
#######################################################
#                                                     #
#                        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   44 (   44),  selected   44 , name T0301TS464_5_2-D2
# Molecule2: number of CA atoms  191 ( 1389),  selected  191 , name T0301_D2.pdb
# PARAMETERS: T0301TS464_5_2-D2.T0301_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      D     187           -
LGA    -       -      G     188           -
LGA    -       -      G     189           -
LGA    -       -      A     190           -
LGA    -       -      I     191           -
LGA    -       -      F     192           -
LGA    -       -      P     193           -
LGA    -       -      T     194           -
LGA    -       -      G     195           -
LGA    -       -      N     196           -
LGA    -       -      L     197           -
LGA    -       -      V     198           -
LGA    -       -      D     199           -
LGA    -       -      D     200           -
LGA    -       -      L     201           -
LGA    -       -      E     202           -
LGA    -       -      V     203           -
LGA    -       -      P     204           -
LGA    -       -      G     205           -
LGA    -       -      V     206           -
LGA    -       -      G     207           -
LGA    -       -      T     208           -
LGA    E     227      F     209          3.013
LGA    I     228      K     210          3.978
LGA    G     229      A     211          2.951
LGA    Y     230      T     212          4.198
LGA    R     231      -       -           -
LGA    G     232      -       -           -
LGA    T     233      -       -           -
LGA    A     247      M     213          3.945
LGA    R     248      I     214          3.263
LGA    F     249      -       -           -
LGA    E     250      N     215          4.435
LGA    R     251      A     216          4.006
LGA    I     252      G     217          5.541
LGA    R     253      I     218          4.504
LGA    V     254      P     219          4.204
LGA    -       -      T     220           -
LGA    -       -      V     221           -
LGA    -       -      F     222           -
LGA    -       -      V     223           -
LGA    -       -      N     224           -
LGA    -       -      A     225           -
LGA    -       -      E     226           -
LGA    -       -      E     227           -
LGA    -       -      I     228           -
LGA    -       -      G     229           -
LGA    -       -      Y     230           -
LGA    -       -      R     231           -
LGA    -       -      G     232           -
LGA    -       -      T     233           -
LGA    -       -      E     234           -
LGA    -       -      L     235           -
LGA    -       -      R     236           -
LGA    -       -      E     237           -
LGA    -       -      E     238           -
LGA    -       -      I     239           -
LGA    -       -      N     240           -
LGA    -       -      G     241           -
LGA    -       -      D     242           -
LGA    -       -      P     243           -
LGA    -       -      Q     244           -
LGA    -       -      Q     245           -
LGA    -       -      L     246           -
LGA    -       -      A     247           -
LGA    -       -      R     248           -
LGA    -       -      F     249           -
LGA    -       -      E     250           -
LGA    -       -      R     251           -
LGA    -       -      I     252           -
LGA    -       -      R     253           -
LGA    -       -      V     254           -
LGA    -       -      A     255           -
LGA    -       -      G     256           -
LGA    -       -      A     257           -
LGA    -       -      L     258           -
LGA    -       -      R     259           -
LGA    -       -      M     260           -
LGA    -       -      G     261           -
LGA    -       -      L     262           -
LGA    -       -      I     263           -
LGA    -       -      K     264           -
LGA    -       -      T     265           -
LGA    -       -      P     266           -
LGA    -       -      E     267           -
LGA    -       -      E     268           -
LGA    -       -      A     269           -
LGA    -       -      A     270           -
LGA    -       -      T     271           -
LGA    -       -      R     272           -
LGA    -       -      Q     273           -
LGA    -       -      H     274           -
LGA    -       -      T     275           -
LGA    -       -      P     276           -
LGA    -       -      K     277           -
LGA    -       -      I     278           -
LGA    -       -      A     279           -
LGA    -       -      F     280           -
LGA    -       -      V     281           -
LGA    -       -      A     282           -
LGA    -       -      P     283           -
LGA    -       -      P     284           -
LGA    -       -      R     285           -
LGA    -       -      D     286           -
LGA    -       -      Y     287           -
LGA    -       -      R     288           -
LGA    -       -      T     289           -
LGA    -       -      A     290           -
LGA    -       -      S     291           -
LGA    -       -      G     292           -
LGA    -       -      K     293           -
LGA    -       -      L     294           -
LGA    -       -      V     295           -
LGA    -       -      A     296           -
LGA    -       -      A     297           -
LGA    -       -      G     298           -
LGA    -       -      D     299           -
LGA    -       -      I     300           -
LGA    -       -      D     301           -
LGA    -       -      L     302           -
LGA    -       -      L     303           -
LGA    -       -      V     304           -
LGA    -       -      R     305           -
LGA    -       -      A     306           -
LGA    -       -      L     307           -
LGA    -       -      S     308           -
LGA    -       -      M     309           -
LGA    -       -      G     310           -
LGA    -       -      K     311           -
LGA    -       -      L     312           -
LGA    -       -      H     313           -
LGA    -       -      H     314           -
LGA    -       -      A     315           -
LGA    -       -      M     316           -
LGA    -       -      M     317           -
LGA    -       -      G     318           -
LGA    -       -      T     319           -
LGA    -       -      A     320           -
LGA    -       -      A     321           -
LGA    A     255      V     322          3.208
LGA    G     256      A     323          3.260
LGA    A     257      I     324          2.930
LGA    L     258      G     325          3.138
LGA    -       -      T     326           -
LGA    -       -      A     327           -
LGA    -       -      A     328           -
LGA    -       -      A     329           -
LGA    -       -      I     330           -
LGA    -       -      P     331           -
LGA    -       -      G     332           -
LGA    -       -      T     333           -
LGA    -       -      L     334           -
LGA    R     259      V     335          3.297
LGA    M     260      N     336          2.073
LGA    G     261      L     337          3.495
LGA    V     335      A     338           -
LGA    -       -      A     339           -
LGA    -       -      G     340           -
LGA    -       -      G     341           -
LGA    -       -      G     342           -
LGA    -       -      E     343           -
LGA    -       -      R     344           -
LGA    -       -      S     345           -
LGA    -       -      A     346           -
LGA    -       -      V     347           -
LGA    -       -      R     348           -
LGA    -       -      F     349           -
LGA    -       -      G     350           -
LGA    -       -      H     351           -
LGA    -       -      P     352           -
LGA    -       -      S     353           -
LGA    -       -      G     354           -
LGA    -       -      T     355           -
LGA    -       -      L     356           -
LGA    -       -      R     357           -
LGA    -       -      V     358           -
LGA    -       -      G     359           -
LGA    -       -      A     360           -
LGA    -       -      E     361           -
LGA    -       -      A     362           -
LGA    N     336      S     363          5.638
LGA    L     337      Q     364          2.416
LGA    A     338      A     365          1.873
LGA    A     339      N     366          4.012
LGA    S     353      G     367           #
LGA    G     354      E     368          3.785
LGA    T     355      W     369          2.590
LGA    L     356      -       -           -
LGA    R     357      T     370          2.214
LGA    V     358      V     371          1.488
LGA    G     359      -       -           -
LGA    A     360      -       -           -
LGA    E     361      T     372          3.127
LGA    A     362      K     373          1.480
LGA    S     363      A     374          1.435
LGA    Q     364      -       -           -
LGA    A     365      -       -           -
LGA    N     366      I     375          1.933
LGA    G     367      M     376          4.502
LGA    E     368      S     377           -
LGA    W     369      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   44  191    5.0     31    3.46     6.45      8.587     0.870

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.726249 * X  +   0.000694 * Y  +   0.687431 * Z  +  64.199112
  Y_new =  -0.246954 * X  +  -0.933508 * Y  +  -0.259957 * Z  +  31.402689
  Z_new =   0.641542 * X  +  -0.358557 * Y  +   0.678130 * Z  +  11.224328 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.486377    2.655215  [ DEG:   -27.8674    152.1326 ]
  Theta =  -0.696507   -2.445086  [ DEG:   -39.9069   -140.0931 ]
  Phi   =  -2.813818    0.327775  [ DEG:  -161.2199     18.7801 ]
 
# 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: T0301TS464_5_2-D2                             
REMARK     2: T0301_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301TS464_5_2-D2.T0301_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   44  191   5.0   31   3.46    6.45   8.587
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS464_5_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM     33  CA  GLU   227     105.837  -0.751  11.974  1.00  0.00
ATOM     34  CA  ILE   228     102.772  -1.059   9.736  1.00  0.00
ATOM     35  CA  GLY   229     101.297   2.015  11.434  1.00  0.00
ATOM     36  CA  TYR   230      98.448   0.488  13.437  1.00  0.00
ATOM     37  CA  ARG   231      97.365   2.423  16.535  1.00  0.00
ATOM     38  CA  GLY   232      96.523  -0.703  18.563  1.00  0.00
ATOM     39  CA  THR   233      96.336  -4.490  18.234  1.00  0.00
ATOM     40  CA  ALA   247      99.284   2.108   2.856  1.00  0.00
ATOM     41  CA  ARG   248      95.971   1.137   4.464  1.00  0.00
ATOM     42  CA  PHE   249      96.717   2.618   7.893  1.00  0.00
ATOM     43  CA  GLU   250      98.084   5.749   6.181  1.00  0.00
ATOM     44  CA  ARG   251      94.759   6.142   4.383  1.00  0.00
ATOM     45  CA  ILE   252      92.793   5.911   7.626  1.00  0.00
ATOM     46  CA  ARG   253      95.140   8.404   9.286  1.00  0.00
ATOM     47  CA  VAL   254      93.264  10.622   6.874  1.00  0.00
ATOM     48  CA  ALA   255      89.887  10.295   8.604  1.00  0.00
ATOM     49  CA  GLY   256      90.953  10.067  12.250  1.00  0.00
ATOM     50  CA  ALA   257      89.231   6.699  12.491  1.00  0.00
ATOM     51  CA  LEU   258      90.633   4.355  15.138  1.00  0.00
ATOM     52  CA  ARG   259      92.746   1.621  13.372  1.00  0.00
ATOM     53  CA  MET   260      93.596  -1.526  15.331  1.00  0.00
ATOM     54  CA  GLY   261      94.626  -4.798  13.704  1.00  0.00
ATOM     55  CA  VAL   335      78.300  -7.898   3.092  1.00  0.00
ATOM     56  CA  ASN   336      81.843  -8.579   1.776  1.00  0.00
ATOM     57  CA  LEU   337      84.077  -6.248  -0.187  1.00  0.00
ATOM     58  CA  ALA   338      87.308  -7.577  -1.670  1.00  0.00
ATOM     59  CA  ALA   339      90.722  -5.939  -1.744  1.00  0.00
ATOM     60  CA  SER   353      90.770  -1.622  -0.937  1.00  0.00
ATOM     61  CA  GLY   354      87.154  -2.096   0.256  1.00  0.00
ATOM     62  CA  THR   355      88.418  -1.037   3.646  1.00  0.00
ATOM     63  CA  LEU   356      89.291   2.406   2.346  1.00  0.00
ATOM     64  CA  ARG   357      85.723   2.966   1.276  1.00  0.00
ATOM     65  CA  VAL   358      84.296   1.696   4.553  1.00  0.00
ATOM     66  CA  GLY   359      86.581   4.062   6.487  1.00  0.00
ATOM     67  CA  ALA   360      85.507   6.983   4.319  1.00  0.00
ATOM     68  CA  GLU   361      81.811   6.125   4.509  1.00  0.00
ATOM     69  CA  ALA   362      81.566   5.264   8.207  1.00  0.00
ATOM     70  CA  SER   363      83.705   8.214   9.281  1.00  0.00
ATOM     71  CA  GLN   364      81.315  10.593   7.380  1.00  0.00
ATOM     72  CA  ALA   365      78.456   8.948   9.281  1.00  0.00
ATOM     73  CA  ASN   366      80.116   9.923  12.599  1.00  0.00
ATOM     74  CA  GLY   367      81.768   6.669  13.625  1.00  0.00
ATOM     75  CA  GLU   368      84.801   6.558  16.010  1.00  0.00
ATOM     76  CA  TRP   369      86.508   3.546  14.416  1.00  0.00
TER
END
