
#######################################################
#                                                     #
#                        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   55 (   55),  selected   55 , name T0356TS464_4-D2
# Molecule2: number of CA atoms  192 ( 1487),  selected  192 , name T0356_D2.pdb
# PARAMETERS: T0356TS464_4-D2.T0356_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    T     122      T     122           -
LGA    K     123      K     123           -
LGA    R     124      R     124           -
LGA    L     125      L     125           -
LGA    R     126      R     126           -
LGA    G     127      -       -           -
LGA    A     128      -       -           -
LGA    P     129      -       -           -
LGA    C     130      -       -           -
LGA    Q     131      -       -           -
LGA    W     161      -       -           -
LGA    G     162      -       -           -
LGA    L     163      -       -           -
LGA    T     164      -       -           -
LGA    V     165      -       -           -
LGA    A     220      -       -           -
LGA    L     221      -       -           -
LGA    G     222      -       -           -
LGA    A     223      -       -           -
LGA    D     224      -       -           -
LGA    P     225      -       -           -
LGA    A     226      -       -           -
LGA    T     227      G     127          4.159
LGA    -       -      A     128           -
LGA    -       -      P     129           -
LGA    -       -      C     130           -
LGA    -       -      Q     131           -
LGA    -       -      Q     132           -
LGA    T     233      K     133          2.376
LGA    P     234      I     134          1.293
LGA    V     235      V     135          0.738
LGA    P     236      S     136          0.979
LGA    D     237      G     137          3.272
LGA    T     238      D     138           #
LGA    -       -      D     139           -
LGA    L     239      V     140          1.991
LGA    S     240      D     141          1.392
LGA    E     241      L     142          1.887
LGA    Y     242      N     143          2.188
LGA    A     243      R     144          2.019
LGA    F     244      I     145          2.134
LGA    A     245      P     146          3.078
LGA    G     246      -       -           -
LGA    L     247      -       -           -
LGA    L     248      -       -           -
LGA    R     249      I     147          5.397
LGA    G     250      M     148          1.042
LGA    T     251      T     149          3.994
LGA    -       -      C     150           -
LGA    -       -      W     151           -
LGA    -       -      P     152           -
LGA    -       -      E     153           -
LGA    -       -      D     154           -
LGA    -       -      A     155           -
LGA    K     252      A     156          4.171
LGA    T     253      P     157          2.917
LGA    E     254      -       -           -
LGA    V     255      L     158          1.829
LGA    V     256      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    K     257      Q     182          3.933
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    G     275      H     196          2.282
LGA    -       -      R     197           -
LGA    Y     276      G     198          2.572
LGA    I     277      G     199          1.588
LGA    -       -      A     200           -
LGA    -       -      L     201           -
LGA    -       -      D     202           -
LGA    E     278      Y     203          1.449
LGA    -       -      Q     204           -
LGA    -       -      E     205           -
LGA    Q     279      W     206          5.539
LGA    G     280      C     207           #
LGA    -       -      A     208           -
LGA    -       -      A     209           -
LGA    -       -      H     210           -
LGA    -       -      P     211           -
LGA    -       -      G     212           -
LGA    -       -      E     213           -
LGA    E     281      R     214          2.700
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    -       -      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)   55  192    5.0     26    2.87     7.69      9.057     0.875

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.842874 * X  +   0.134009 * Y  +   0.521158 * Z  +  71.555481
  Y_new =  -0.422397 * X  +  -0.764792 * Y  +  -0.486491 * Z  + 101.354736
  Z_new =   0.333383 * X  +  -0.630187 * Y  +   0.701228 * Z  + 100.227318 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.732091    2.409502  [ DEG:   -41.9457    138.0543 ]
  Theta =  -0.339889   -2.801703  [ DEG:   -19.4742   -160.5258 ]
  Phi   =  -2.677034    0.464559  [ DEG:  -153.3827     26.6173 ]
 
# 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: T0356TS464_4-D2                               
REMARK     2: T0356_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS464_4-D2.T0356_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   55  192   5.0   26   2.87    7.69   9.057
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS464_4-D2
PFRMAT TS
TARGET T0356
MODEL 4
PARENT N/A
ATOM     59  CA  THR   122      57.608  70.128  58.790  1.00  0.00
ATOM     60  CA  LYS   123      55.922  67.181  60.518  1.00  0.00
ATOM     61  CA  ARG   124      58.730  67.134  63.098  1.00  0.00
ATOM     62  CA  LEU   125      58.125  70.749  64.138  1.00  0.00
ATOM     63  CA  ARG   126      54.362  70.271  64.540  1.00  0.00
ATOM     64  CA  GLY   127      55.008  67.056  66.483  1.00  0.00
ATOM     65  CA  ALA   128      57.172  68.975  68.974  1.00  0.00
ATOM     66  CA  PRO   129      54.828  71.979  68.908  1.00  0.00
ATOM     67  CA  CYS   130      51.887  69.757  69.874  1.00  0.00
ATOM     68  CA  GLN   131      53.990  68.392  72.751  1.00  0.00
ATOM     69  CA  TRP   161      58.042  79.487  72.071  1.00  0.00
ATOM     70  CA  GLY   162      60.944  81.929  71.699  1.00  0.00
ATOM     71  CA  LEU   163      64.429  80.766  72.660  1.00  0.00
ATOM     72  CA  THR   164      67.482  83.025  72.629  1.00  0.00
ATOM     73  CA  VAL   165      69.784  81.854  69.848  1.00  0.00
ATOM     74  CA  ALA   220      96.033  84.709 102.137  1.00  0.00
ATOM     75  CA  LEU   221      92.339  84.758 102.977  1.00  0.00
ATOM     76  CA  GLY   222      91.645  81.015 103.126  1.00  0.00
ATOM     77  CA  ALA   223      92.257  79.535  99.660  1.00  0.00
ATOM     78  CA  ASP   224      94.429  76.400  99.594  1.00  0.00
ATOM     79  CA  PRO   225      94.676  76.426  95.827  1.00  0.00
ATOM     80  CA  ALA   226      93.952  78.653  92.837  1.00  0.00
ATOM     81  CA  THR   227      92.060  77.445  89.788  1.00  0.00
ATOM     82  CA  THR   233      84.863  69.419  93.572  1.00  0.00
ATOM     83  CA  PRO   234      87.754  67.002  94.219  1.00  0.00
ATOM     84  CA  VAL   235      86.870  63.595  95.687  1.00  0.00
ATOM     85  CA  PRO   236      87.750  59.850  95.640  1.00  0.00
ATOM     86  CA  ASP   237      87.091  57.952  92.400  1.00  0.00
ATOM     87  CA  THR   238      84.964  55.209  94.016  1.00  0.00
ATOM     88  CA  LEU   239      82.466  57.942  94.959  1.00  0.00
ATOM     89  CA  SER   240      79.308  58.497  97.041  1.00  0.00
ATOM     90  CA  GLU   241      76.888  57.865  94.147  1.00  0.00
ATOM     91  CA  TYR   242      74.217  57.666  96.878  1.00  0.00
ATOM     92  CA  ALA   243      74.673  61.252  98.128  1.00  0.00
ATOM     93  CA  PHE   244      74.075  62.409  94.532  1.00  0.00
ATOM     94  CA  ALA   245      70.479  61.273  95.146  1.00  0.00
ATOM     95  CA  GLY   246      69.469  64.023  97.607  1.00  0.00
ATOM     96  CA  LEU   247      71.701  66.367  95.572  1.00  0.00
ATOM     97  CA  LEU   248      69.250  66.078  92.649  1.00  0.00
ATOM     98  CA  ARG   249      66.075  65.662  94.741  1.00  0.00
ATOM     99  CA  GLY   250      66.271  61.988  93.699  1.00  0.00
ATOM    100  CA  THR   251      66.494  58.758  95.728  1.00  0.00
ATOM    101  CA  LYS   252      68.441  55.475  95.536  1.00  0.00
ATOM    102  CA  THR   253      65.935  53.755  93.221  1.00  0.00
ATOM    103  CA  GLU   254      65.760  56.640  90.723  1.00  0.00
ATOM    104  CA  VAL   255      69.539  57.226  90.634  1.00  0.00
ATOM    105  CA  VAL   256      69.857  53.505  89.814  1.00  0.00
ATOM    106  CA  LYS   257      66.702  53.052  87.706  1.00  0.00
ATOM    107  CA  GLY   275      74.719  51.952  70.932  1.00  0.00
ATOM    108  CA  TYR   276      75.834  55.433  72.320  1.00  0.00
ATOM    109  CA  ILE   277      78.646  55.172  74.839  1.00  0.00
ATOM    110  CA  GLU   278      81.563  52.788  75.070  1.00  0.00
ATOM    111  CA  GLN   279      84.479  52.258  77.441  1.00  0.00
ATOM    112  CA  GLY   280      88.081  52.478  76.357  1.00  0.00
ATOM    113  CA  GLU   281      89.955  51.779  79.563  1.00  0.00
TER
END
