
#######################################################
#                                                     #
#                        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   32 (  128),  selected   32 , name T0320AL044_4-D2
# Molecule2: number of CA atoms   73 (  604),  selected   73 , name T0320_D2.pdb
# PARAMETERS: T0320AL044_4-D2.T0320_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    N     228      N     228          3.538
LGA    N     229      N     229          2.956
LGA    S     230      S     230          4.010
LGA    L     231      L     231          3.282
LGA    P     232      -       -           -
LGA    N     233      -       -           -
LGA    P     234      P     232          3.577
LGA    L     236      N     233          4.383
LGA    S     240      P     234          3.068
LGA    P     243      H     235          4.228
LGA    L     245      L     236          3.617
LGA    -       -      R     237           -
LGA    -       -      K     238           -
LGA    -       -      D     239           -
LGA    -       -      S     240           -
LGA    H     246      N     241          4.026
LGA    W     249      N     242           #
LGA    E     250      P     243          3.000
LGA    I     251      A     244          3.828
LGA    I     252      L     245          2.809
LGA    G     256      -       -           -
LGA    K     257      H     246          3.143
LGA    D     258      F     247          0.959
LGA    A     259      E     248          2.787
LGA    E     260      W     249          3.463
LGA    G     261      E     250          3.425
LGA    E     262      I     251          3.080
LGA    -       -      I     252           -
LGA    R     263      H     253          2.870
LGA    S     264      A     254          3.149
LGA    S     265      F     255          3.264
LGA    A     266      G     256          3.185
LGA    I     267      K     257           -
LGA    T     269      D     258           -
LGA    V     274      R     263           -
LGA    K     277      S     264           -
LGA    S     281      S     265           -
LGA    -       -      A     266           -
LGA    -       -      I     267           -
LGA    -       -      N     268           -
LGA    -       -      T     269           -
LGA    -       -      S     270           -
LGA    -       -      P     271           -
LGA    -       -      I     272           -
LGA    -       -      S     273           -
LGA    -       -      V     274           -
LGA    -       -      V     275           -
LGA    -       -      D     276           -
LGA    -       -      K     277           -
LGA    -       -      E     278           -
LGA    -       -      R     279           -
LGA    -       -      F     280           -
LGA    -       -      S     281           -
LGA    -       -      K     282           -
LGA    -       -      Y     283           -
LGA    -       -      H     284           -
LGA    -       -      D     285           -
LGA    -       -      N     286           -
LGA    -       -      Y     287           -
LGA    -       -      Y     288           -
LGA    -       -      P     289           -
LGA    -       -      G     290           -
LGA    -       -      W     291           -
LGA    -       -      Y     292           -
LGA    -       -      L     293           -
LGA    -       -      V     294           -
LGA    -       -      D     295           -
LGA    -       -      D     296           -
LGA    -       -      T     297           -
LGA    -       -      L     298           -
LGA    -       -      E     299           -
LGA    -       -      R     300           -
LGA    -       -      A     301           -
LGA    -       -      G     302           -
LGA    -       -      R     303           -
LGA    -       -      I     304           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   32   73    5.0     23    3.36    26.09     18.265     0.666

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.048339 * X  +  -0.155010 * Y  +  -0.986730 * Z  +  97.047920
  Y_new =   0.178532 * X  +  -0.973317 * Y  +   0.144157 * Z  +  76.525154
  Z_new =  -0.982746 * X  +  -0.169194 * Y  +   0.074723 * Z  +  42.320164 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.154916    1.986677  [ DEG:   -66.1718    113.8282 ]
  Theta =   1.384765    1.756827  [ DEG:    79.3412    100.6588 ]
  Phi   =   1.835213   -1.306380  [ DEG:   105.1500    -74.8500 ]
 
# 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: T0320AL044_4-D2                               
REMARK     2: T0320_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320AL044_4-D2.T0320_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   32   73   5.0   23   3.36   26.09  18.265
REMARK  ---------------------------------------------------------- 
MOLECULE T0320AL044_4-D2
REMARK Aligment from pdb entry: 2c5s_A
ATOM    753  N   ASN   228      29.151  19.926  10.887  1.00  0.00              
ATOM    754  CA  ASN   228      28.818  20.657   9.659  1.00  0.00              
ATOM    755  C   ASN   228      28.040  19.753   8.696  1.00  0.00              
ATOM    756  O   ASN   228      28.639  18.987   7.932  1.00  0.00              
ATOM    757  N   ASN   229      26.701  19.823   8.743  1.00  0.00              
ATOM    758  CA  ASN   229      25.880  18.980   7.876  1.00  0.00              
ATOM    759  C   ASN   229      26.038  19.313   6.393  1.00  0.00              
ATOM    760  O   ASN   229      26.081  20.489   6.019  1.00  0.00              
ATOM    761  N   SER   230      26.133  18.273   5.570  1.00  0.00              
ATOM    762  CA  SER   230      26.209  18.418   4.125  1.00  0.00              
ATOM    763  C   SER   230      24.881  17.993   3.489  1.00  0.00              
ATOM    764  O   SER   230      24.184  17.125   4.019  1.00  0.00              
ATOM    765  N   LEU   231      24.548  18.604   2.351  1.00  0.00              
ATOM    766  CA  LEU   231      23.353  18.256   1.563  1.00  0.00              
ATOM    767  C   LEU   231      23.340  16.796   1.028  1.00  0.00              
ATOM    768  O   LEU   231      22.314  16.115   1.082  1.00  0.00              
ATOM    769  N   PRO   232      24.489  16.325   0.554  1.00  0.00              
ATOM    770  CA  PRO   232      24.655  14.955   0.078  1.00  0.00              
ATOM    771  C   PRO   232      24.230  13.898   1.107  1.00  0.00              
ATOM    772  O   PRO   232      23.513  12.955   0.771  1.00  0.00              
ATOM    773  N   ASN   233      24.669  14.057   2.353  1.00  0.00              
ATOM    774  CA  ASN   233      24.325  13.099   3.395  1.00  0.00              
ATOM    775  C   ASN   233      22.879  13.273   3.836  1.00  0.00              
ATOM    776  O   ASN   233      22.183  12.280   4.064  1.00  0.00              
ATOM    777  N   PRO   234      22.417  14.516   3.943  1.00  0.00              
ATOM    778  CA  PRO   234      21.028  14.756   4.311  1.00  0.00              
ATOM    779  C   PRO   234      20.084  14.072   3.318  1.00  0.00              
ATOM    780  O   PRO   234      19.087  13.466   3.710  1.00  0.00              
ATOM    781  N   LEU   236      20.414  14.160   2.031  1.00  0.00              
ATOM    782  CA  LEU   236      19.585  13.564   0.988  1.00  0.00              
ATOM    783  C   LEU   236      19.661  12.041   0.994  1.00  0.00              
ATOM    784  O   LEU   236      18.634  11.364   0.918  1.00  0.00              
ATOM    785  N   SER   240      20.883  11.525   1.117  1.00  0.00              
ATOM    786  CA  SER   240      21.160  10.087   1.135  1.00  0.00              
ATOM    787  C   SER   240      20.452   9.372   2.284  1.00  0.00              
ATOM    788  O   SER   240      19.959   8.255   2.112  1.00  0.00              
ATOM    789  N   PRO   243      20.406  10.011   3.452  1.00  0.00              
ATOM    790  CA  PRO   243      19.702   9.432   4.596  1.00  0.00              
ATOM    791  C   PRO   243      18.180   9.498   4.399  1.00  0.00              
ATOM    792  O   PRO   243      17.484   8.516   4.635  1.00  0.00              
ATOM    793  N   LEU   245      17.675  10.645   3.947  1.00  0.00              
ATOM    794  CA  LEU   245      16.237  10.808   3.707  1.00  0.00              
ATOM    795  C   LEU   245      15.706   9.878   2.608  1.00  0.00              
ATOM    796  O   LEU   245      14.524   9.517   2.601  1.00  0.00              
ATOM    797  N   HIS   246      10.184   7.210   3.122  1.00  0.00              
ATOM    798  CA  HIS   246       9.293   8.214   2.534  1.00  0.00              
ATOM    799  C   HIS   246       8.498   8.981   3.613  1.00  0.00              
ATOM    800  O   HIS   246       7.550   8.456   4.207  1.00  0.00              
ATOM    801  N   TRP   249       8.896  10.231   3.840  1.00  0.00              
ATOM    802  CA  TRP   249       8.328  11.081   4.884  1.00  0.00              
ATOM    803  C   TRP   249       7.094  11.837   4.411  1.00  0.00              
ATOM    804  O   TRP   249       6.457  12.553   5.193  1.00  0.00              
ATOM    805  N   GLU   250       6.752  11.671   3.136  1.00  0.00              
ATOM    806  CA  GLU   250       5.609  12.378   2.544  1.00  0.00              
ATOM    807  C   GLU   250       4.273  12.160   3.276  1.00  0.00              
ATOM    808  O   GLU   250       3.554  13.133   3.524  1.00  0.00              
ATOM    809  N   ILE   251       3.847  11.339   6.448  1.00  0.00              
ATOM    810  CA  ILE   251       4.053  12.061   7.698  1.00  0.00              
ATOM    811  C   ILE   251       3.922  13.581   7.524  1.00  0.00              
ATOM    812  O   ILE   251       3.250  14.238   8.314  1.00  0.00              
ATOM    813  N   ILE   252       4.565  14.124   6.492  1.00  0.00              
ATOM    814  CA  ILE   252       4.491  15.549   6.175  1.00  0.00              
ATOM    815  C   ILE   252       3.041  15.982   5.937  1.00  0.00              
ATOM    816  O   ILE   252       2.581  16.975   6.514  1.00  0.00              
ATOM    817  N   GLY   256       2.322  15.223   5.110  1.00  0.00              
ATOM    818  CA  GLY   256       0.941  15.553   4.753  1.00  0.00              
ATOM    819  C   GLY   256      -0.024  15.454   5.946  1.00  0.00              
ATOM    820  O   GLY   256      -0.948  16.268   6.065  1.00  0.00              
ATOM    821  N   LYS   257       0.203  14.476   6.828  1.00  0.00              
ATOM    822  CA  LYS   257      -0.664  14.285   7.989  1.00  0.00              
ATOM    823  C   LYS   257      -0.455  15.398   9.011  1.00  0.00              
ATOM    824  O   LYS   257      -1.409  15.885   9.615  1.00  0.00              
ATOM    825  N   ASP   258       0.798  15.811   9.183  1.00  0.00              
ATOM    826  CA  ASP   258       1.139  16.900  10.091  1.00  0.00              
ATOM    827  C   ASP   258       0.451  18.196   9.668  1.00  0.00              
ATOM    828  O   ASP   258      -0.091  18.920  10.495  1.00  0.00              
ATOM    829  N   ALA   259       0.473  18.481   8.371  1.00  0.00              
ATOM    830  CA  ALA   259      -0.266  19.616   7.823  1.00  0.00              
ATOM    831  C   ALA   259      -1.765  19.459   8.122  1.00  0.00              
ATOM    832  O   ALA   259      -2.397  20.390   8.617  1.00  0.00              
ATOM    833  N   GLU   260      -2.309  18.275   7.847  1.00  0.00              
ATOM    834  CA  GLU   260      -3.735  17.984   8.078  1.00  0.00              
ATOM    835  C   GLU   260      -4.146  18.045   9.542  1.00  0.00              
ATOM    836  O   GLU   260      -5.325  18.251   9.831  1.00  0.00              
ATOM    837  N   GLY   261      -3.174  17.862  10.443  1.00  0.00              
ATOM    838  CA  GLY   261      -3.420  17.732  11.883  1.00  0.00              
ATOM    839  C   GLY   261      -3.176  19.022  12.678  1.00  0.00              
ATOM    840  O   GLY   261      -3.486  19.094  13.873  1.00  0.00              
ATOM    841  N   GLU   262      -2.639  20.044  12.020  1.00  0.00              
ATOM    842  CA  GLU   262      -2.390  21.321  12.697  1.00  0.00              
ATOM    843  C   GLU   262      -3.659  21.889  13.336  1.00  0.00              
ATOM    844  O   GLU   262      -4.755  21.783  12.790  1.00  0.00              
ATOM    845  N   ARG   263      -3.500  22.477  14.508  1.00  0.00              
ATOM    846  CA  ARG   263      -4.601  23.138  15.166  1.00  0.00              
ATOM    847  C   ARG   263      -4.369  24.628  15.071  1.00  0.00              
ATOM    848  O   ARG   263      -3.221  25.079  15.022  1.00  0.00              
ATOM    849  N   SER   264      -5.455  25.391  15.012  1.00  0.00              
ATOM    850  CA  SER   264      -5.351  26.825  14.843  1.00  0.00              
ATOM    851  C   SER   264      -6.065  27.554  15.969  1.00  0.00              
ATOM    852  O   SER   264      -7.249  27.356  16.193  1.00  0.00              
ATOM    853  N   SER   265      -5.309  28.392  16.675  1.00  0.00              
ATOM    854  CA  SER   265      -5.860  29.327  17.655  1.00  0.00              
ATOM    855  C   SER   265      -5.788  30.715  17.060  1.00  0.00              
ATOM    856  O   SER   265      -4.875  31.012  16.295  1.00  0.00              
ATOM    857  N   ALA   266      -6.744  31.565  17.412  1.00  0.00              
ATOM    858  CA  ALA   266      -6.746  32.955  16.973  1.00  0.00              
ATOM    859  C   ALA   266      -6.776  33.857  18.191  1.00  0.00              
ATOM    860  O   ALA   266      -7.734  33.850  18.941  1.00  0.00              
ATOM    861  N   ILE   267      -5.704  34.622  18.382  1.00  0.00              
ATOM    862  CA  ILE   267      -5.546  35.450  19.568  1.00  0.00              
ATOM    863  C   ILE   267      -5.743  36.944  19.292  1.00  0.00              
ATOM    864  O   ILE   267      -5.377  37.454  18.237  1.00  0.00              
ATOM    865  N   THR   269      -6.326  37.629  20.264  1.00  0.00              
ATOM    866  CA  THR   269      -6.647  39.045  20.182  1.00  0.00              
ATOM    867  C   THR   269      -6.212  39.657  21.476  1.00  0.00              
ATOM    868  O   THR   269      -6.082  38.948  22.464  1.00  0.00              
ATOM    869  N   VAL   274      -6.011  40.969  21.488  1.00  0.00              
ATOM    870  CA  VAL   274      -5.788  41.666  22.740  1.00  0.00              
ATOM    871  C   VAL   274      -7.121  41.828  23.441  1.00  0.00              
ATOM    872  O   VAL   274      -8.071  42.404  22.899  1.00  0.00              
ATOM    873  N   LYS   277      -7.161  41.291  24.656  1.00  0.00              
ATOM    874  CA  LYS   277      -8.379  41.162  25.429  1.00  0.00              
ATOM    875  C   LYS   277      -8.525  42.349  26.403  1.00  0.00              
ATOM    876  O   LYS   277      -8.461  42.192  27.633  1.00  0.00              
ATOM    877  N   SER   281      -8.715  43.533  25.815  1.00  0.00              
ATOM    878  CA  SER   281      -8.966  44.799  26.522  1.00  0.00              
ATOM    879  C   SER   281      -9.178  44.703  28.047  1.00  0.00              
ATOM    880  O   SER   281     -10.308  44.644  28.545  1.00  0.00              
END
