
#######################################################
#                                                     #
#                        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   12 (   48),  selected   12 , name T0356AL243_4-D2
# Molecule2: number of CA atoms  192 ( 1487),  selected  192 , name T0356_D2.pdb
# PARAMETERS: T0356AL243_4-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    -       -      A     128           -
LGA    -       -      P     129           -
LGA    -       -      C     130           -
LGA    -       -      Q     131           -
LGA    -       -      Q     132           -
LGA    -       -      K     133           -
LGA    -       -      I     134           -
LGA    -       -      V     135           -
LGA    -       -      S     136           -
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    -       -      T     149           -
LGA    -       -      C     150           -
LGA    -       -      W     151           -
LGA    -       -      P     152           -
LGA    -       -      E     153           -
LGA    -       -      D     154           -
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    Q     132      L     194          2.381
LGA    K     133      S     195          3.387
LGA    -       -      H     196           -
LGA    I     134      R     197          2.954
LGA    V     135      G     198          2.083
LGA    -       -      G     199           -
LGA    -       -      A     200           -
LGA    S     136      L     201          1.178
LGA    V     140      D     202          1.903
LGA    -       -      Y     203           -
LGA    -       -      Q     204           -
LGA    -       -      E     205           -
LGA    D     141      W     206          1.578
LGA    L     142      C     207          1.766
LGA    N     143      A     208          2.166
LGA    -       -      A     209           -
LGA    R     144      H     210          2.155
LGA    -       -      P     211           -
LGA    -       -      G     212           -
LGA    P     146      E     213          2.779
LGA    I     147      R     214          4.049
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    -       -      Y     288           -
LGA    -       -      G     289           -
LGA    -       -      D     290           -
LGA    -       -      H     291           -
LGA    -       -      T     292           -
LGA    -       -      G     293           -
LGA    -       -      Y     294           -
LGA    -       -      Y     295           -
LGA    -       -      N     296           -
LGA    -       -      E     297           -
LGA    -       -      V     298           -
LGA    -       -      D     299           -
LGA    -       -      S     300           -
LGA    -       -      F     301           -
LGA    -       -      P     302           -
LGA    -       -      V     303           -
LGA    -       -      F     304           -
LGA    -       -      T     305           -
LGA    -       -      V     306           -
LGA    -       -      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)   12  192    5.0     12    2.49     0.00      4.713     0.464

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.554534 * X  +   0.830382 * Y  +   0.054377 * Z  +  69.218346
  Y_new =   0.651762 * X  +  -0.392764 * Y  +  -0.648801 * Z  +  37.908787
  Z_new =  -0.517395 * X  +   0.395223 * Y  +  -0.759013 * Z  +  73.509315 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.661517   -0.480076  [ DEG:   152.4937    -27.5063 ]
  Theta =   0.543804    2.597788  [ DEG:    31.1577    148.8423 ]
  Phi   =   0.865824   -2.275768  [ DEG:    49.6081   -130.3919 ]
 
# 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: T0356AL243_4-D2                               
REMARK     2: T0356_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356AL243_4-D2.T0356_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   12  192   5.0   12   2.49    0.00   4.713
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL243_4-D2
REMARK Aligment from pdb entry: 1f1zA
ATOM    381  N   GLN   132      72.711  51.601  75.743  1.00  0.00              
ATOM    382  CA  GLN   132      71.533  51.633  74.887  1.00  0.00              
ATOM    383  C   GLN   132      71.865  51.825  73.420  1.00  0.00              
ATOM    384  O   GLN   132      70.978  51.768  72.574  1.00  0.00              
ATOM    385  N   LYS   133      73.134  52.100  73.123  1.00  0.00              
ATOM    386  CA  LYS   133      73.561  52.241  71.735  1.00  0.00              
ATOM    387  C   LYS   133      73.625  53.628  71.131  1.00  0.00              
ATOM    388  O   LYS   133      73.971  53.785  69.953  1.00  0.00              
ATOM    389  N   ILE   134      73.327  54.640  71.935  1.00  0.00              
ATOM    390  CA  ILE   134      73.358  56.017  71.459  1.00  0.00              
ATOM    391  C   ILE   134      74.808  56.502  71.359  1.00  0.00              
ATOM    392  O   ILE   134      75.127  57.402  70.569  1.00  0.00              
ATOM    393  N   VAL   135      75.679  55.849  72.127  1.00  0.00              
ATOM    394  CA  VAL   135      77.112  56.137  72.155  1.00  0.00              
ATOM    395  C   VAL   135      77.830  54.824  71.797  1.00  0.00              
ATOM    396  O   VAL   135      77.503  53.780  72.363  1.00  0.00              
ATOM    397  N   SER   136      78.762  54.869  70.844  1.00  0.00              
ATOM    398  CA  SER   136      79.543  53.692  70.429  1.00  0.00              
ATOM    399  C   SER   136      80.993  53.973  70.804  1.00  0.00              
ATOM    400  O   SER   136      81.451  55.109  70.692  1.00  0.00              
ATOM    401  N   VAL   140      81.725  52.951  71.229  1.00  0.00              
ATOM    402  CA  VAL   140      83.130  53.124  71.586  1.00  0.00              
ATOM    403  C   VAL   140      83.979  51.953  71.078  1.00  0.00              
ATOM    404  O   VAL   140      83.462  51.014  70.465  1.00  0.00              
ATOM    405  N   ASP   141      85.277  51.999  71.348  1.00  0.00              
ATOM    406  CA  ASP   141      86.163  50.934  70.922  1.00  0.00              
ATOM    407  C   ASP   141      86.004  49.770  71.898  1.00  0.00              
ATOM    408  O   ASP   141      86.680  49.710  72.919  1.00  0.00              
ATOM    409  N   LEU   142      85.082  48.866  71.585  1.00  0.00              
ATOM    410  CA  LEU   142      84.797  47.699  72.421  1.00  0.00              
ATOM    411  C   LEU   142      85.984  46.764  72.659  1.00  0.00              
ATOM    412  O   LEU   142      85.972  45.967  73.592  1.00  0.00              
ATOM    413  N   ASN   143      86.991  46.830  71.798  1.00  0.00              
ATOM    414  CA  ASN   143      88.165  45.977  71.946  1.00  0.00              
ATOM    415  C   ASN   143      89.182  46.555  72.927  1.00  0.00              
ATOM    416  O   ASN   143      90.261  45.991  73.135  1.00  0.00              
ATOM    417  N   ARG   144      88.823  47.674  73.538  1.00  0.00              
ATOM    418  CA  ARG   144      89.674  48.331  74.510  1.00  0.00              
ATOM    419  C   ARG   144      88.729  48.553  75.668  1.00  0.00              
ATOM    420  O   ARG   144      87.533  48.732  75.451  1.00  0.00              
ATOM    421  N   PRO   146      89.231  48.459  76.893  1.00  0.00              
ATOM    422  CA  PRO   146      88.379  48.686  78.048  1.00  0.00              
ATOM    423  C   PRO   146      87.800  50.074  77.898  1.00  0.00              
ATOM    424  O   PRO   146      88.469  50.989  77.403  1.00  0.00              
ATOM    425  N   ILE   147      86.567  50.237  78.352  1.00  0.00              
ATOM    426  CA  ILE   147      85.909  51.520  78.254  1.00  0.00              
ATOM    427  C   ILE   147      86.724  52.572  78.992  1.00  0.00              
ATOM    428  O   ILE   147      86.936  53.683  78.494  1.00  0.00              
END
