
#######################################################
#                                                     #
#                        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   15 (   60),  selected   15 , name T0295AL044_5-D2
# Molecule2: number of CA atoms   95 (  803),  selected   95 , name T0295_D2.pdb
# PARAMETERS: T0295AL044_5-D2.T0295_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     181           -
LGA    -       -      N     182           -
LGA    -       -      F     183           -
LGA    -       -      D     184           -
LGA    -       -      E     185           -
LGA    -       -      W     186           -
LGA    -       -      D     187           -
LGA    -       -      N     188           -
LGA    -       -      L     189           -
LGA    -       -      L     190           -
LGA    -       -      R     191           -
LGA    -       -      I     192           -
LGA    -       -      C     193           -
LGA    -       -      F     194           -
LGA    -       -      S     195           -
LGA    -       -      R     196           -
LGA    -       -      K     197           -
LGA    -       -      R     198           -
LGA    -       -      K     199           -
LGA    T     181      T     200          1.984
LGA    D     184      L     201          3.713
LGA    -       -      H     202           -
LGA    -       -      A     203           -
LGA    -       -      I     204           -
LGA    E     185      F     205          0.821
LGA    -       -      K     206           -
LGA    -       -      R     207           -
LGA    -       -      N     208           -
LGA    -       -      A     209           -
LGA    W     186      V     210          3.577
LGA    N     188      L     211          1.337
LGA    -       -      N     212           -
LGA    -       -      M     213           -
LGA    -       -      L     214           -
LGA    L     189      E     215          2.764
LGA    L     190      H     216           -
LGA    -       -      N     217           -
LGA    -       -      Y     218           -
LGA    -       -      K     219           -
LGA    -       -      N     220           -
LGA    -       -      W     221           -
LGA    -       -      C     222           -
LGA    -       -      T     223           -
LGA    -       -      L     224           -
LGA    -       -      N     225           -
LGA    -       -      K     226           -
LGA    -       -      Q     227           -
LGA    -       -      V     228           -
LGA    -       -      P     229           -
LGA    -       -      V     230           -
LGA    -       -      N     231           -
LGA    -       -      F     232           -
LGA    R     191      P     233          2.908
LGA    I     192      F     234          0.674
LGA    C     193      K     235          2.603
LGA    -       -      K     236           -
LGA    -       -      Y     237           -
LGA    F     194      C     238          2.745
LGA    S     195      L     239           #
LGA    -       -      D     240           -
LGA    -       -      V     241           -
LGA    -       -      L     242           -
LGA    -       -      E     243           -
LGA    -       -      H     244           -
LGA    -       -      L     245           -
LGA    -       -      D     246           -
LGA    -       -      M     247           -
LGA    R     196      C     248          1.574
LGA    K     197      E     249          2.212
LGA    R     198      K     250          4.941
LGA    -       -      R     251           -
LGA    -       -      S     252           -
LGA    -       -      I     253           -
LGA    -       -      N     254           -
LGA    -       -      L     255           -
LGA    -       -      D     256           -
LGA    -       -      E     257           -
LGA    -       -      N     258           -
LGA    -       -      D     259           -
LGA    -       -      F     260           -
LGA    -       -      L     261           -
LGA    -       -      K     262           -
LGA    -       -      L     263           -
LGA    -       -      L     264           -
LGA    -       -      L     265           -
LGA    -       -      E     266           -
LGA    -       -      F     267           -
LGA    -       -      N     268           -
LGA    -       -      K     269           -
LGA    -       -      K     270           -
LGA    -       -      G     271           -
LGA    -       -      I     272           -
LGA    -       -      H     273           -
LGA    -       -      F     274           -
LGA    -       -      F     275           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   15   95    5.0     13    2.71     7.69      9.651     0.462

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.338689 * X  +  -0.554031 * Y  +  -0.760486 * Z  + 102.072624
  Y_new =  -0.939767 * X  +  -0.238813 * Y  +  -0.244553 * Z  +  69.477859
  Z_new =  -0.046124 * X  +   0.797507 * Y  +  -0.601544 * Z  +  42.807468 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.217031   -0.924562  [ DEG:   127.0265    -52.9735 ]
  Theta =   0.046141    3.095452  [ DEG:     2.6437    177.3563 ]
  Phi   =  -1.224890    1.916703  [ DEG:   -70.1810    109.8190 ]
 
# 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: T0295AL044_5-D2                               
REMARK     2: T0295_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0295AL044_5-D2.T0295_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   15   95   5.0   13   2.71    7.69   9.651
REMARK  ---------------------------------------------------------- 
MOLECULE T0295AL044_5-D2
REMARK Aligment from pdb entry: 1ve3_A
ATOM    645  N   THR   181      19.017  16.522 -13.804  1.00  0.00              
ATOM    646  CA  THR   181      17.839  16.234 -12.995  1.00  0.00              
ATOM    647  C   THR   181      17.290  17.532 -12.399  1.00  0.00              
ATOM    648  O   THR   181      16.103  17.815 -12.508  1.00  0.00              
ATOM    649  N   ASP   184      18.165  18.324 -11.780  1.00  0.00              
ATOM    650  CA  ASP   184      17.756  19.582 -11.162  1.00  0.00              
ATOM    651  C   ASP   184      18.916  20.574 -11.087  1.00  0.00              
ATOM    652  O   ASP   184      20.062  20.224 -11.363  1.00  0.00              
ATOM    653  N   GLU   185      18.608  21.809 -10.700  1.00  0.00              
ATOM    654  CA  GLU   185      19.625  22.844 -10.582  1.00  0.00              
ATOM    655  C   GLU   185      19.179  23.925  -9.606  1.00  0.00              
ATOM    656  O   GLU   185      18.072  24.451  -9.715  1.00  0.00              
ATOM    657  N   TRP   186      20.043  24.245  -8.648  1.00  0.00              
ATOM    658  CA  TRP   186      19.742  25.258  -7.644  1.00  0.00              
ATOM    659  C   TRP   186      20.756  26.393  -7.736  1.00  0.00              
ATOM    660  O   TRP   186      21.965  26.149  -7.759  1.00  0.00              
ATOM    661  N   ASN   188      20.271  27.630  -7.779  1.00  0.00              
ATOM    662  CA  ASN   188      21.170  28.774  -7.831  1.00  0.00              
ATOM    663  C   ASN   188      21.534  29.143  -6.396  1.00  0.00              
ATOM    664  O   ASN   188      20.661  29.319  -5.553  1.00  0.00              
ATOM    665  N   LEU   189      23.705  31.819  -3.977  1.00  0.00              
ATOM    666  CA  LEU   189      24.389  33.094  -3.944  1.00  0.00              
ATOM    667  C   LEU   189      24.176  33.853  -5.237  1.00  0.00              
ATOM    668  O   LEU   189      23.173  33.654  -5.924  1.00  0.00              
ATOM    669  N   LEU   190      25.126  34.714  -5.578  1.00  0.00              
ATOM    670  CA  LEU   190      25.023  35.515  -6.789  1.00  0.00              
ATOM    671  C   LEU   190      25.433  34.791  -8.060  1.00  0.00              
ATOM    672  O   LEU   190      24.891  35.067  -9.129  1.00  0.00              
ATOM    673  N   ARG   191      26.378  33.862  -7.957  1.00  0.00              
ATOM    674  CA  ARG   191      26.808  33.138  -9.145  1.00  0.00              
ATOM    675  C   ARG   191      27.293  31.712  -8.938  1.00  0.00              
ATOM    676  O   ARG   191      28.179  31.247  -9.648  1.00  0.00              
ATOM    677  N   ILE   192      26.703  31.011  -7.979  1.00  0.00              
ATOM    678  CA  ILE   192      27.083  29.627  -7.721  1.00  0.00              
ATOM    679  C   ILE   192      25.915  28.701  -8.015  1.00  0.00              
ATOM    680  O   ILE   192      24.749  29.105  -7.926  1.00  0.00              
ATOM    681  N   CYS   193      26.228  27.459  -8.371  1.00  0.00              
ATOM    682  CA  CYS   193      25.191  26.489  -8.721  1.00  0.00              
ATOM    683  C   CYS   193      25.380  25.092  -8.179  1.00  0.00              
ATOM    684  O   CYS   193      26.494  24.568  -8.145  1.00  0.00              
ATOM    685  N   PHE   194      24.275  24.488  -7.752  1.00  0.00              
ATOM    686  CA  PHE   194      24.276  23.116  -7.280  1.00  0.00              
ATOM    687  C   PHE   194      23.511  22.406  -8.381  1.00  0.00              
ATOM    688  O   PHE   194      22.345  22.715  -8.616  1.00  0.00              
ATOM    689  N   SER   195      22.258  18.675 -10.244  1.00  0.00              
ATOM    690  CA  SER   195      22.042  17.245 -10.069  1.00  0.00              
ATOM    691  C   SER   195      21.992  16.584 -11.449  1.00  0.00              
ATOM    692  O   SER   195      21.148  16.915 -12.276  1.00  0.00              
ATOM    693  N   ARG   196      22.903  15.647 -11.686  1.00  0.00              
ATOM    694  CA  ARG   196      22.992  14.961 -12.973  1.00  0.00              
ATOM    695  C   ARG   196      22.744  13.457 -12.901  1.00  0.00              
ATOM    696  O   ARG   196      23.030  12.816 -11.894  1.00  0.00              
ATOM    697  N   LYS   197      22.219  12.905 -13.990  1.00  0.00              
ATOM    698  CA  LYS   197      21.970  11.472 -14.092  1.00  0.00              
ATOM    699  C   LYS   197      22.832  10.996 -15.260  1.00  0.00              
ATOM    700  O   LYS   197      22.848  11.623 -16.317  1.00  0.00              
ATOM    701  N   ARG   198      23.559   9.884 -15.079  1.00  0.00              
ATOM    702  CA  ARG   198      24.430   9.317 -16.110  1.00  0.00              
ATOM    703  C   ARG   198      23.686   8.736 -17.307  1.00  0.00              
ATOM    704  O   ARG   198      22.552   8.279 -17.181  1.00  0.00              
END
