
#######################################################
#                                                     #
#                        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   27 (  108),  selected   27 , name T0301AL044_1-D2
# Molecule2: number of CA atoms  191 ( 1389),  selected  191 , name T0301_D2.pdb
# PARAMETERS: T0301AL044_1-D2.T0301_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    T     194      D     187           -
LGA    G     195      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    N     196      F     209          5.145
LGA    L     197      K     210          4.157
LGA    V     198      A     211          1.567
LGA    D     199      T     212          1.559
LGA    D     200      M     213          2.541
LGA    V     203      I     214          2.014
LGA    P     204      N     215          2.063
LGA    G     205      A     216          4.041
LGA    -       -      G     217           -
LGA    V     206      I     218          2.633
LGA    T     208      P     219          2.640
LGA    K     210      T     220          4.320
LGA    T     212      V     221          1.004
LGA    M     213      F     222          1.847
LGA    I     214      V     223          2.667
LGA    N     215      N     224          2.533
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     216      A     282          1.806
LGA    G     217      P     283          2.892
LGA    I     218      P     284          2.012
LGA    P     219      R     285          0.889
LGA    T     220      D     286          4.391
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    E     227      I     300          2.813
LGA    I     228      D     301          3.346
LGA    G     229      L     302          2.539
LGA    -       -      L     303           -
LGA    Y     230      V     304          2.931
LGA    R     231      R     305          3.136
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)   27  191    5.0     25    2.90    12.00      8.730     0.834

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.198886 * X  +  -0.890131 * Y  +   0.410014 * Z  + 107.436722
  Y_new =  -0.974847 * X  +  -0.222630 * Y  +  -0.010455 * Z  +  30.368765
  Z_new =   0.100588 * X  +  -0.397621 * Y  +  -0.912019 * Z  +  63.314953 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.730459    0.411133  [ DEG:  -156.4438     23.5562 ]
  Theta =  -0.100759   -3.040834  [ DEG:    -5.7730   -174.2270 ]
  Phi   =  -1.369541    1.772052  [ DEG:   -78.4689    101.5311 ]
 
# 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_1-D2                               
REMARK     2: T0301_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301AL044_1-D2.T0301_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   27  191   5.0   25   2.90   12.00   8.730
REMARK  ---------------------------------------------------------- 
MOLECULE T0301AL044_1-D2
REMARK Aligment from pdb entry: 2azp_A
ATOM    281  N   THR   194     101.179  -3.996  21.427  1.00  0.00              
ATOM    282  CA  THR   194     101.968  -4.081  20.205  1.00  0.00              
ATOM    283  C   THR   194     102.682  -2.764  19.966  1.00  0.00              
ATOM    284  O   THR   194     102.173  -1.699  20.306  1.00  0.00              
ATOM    285  N   GLY   195     103.868  -2.841  19.377  1.00  0.00              
ATOM    286  CA  GLY   195     104.661  -1.648  19.121  1.00  0.00              
ATOM    287  C   GLY   195     104.802  -1.317  17.644  1.00  0.00              
ATOM    288  O   GLY   195     104.755  -2.197  16.791  1.00  0.00              
ATOM    289  N   ASN   196     104.989  -0.032  17.364  1.00  0.00              
ATOM    290  CA  ASN   196     105.167   0.464  16.007  1.00  0.00              
ATOM    291  C   ASN   196     104.343  -0.280  14.964  1.00  0.00              
ATOM    292  O   ASN   196     104.880  -0.859  14.023  1.00  0.00              
ATOM    293  N   LEU   197     103.030  -0.252  15.144  1.00  0.00              
ATOM    294  CA  LEU   197     102.110  -0.901  14.226  1.00  0.00              
ATOM    295  C   LEU   197     101.747   0.101  13.139  1.00  0.00              
ATOM    296  O   LEU   197     101.246   1.187  13.431  1.00  0.00              
ATOM    297  N   VAL   198     102.012  -0.259  11.887  1.00  0.00              
ATOM    298  CA  VAL   198     101.712   0.622  10.764  1.00  0.00              
ATOM    299  C   VAL   198     100.335   0.336  10.193  1.00  0.00              
ATOM    300  O   VAL   198      99.943  -0.820  10.043  1.00  0.00              
ATOM    301  N   ASP   199      99.604   1.396   9.873  1.00  0.00              
ATOM    302  CA  ASP   199      98.266   1.256   9.315  1.00  0.00              
ATOM    303  C   ASP   199      98.051   2.233   8.169  1.00  0.00              
ATOM    304  O   ASP   199      98.412   3.408   8.267  1.00  0.00              
ATOM    305  N   ASP   200      97.471   1.742   7.080  1.00  0.00              
ATOM    306  CA  ASP   200      97.182   2.592   5.936  1.00  0.00              
ATOM    307  C   ASP   200      95.846   3.256   6.216  1.00  0.00              
ATOM    308  O   ASP   200      94.807   2.596   6.214  1.00  0.00              
ATOM    309  N   VAL   203      95.870   4.560   6.466  1.00  0.00              
ATOM    310  CA  VAL   203      94.645   5.291   6.764  1.00  0.00              
ATOM    311  C   VAL   203      94.187   6.161   5.597  1.00  0.00              
ATOM    312  O   VAL   203      94.912   7.041   5.138  1.00  0.00              
ATOM    313  N   PRO   204      92.970   5.916   5.097  1.00  0.00              
ATOM    314  CA  PRO   204      92.427   6.692   3.980  1.00  0.00              
ATOM    315  C   PRO   204      92.423   8.191   4.263  1.00  0.00              
ATOM    316  O   PRO   204      91.977   8.632   5.327  1.00  0.00              
ATOM    317  N   GLY   205      92.925   8.968   3.309  1.00  0.00              
ATOM    318  CA  GLY   205      92.959  10.410   3.466  1.00  0.00              
ATOM    319  C   GLY   205      94.188  10.923   4.186  1.00  0.00              
ATOM    320  O   GLY   205      94.452  12.126   4.199  1.00  0.00              
ATOM    321  N   VAL   206      94.946  10.015   4.790  1.00  0.00              
ATOM    322  CA  VAL   206      96.149  10.400   5.513  1.00  0.00              
ATOM    323  C   VAL   206      97.361   9.645   4.989  1.00  0.00              
ATOM    324  O   VAL   206      98.422  10.226   4.770  1.00  0.00              
ATOM    325  N   THR   208      97.194   8.343   4.790  1.00  0.00              
ATOM    326  CA  THR   208      98.287   7.521   4.314  1.00  0.00              
ATOM    327  C   THR   208      98.751   6.597   5.423  1.00  0.00              
ATOM    328  O   THR   208      97.968   6.225   6.300  1.00  0.00              
ATOM    329  N   LYS   210     100.028   6.234   5.393  1.00  0.00              
ATOM    330  CA  LYS   210     100.596   5.345   6.395  1.00  0.00              
ATOM    331  C   LYS   210     100.796   6.013   7.749  1.00  0.00              
ATOM    332  O   LYS   210     101.448   7.052   7.860  1.00  0.00              
ATOM    333  N   THR   212     100.224   5.393   8.775  1.00  0.00              
ATOM    334  CA  THR   212     100.313   5.878  10.147  1.00  0.00              
ATOM    335  C   THR   212     100.757   4.720  11.031  1.00  0.00              
ATOM    336  O   THR   212     100.264   3.604  10.884  1.00  0.00              
ATOM    337  N   MET   213     101.688   4.973  11.943  1.00  0.00              
ATOM    338  CA  MET   213     102.141   3.910  12.833  1.00  0.00              
ATOM    339  C   MET   213     102.112   4.373  14.284  1.00  0.00              
ATOM    340  O   MET   213     102.283   5.557  14.573  1.00  0.00              
ATOM    341  N   ILE   214     101.888   3.434  15.195  1.00  0.00              
ATOM    342  CA  ILE   214     101.850   3.784  16.600  1.00  0.00              
ATOM    343  C   ILE   214     101.770   2.561  17.482  1.00  0.00              
ATOM    344  O   ILE   214     101.748   1.430  16.991  1.00  0.00              
ATOM    345  N   ASN   215     101.729   2.783  18.790  1.00  0.00              
ATOM    346  CA  ASN   215     101.641   1.684  19.734  1.00  0.00              
ATOM    347  C   ASN   215     100.201   1.439  20.135  1.00  0.00              
ATOM    348  O   ASN   215      99.379   2.353  20.126  1.00  0.00              
ATOM    349  N   ALA   216      99.905   0.192  20.477  1.00  0.00              
ATOM    350  CA  ALA   216      98.582  -0.195  20.932  1.00  0.00              
ATOM    351  C   ALA   216      98.799  -0.581  22.387  1.00  0.00              
ATOM    352  O   ALA   216      99.474  -1.570  22.675  1.00  0.00              
ATOM    353  N   GLY   217      98.243   0.205  23.306  1.00  0.00              
ATOM    354  CA  GLY   217      98.429  -0.069  24.722  1.00  0.00              
ATOM    355  C   GLY   217      97.148   0.000  25.543  1.00  0.00              
ATOM    356  O   GLY   217      96.195   0.687  25.185  1.00  0.00              
ATOM    357  N   ILE   218      97.147  -0.719  26.658  1.00  0.00              
ATOM    358  CA  ILE   218      96.005  -0.745  27.553  1.00  0.00              
ATOM    359  C   ILE   218      96.292   0.097  28.789  1.00  0.00              
ATOM    360  O   ILE   218      97.366  -0.009  29.387  1.00  0.00              
ATOM    361  N   PRO   219      95.326   0.934  29.159  1.00  0.00              
ATOM    362  CA  PRO   219      95.465   1.775  30.335  1.00  0.00              
ATOM    363  C   PRO   219      94.141   1.881  31.071  1.00  0.00              
ATOM    364  O   PRO   219      93.932   2.794  31.865  1.00  0.00              
ATOM    365  N   THR   220      93.251   0.928  30.818  1.00  0.00              
ATOM    366  CA  THR   220      91.938   0.947  31.441  1.00  0.00              
ATOM    367  C   THR   220      90.927   0.979  30.313  1.00  0.00              
ATOM    368  O   THR   220      89.723   0.804  30.514  1.00  0.00              
ATOM    369  N   GLU   227      91.459   1.228  29.117  1.00  0.00              
ATOM    370  CA  GLU   227      90.726   1.269  27.852  1.00  0.00              
ATOM    371  C   GLU   227      91.846   1.066  26.833  1.00  0.00              
ATOM    372  O   GLU   227      93.019   1.257  27.168  1.00  0.00              
ATOM    373  N   ILE   228      91.499   0.685  25.608  1.00  0.00              
ATOM    374  CA  ILE   228      92.506   0.490  24.572  1.00  0.00              
ATOM    375  C   ILE   228      92.801   1.794  23.848  1.00  0.00              
ATOM    376  O   ILE   228      91.887   2.524  23.449  1.00  0.00              
ATOM    377  N   GLY   229      94.089   2.081  23.685  1.00  0.00              
ATOM    378  CA  GLY   229      94.530   3.289  23.011  1.00  0.00              
ATOM    379  C   GLY   229      95.513   2.973  21.901  1.00  0.00              
ATOM    380  O   GLY   229      96.234   1.974  21.944  1.00  0.00              
ATOM    381  N   TYR   230      95.526   3.841  20.901  1.00  0.00              
ATOM    382  CA  TYR   230      96.464   3.737  19.801  1.00  0.00              
ATOM    383  C   TYR   230      97.225   5.050  19.918  1.00  0.00              
ATOM    384  O   TYR   230      96.653   6.120  19.706  1.00  0.00              
ATOM    385  N   ARG   231      98.496   4.974  20.296  1.00  0.00              
ATOM    386  CA  ARG   231      99.317   6.170  20.440  1.00  0.00              
ATOM    387  C   ARG   231     100.087   6.386  19.146  1.00  0.00              
ATOM    388  O   ARG   231     101.063   5.690  18.863  1.00  0.00              
END
