
#######################################################
#                                                     #
#                        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   30 (   30),  selected   30 , name T0356TS464_2-D2
# Molecule2: number of CA atoms  192 ( 1487),  selected  192 , name T0356_D2.pdb
# PARAMETERS: T0356TS464_2-D2.T0356_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    -       -      T     122           -
LGA    -       -      K     123           -
LGA    -       -      R     124           -
LGA    -       -      L     125           -
LGA    -       -      R     126           -
LGA    -       -      G     127           -
LGA    T     122      A     128          1.487
LGA    K     123      P     129          2.389
LGA    R     124      C     130          1.257
LGA    L     125      Q     131          1.955
LGA    R     126      Q     132          3.494
LGA    G     127      K     133          2.445
LGA    A     128      -       -           -
LGA    P     129      I     134          2.874
LGA    C     130      V     135          2.246
LGA    Q     131      S     136          5.579
LGA    -       -      G     137           -
LGA    -       -      D     138           -
LGA    -       -      D     139           -
LGA    -       -      V     140           -
LGA    -       -      D     141           -
LGA    -       -      L     142           -
LGA    -       -      N     143           -
LGA    -       -      R     144           -
LGA    -       -      I     145           -
LGA    -       -      P     146           -
LGA    -       -      I     147           -
LGA    -       -      M     148           -
LGA    A     220      T     149           #
LGA    -       -      C     150           -
LGA    -       -      W     151           -
LGA    L     221      P     152          2.288
LGA    G     222      E     153          1.854
LGA    A     223      D     154          2.115
LGA    -       -      A     155           -
LGA    -       -      A     156           -
LGA    -       -      P     157           -
LGA    -       -      L     158           -
LGA    -       -      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    -       -      Q     182           -
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    -       -      H     196           -
LGA    -       -      R     197           -
LGA    -       -      G     198           -
LGA    -       -      G     199           -
LGA    -       -      A     200           -
LGA    -       -      L     201           -
LGA    -       -      D     202           -
LGA    -       -      Y     203           -
LGA    -       -      Q     204           -
LGA    -       -      E     205           -
LGA    -       -      W     206           -
LGA    -       -      C     207           -
LGA    -       -      A     208           -
LGA    -       -      A     209           -
LGA    -       -      H     210           -
LGA    -       -      P     211           -
LGA    -       -      G     212           -
LGA    -       -      E     213           -
LGA    -       -      R     214           -
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    D     224      Y     288          2.047
LGA    P     225      G     289           -
LGA    A     226      D     290           -
LGA    -       -      H     291           -
LGA    -       -      T     292           -
LGA    I     277      G     293           #
LGA    E     278      Y     294           -
LGA    Q     279      Y     295           -
LGA    G     280      N     296           -
LGA    E     281      E     297           -
LGA    V     306      V     298           -
LGA    T     307      D     299           -
LGA    -       -      S     300           -
LGA    -       -      F     301           -
LGA    H     308      P     302           #
LGA    I     309      V     303           -
LGA    T     310      F     304           -
LGA    Q     311      T     305           -
LGA    R     312      V     306           -
LGA    E     313      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)   30  192    5.0     13    2.68     0.00      4.873     0.468

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.292081 * X  +   0.911552 * Y  +   0.289416 * Z  +  33.089149
  Y_new =   0.819069 * X  +  -0.394650 * Y  +   0.416387 * Z  +  66.401871
  Z_new =   0.493776 * X  +   0.115433 * Y  +  -0.861893 * Z  +  71.823097 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.008455   -0.133138  [ DEG:   172.3718     -7.6282 ]
  Theta =  -0.516427   -2.625165  [ DEG:   -29.5891   -150.4109 ]
  Phi   =   1.228252   -1.913340  [ DEG:    70.3737   -109.6263 ]
 
# 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_2-D2                               
REMARK     2: T0356_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS464_2-D2.T0356_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   30  192   5.0   13   2.68    0.00   4.873
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS464_2-D2
PFRMAT TS
TARGET T0356
MODEL 2
PARENT N/A
ATOM     69  CA  THR   122      86.773  75.296  88.088  1.00  0.00
ATOM     70  CA  LYS   123      84.936  75.056  91.416  1.00  0.00
ATOM     71  CA  ARG   124      82.579  72.477  89.886  1.00  0.00
ATOM     72  CA  LEU   125      85.423  70.129  88.931  1.00  0.00
ATOM     73  CA  ARG   126      87.048  70.283  92.378  1.00  0.00
ATOM     74  CA  GLY   127      83.631  69.750  93.981  1.00  0.00
ATOM     75  CA  ALA   128      83.186  66.519  91.999  1.00  0.00
ATOM     76  CA  PRO   129      86.852  65.576  92.449  1.00  0.00
ATOM     77  CA  CYS   130      86.500  65.848  96.233  1.00  0.00
ATOM     78  CA  GLN   131      83.431  63.590  96.012  1.00  0.00
ATOM     79  CA  ALA   220      61.805  51.988  96.918  1.00  0.00
ATOM     80  CA  LEU   221      58.538  53.181  95.337  1.00  0.00
ATOM     81  CA  GLY   222      59.410  51.255  92.191  1.00  0.00
ATOM     82  CA  ALA   223      60.759  53.845  89.781  1.00  0.00
ATOM     83  CA  ASP   224      63.140  52.497  87.137  1.00  0.00
ATOM     84  CA  PRO   225      65.015  55.772  86.775  1.00  0.00
ATOM     85  CA  ALA   226      65.154  59.264  88.197  1.00  0.00
ATOM     86  CA  ILE   277      56.224  60.244  92.694  1.00  0.00
ATOM     87  CA  GLU   278      57.659  62.782  95.063  1.00  0.00
ATOM     88  CA  GLN   279      60.386  61.228  97.245  1.00  0.00
ATOM     89  CA  GLY   280      59.310  62.890 100.461  1.00  0.00
ATOM     90  CA  GLU   281      56.144  63.341 102.548  1.00  0.00
ATOM     91  CA  VAL   306      83.737  43.418  72.315  1.00  0.00
ATOM     92  CA  THR   307      80.413  43.866  74.096  1.00  0.00
ATOM     93  CA  HIS   308      78.980  46.184  71.462  1.00  0.00
ATOM     94  CA  ILE   309      80.067  47.454  68.000  1.00  0.00
ATOM     95  CA  THR   310      78.646  50.589  66.308  1.00  0.00
ATOM     96  CA  GLN   311      79.347  51.185  62.618  1.00  0.00
ATOM     97  CA  ARG   312      79.161  54.982  62.405  1.00  0.00
ATOM     98  CA  GLU   313      80.001  56.908  59.186  1.00  0.00
TER
END
