
#######################################################
#                                                     #
#                        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   20 (   80),  selected   20 , name T0301AL044_4-D2
# Molecule2: number of CA atoms  191 ( 1389),  selected  191 , name T0301_D2.pdb
# PARAMETERS: T0301AL044_4-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    D     187      K     210           #
LGA    T     194      A     211          4.016
LGA    D     200      T     212          3.724
LGA    V     203      M     213          1.799
LGA    P     204      I     214          1.529
LGA    G     205      N     215          5.111
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    -       -      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    V     206      K     277          4.835
LGA    T     208      I     278          2.160
LGA    K     210      A     279          0.949
LGA    T     212      F     280          0.691
LGA    M     213      V     281          0.686
LGA    I     214      A     282          3.027
LGA    N     215      P     283          2.908
LGA    A     216      P     284          2.970
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    G     217      I     300          3.852
LGA    E     227      D     301          1.260
LGA    I     228      L     302          1.965
LGA    G     229      L     303          3.941
LGA    Y     230      V     304          3.818
LGA    R     231      R     305          3.724
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    -       -      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)   20  191    5.0     19    3.10     5.26      6.910     0.594

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.208362 * X  +   0.382376 * Y  +   0.900208 * Z  +  59.671410
  Y_new =  -0.942314 * X  +   0.325017 * Y  +   0.080053 * Z  +  16.994337
  Z_new =  -0.261973 * X  +  -0.864958 * Y  +   0.428039 * Z  +  45.451454 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.111264    2.030329  [ DEG:   -63.6707    116.3293 ]
  Theta =   0.265066    2.876527  [ DEG:    15.1872    164.8128 ]
  Phi   =  -1.353180    1.788413  [ DEG:   -77.5315    102.4685 ]
 
# 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: T0301AL044_4-D2                               
REMARK     2: T0301_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301AL044_4-D2.T0301_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   20  191   5.0   19   3.10    5.26   6.910
REMARK  ---------------------------------------------------------- 
MOLECULE T0301AL044_4-D2
REMARK Aligment from pdb entry: 1ym5_A
ATOM    277  N   ASP   187     103.098   0.385   7.648  1.00  0.00              
ATOM    278  CA  ASP   187     102.034  -0.141   6.802  1.00  0.00              
ATOM    279  C   ASP   187     100.636   0.167   7.372  1.00  0.00              
ATOM    280  O   ASP   187      99.807   0.755   6.690  1.00  0.00              
ATOM    281  N   THR   194     100.414  -0.212   8.632  1.00  0.00              
ATOM    282  CA  THR   194      99.224   0.231   9.383  1.00  0.00              
ATOM    283  C   THR   194      99.009   1.728   9.255  1.00  0.00              
ATOM    284  O   THR   194      97.889   2.181   8.994  1.00  0.00              
ATOM    285  N   ASP   200     100.088   2.495   9.396  1.00  0.00              
ATOM    286  CA  ASP   200     100.024   3.951   9.435  1.00  0.00              
ATOM    287  C   ASP   200      99.469   4.461   8.134  1.00  0.00              
ATOM    288  O   ASP   200      98.597   5.334   8.130  1.00  0.00              
ATOM    289  N   VAL   203      99.981   3.916   7.023  1.00  0.00              
ATOM    290  CA  VAL   203      99.678   4.440   5.675  1.00  0.00              
ATOM    291  C   VAL   203      98.230   4.153   5.320  1.00  0.00              
ATOM    292  O   VAL   203      97.540   4.973   4.707  1.00  0.00              
ATOM    293  N   PRO   204      97.782   2.976   5.728  1.00  0.00              
ATOM    294  CA  PRO   204      96.404   2.609   5.578  1.00  0.00              
ATOM    295  C   PRO   204      95.457   3.518   6.365  1.00  0.00              
ATOM    296  O   PRO   204      94.461   3.996   5.818  1.00  0.00              
ATOM    297  N   GLY   205      95.778   3.766   7.647  1.00  0.00              
ATOM    298  CA  GLY   205      94.959   4.684   8.445  1.00  0.00              
ATOM    299  C   GLY   205      94.909   6.060   7.862  1.00  0.00              
ATOM    300  O   GLY   205      93.873   6.724   7.903  1.00  0.00              
ATOM    301  N   VAL   206     103.198  13.066  12.697  1.00  0.00              
ATOM    302  CA  VAL   206     104.074  12.255  13.502  1.00  0.00              
ATOM    303  C   VAL   206     103.577  10.855  13.330  1.00  0.00              
ATOM    304  O   VAL   206     102.451  10.667  12.898  1.00  0.00              
ATOM    305  N   THR   208     104.414   9.865  13.622  1.00  0.00              
ATOM    306  CA  THR   208     103.915   8.499  13.587  1.00  0.00              
ATOM    307  C   THR   208     102.823   8.221  14.607  1.00  0.00              
ATOM    308  O   THR   208     103.103   8.331  15.819  1.00  0.00              
ATOM    309  N   LYS   210     101.612   7.823  14.142  1.00  0.00              
ATOM    310  CA  LYS   210     100.601   7.262  15.082  1.00  0.00              
ATOM    311  C   LYS   210     101.150   6.152  15.909  1.00  0.00              
ATOM    312  O   LYS   210     102.157   5.574  15.553  1.00  0.00              
ATOM    313  N   THR   212     100.473   5.811  16.986  1.00  0.00              
ATOM    314  CA  THR   212     100.895   4.672  17.773  1.00  0.00              
ATOM    315  C   THR   212      99.701   4.053  18.439  1.00  0.00              
ATOM    316  O   THR   212      98.623   4.652  18.460  1.00  0.00              
ATOM    317  N   MET   213      99.864   2.835  18.940  1.00  0.00              
ATOM    318  CA  MET   213      98.791   2.162  19.654  1.00  0.00              
ATOM    319  C   MET   213      98.888   2.489  21.159  1.00  0.00              
ATOM    320  O   MET   213      99.940   2.261  21.784  1.00  0.00              
ATOM    321  N   ILE   214      97.810   3.069  21.705  1.00  0.00              
ATOM    322  CA  ILE   214      97.679   3.391  23.131  1.00  0.00              
ATOM    323  C   ILE   214      96.613   2.537  23.807  1.00  0.00              
ATOM    324  O   ILE   214      95.487   2.417  23.364  1.00  0.00              
ATOM    325  N   ASN   215      97.054   1.882  24.868  1.00  0.00              
ATOM    326  CA  ASN   215      96.275   0.980  25.667  1.00  0.00              
ATOM    327  C   ASN   215      95.820   1.796  26.875  1.00  0.00              
ATOM    328  O   ASN   215      96.638   2.188  27.724  1.00  0.00              
ATOM    329  N   ALA   216      94.515   2.057  26.936  1.00  0.00              
ATOM    330  CA  ALA   216      93.970   3.031  27.876  1.00  0.00              
ATOM    331  C   ALA   216      92.636   2.497  28.355  1.00  0.00              
ATOM    332  O   ALA   216      91.752   3.236  28.747  1.00  0.00              
ATOM    333  N   GLY   217      92.522   1.178  28.379  1.00  0.00              
ATOM    334  CA  GLY   217      91.244   0.503  28.448  1.00  0.00              
ATOM    335  C   GLY   217      90.881  -0.046  27.068  1.00  0.00              
ATOM    336  O   GLY   217      91.051  -1.230  26.814  1.00  0.00              
ATOM    337  N   GLU   227      90.365   0.814  26.165  1.00  0.00              
ATOM    338  CA  GLU   227      90.240   0.498  24.760  1.00  0.00              
ATOM    339  C   GLU   227      91.557   0.533  24.059  1.00  0.00              
ATOM    340  O   GLU   227      92.517   1.145  24.550  1.00  0.00              
ATOM    341  N   ILE   228      91.606  -0.094  22.882  1.00  0.00              
ATOM    342  CA  ILE   228      92.819  -0.041  22.040  1.00  0.00              
ATOM    343  C   ILE   228      92.651   1.039  21.007  1.00  0.00              
ATOM    344  O   ILE   228      91.977   0.824  19.985  1.00  0.00              
ATOM    345  N   GLY   229      93.272   2.191  21.280  1.00  0.00              
ATOM    346  CA  GLY   229      93.126   3.381  20.463  1.00  0.00              
ATOM    347  C   GLY   229      94.420   3.622  19.668  1.00  0.00              
ATOM    348  O   GLY   229      95.520   3.603  20.213  1.00  0.00              
ATOM    349  N   TYR   230      94.287   3.906  18.386  1.00  0.00              
ATOM    350  CA  TYR   230      95.405   4.485  17.642  1.00  0.00              
ATOM    351  C   TYR   230      95.291   5.944  17.895  1.00  0.00              
ATOM    352  O   TYR   230      94.213   6.498  17.762  1.00  0.00              
ATOM    353  N   ARG   231      96.379   6.599  18.223  1.00  0.00              
ATOM    354  CA  ARG   231      96.376   8.044  18.253  1.00  0.00              
ATOM    355  C   ARG   231      97.150   8.598  17.067  1.00  0.00              
ATOM    356  O   ARG   231      98.248   8.153  16.801  1.00  0.00              
END
