51.0996    128.9004 ]
  Phi   =  -0.970017    2.171575  [ DEG:   -55.5779    124.4221 ]
 
# 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_2_1-D2                             
REMARK     2: T0298_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0298TS268_2_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   1.37    0.00   4.096
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS268_2_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0298
PARENT 1g2i_A
ATOM    928  N   CYS   130      -4.511  87.073  11.941  1.00  0.00
ATOM    929  CA  CYS   130      -4.995  87.955  10.916  1.00  0.00
ATOM    930  C   CYS   130      -4.679  87.468   9.536  1.00  0.00
ATOM    931  O   CYS   130      -4.278  86.327   9.310  1.00  0.00
ATOM    932  CB  CYS   130      -4.367  89.343  11.062  1.00  0.00
ATOM    933  SG  CYS   130      -4.739  90.169  12.626  1.00  0.00
ATOM    934  N   ALA   131      -4.854  88.395   8.571  1.00  0.00
ATOM    935  CA  ALA   131      -4.719  88.144   7.171  1.00  0.00
ATOM    936  C   ALA   131      -3.342  87.657   6.880  1.00  0.00
ATOM    937  O   ALA   131      -2.438  87.770   7.704  1.00  0.00
ATOM    938  CB  ALA   131      -4.969  89.417   6.377  1.00  0.00
ATOM    939  N   VAL   132      -3.206  87.098   5.661  1.00  0.00
ATOM    940  CA  VAL   132      -2.076  86.425   5.090  1.00  0.00
ATOM    941  C   VAL   132      -1.113  85.983   6.134  1.00  0.00
ATOM    942  O   VAL   132      -0.254  86.728   6.605  1.00  0.00
ATOM    943  CB  VAL   132      -1.307  87.339   4.117  1.00  0.00
ATOM    944  CG1 VAL   132      -0.068  86.632   3.591  1.00  0.00
ATOM    945  CG2 VAL   132      -2.185  87.716   2.934  1.00  0.00
ATOM    946  N   ALA   133      -1.290  84.714   6.536  1.00  0.00
ATOM    947  CA  ALA   133      -0.423  84.038   7.450  1.00  0.00
ATOM    948  C   ALA   133      -1.001  82.665   7.566  1.00  0.00
ATOM    949  O   ALA   133      -2.216  82.523   7.689  1.00  0.00
ATOM    950  CB  ALA   133      -0.407  84.753   8.792  1.00  0.00
ATOM    951  N   ALA   134      -0.159  81.611   7.514  1.00  0.00
ATOM    952  CA  ALA   134      -0.692  80.284   7.665  1.00  0.00
ATOM    953  C   ALA   134       0.365  79.277   7.331  1.00  0.00
ATOM    954  O   ALA   134       1.395  79.617   6.750  1.00  0.00
ATOM    955  CB  ALA   134      -1.879  80.081   6.736  1.00  0.00
ATOM    956  N   GLU   135       0.127  78.003   7.728  1.00  0.00
ATOM    957  CA  GLU   135       1.006  76.908   7.417  1.00  0.00
ATOM    958  C   GLU   135       0.148  75.699   7.209  1.00  0.00
ATOM    959  O   GLU   135      -0.833  75.496   7.925  1.00  0.00
ATOM    960  CB  GLU   135       1.988  76.666   8.565  1.00  0.00
ATOM    961  CG  GLU   135       3.008  75.573   8.289  1.00  0.00
ATOM    962  CD  GLU   135       3.992  75.395   9.428  1.00  0.00
ATOM    963  OE1 GLU   135       3.901  76.153  10.417  1.00  0.00
ATOM    964  OE2 GLU   135       4.857  74.498   9.331  1.00  0.00
ATOM    965  N   LEU   136       0.488  74.864   6.207  1.00  0.00
ATOM    966  CA  LEU   136      -0.282  73.678   6.000  1.00  0.00
ATOM    967  C   LEU   136       0.594  72.559   6.448  1.00  0.00
ATOM    968  O   LEU   136       1.483  72.125   5.717  1.00  0.00
ATOM    969  CB  LEU   136      -0.651  73.530   4.523  1.00  0.00
ATOM    970  CG  LEU   136      -1.466  72.289   4.150  1.00  0.00
ATOM    971  CD1 LEU   136      -2.820  72.307   4.842  1.00  0.00
ATOM    972  CD2 LEU   136      -1.701  72.232   2.648  1.00  0.00
ATOM    973  N   CYS   137       0.358  72.048   7.671  1.00  0.00
ATOM    974  CA  CYS   137       1.162  70.971   8.160  1.00  0.00
ATOM    975  C   CYS   137       0.545  69.682   7.633  1.00  0.00
ATOM    976  O   CYS   137      -0.656  69.714   7.264  1.00  0.00
ATOM    977  CB  CYS   137       1.176  70.964   9.689  1.00  0.00
ATOM    978  SG  CYS   137       2.355  69.805  10.421  1.00  0.00
TER
END
