
#######################################################
#                                                     #
#                        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   22 (   22),  selected   22 , name T0301TS464_2_2-D2
# Molecule2: number of CA atoms  191 ( 1389),  selected  191 , name T0301_D2.pdb
# PARAMETERS: T0301TS464_2_2-D2.T0301_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    -       -      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    -       -      F     209           -
LGA    -       -      K     210           -
LGA    -       -      A     211           -
LGA    -       -      T     212           -
LGA    -       -      M     213           -
LGA    -       -      I     214           -
LGA    -       -      N     215           -
LGA    -       -      A     216           -
LGA    -       -      G     217           -
LGA    -       -      I     218           -
LGA    -       -      P     219           -
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    L     312      G     232          0.969
LGA    H     313      T     233          1.011
LGA    H     314      E     234          5.131
LGA    A     315      L     235          4.680
LGA    M     316      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    S     345      F     249          5.587
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     346      A     279          3.388
LGA    V     347      F     280          1.848
LGA    R     348      V     281          1.349
LGA    F     349      A     282          1.849
LGA    G     350      P     283          1.859
LGA    H     351      P     284          2.612
LGA    P     352      R     285          1.624
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    S     353      A     297          0.472
LGA    G     354      G     298          4.781
LGA    -       -      D     299           -
LGA    -       -      I     300           -
LGA    T     355      D     301          3.251
LGA    L     356      L     302          1.586
LGA    R     357      L     303          2.220
LGA    V     358      V     304          1.736
LGA    G     359      R     305          1.235
LGA    A     360      A     306          2.034
LGA    E     361      L     307          1.599
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    -       -      V     322           -
LGA    -       -      A     323           -
LGA    -       -      I     324           -
LGA    -       -      G     325           -
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    -       -      V     335           -
LGA    -       -      N     336           -
LGA    -       -      L     337           -
LGA    -       -      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    -       -      S     363           -
LGA    -       -      Q     364           -
LGA    -       -      A     365           -
LGA    -       -      N     366           -
LGA    -       -      G     367           -
LGA    -       -      E     368           -
LGA    -       -      W     369           -
LGA    -       -      T     370           -
LGA    -       -      V     371           -
LGA    -       -      T     372           -
LGA    -       -      K     373           -
LGA    -       -      A     374           -
LGA    -       -      I     375           -
LGA    -       -      M     376           -
LGA    -       -      S     377           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   22  191    5.0     21    2.82    23.81      8.138     0.720

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.366882 * X  +  -0.692536 * Y  +   0.621120 * Z  +  93.245766
  Y_new =   0.367220 * X  +   0.505642 * Y  +   0.780689 * Z  + -40.912384
  Z_new =  -0.854720 * X  +   0.514509 * Y  +   0.068802 * Z  +  31.612015 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.437861   -1.703732  [ DEG:    82.3834    -97.6166 ]
  Theta =   1.025012    2.116581  [ DEG:    58.7288    121.2712 ]
  Phi   =   2.355734   -0.785858  [ DEG:   134.9736    -45.0264 ]
 
# 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_2_2-D2                             
REMARK     2: T0301_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301TS464_2_2-D2.T0301_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   22  191   5.0   21   2.82   23.81   8.138
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS464_2_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM     16  CA  LEU   312     101.828   4.463  24.187  1.00  0.00
ATOM     17  CA  HIS   313     100.231   5.981  27.273  1.00  0.00
ATOM     18  CA  HIS   314      97.786   8.695  28.200  1.00  0.00
ATOM     19  CA  ALA   315      99.376  10.780  30.962  1.00  0.00
ATOM     20  CA  MET   316      96.605   9.642  33.338  1.00  0.00
ATOM     21  CA  SER   345     104.513   7.478  15.396  1.00  0.00
ATOM     22  CA  ALA   346     101.741   4.935  14.747  1.00  0.00
ATOM     23  CA  VAL   347     101.210   3.316  18.125  1.00  0.00
ATOM     24  CA  ARG   348      97.588   2.515  19.028  1.00  0.00
ATOM     25  CA  PHE   349      98.552   2.376  22.710  1.00  0.00
ATOM     26  CA  GLY   350      96.580   0.047  24.981  1.00  0.00
ATOM     27  CA  HIS   351      95.891   1.907  28.206  1.00  0.00
ATOM     28  CA  PRO   352      95.586   0.217  31.639  1.00  0.00
ATOM     29  CA  SER   353      91.807   0.631  31.482  1.00  0.00
ATOM     30  CA  GLY   354      91.403  -1.120  28.145  1.00  0.00
ATOM     31  CA  THR   355      91.036   2.059  26.124  1.00  0.00
ATOM     32  CA  LEU   356      93.359   2.968  23.231  1.00  0.00
ATOM     33  CA  ARG   357      95.202   6.243  22.537  1.00  0.00
ATOM     34  CA  VAL   358      97.176   7.331  19.472  1.00  0.00
ATOM     35  CA  GLY   359      99.734  10.105  20.170  1.00  0.00
ATOM     36  CA  ALA   360     101.428  11.945  17.244  1.00  0.00
ATOM     37  CA  GLU   361     102.448  15.455  16.025  1.00  0.00
TER
END
