
#######################################################
#                                                     #
#                        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   11 (   44),  selected   11 , name T0372AL044_1-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected  172 , name T0372_D2.pdb
# PARAMETERS: T0372AL044_1-D2.T0372_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      R     118           -
LGA    -       -      A     119           -
LGA    -       -      Y     120           -
LGA    -       -      A     121           -
LGA    -       -      D     122           -
LGA    -       -      Y     123           -
LGA    -       -      I     124           -
LGA    -       -      Y     125           -
LGA    -       -      L     126           -
LGA    -       -      R     127           -
LGA    -       -      S     128           -
LGA    -       -      D     129           -
LGA    -       -      L     130           -
LGA    -       -      A     131           -
LGA    -       -      T     132           -
LGA    -       -      L     133           -
LGA    -       -      K     134           -
LGA    -       -      G     135           -
LGA    -       -      K     136           -
LGA    -       -      K     137           -
LGA    -       -      F     138           -
LGA    R     118      Q     139          0.530
LGA    A     119      A     140          0.598
LGA    Y     120      K     141          0.585
LGA    A     121      R     142          0.844
LGA    D     122      N     143          0.612
LGA    Y     123      H     144          0.636
LGA    I     124      I     145          0.734
LGA    Y     125      N     146          0.513
LGA    L     126      R     147          0.439
LGA    R     127      F     148          0.643
LGA    -       -      R     149           -
LGA    -       -      N     150           -
LGA    -       -      T     151           -
LGA    -       -      Y     152           -
LGA    -       -      P     153           -
LGA    -       -      D     154           -
LGA    -       -      Y     155           -
LGA    -       -      E     156           -
LGA    -       -      Y     157           -
LGA    -       -      T     158           -
LGA    R     142      P     159          0.673
LGA    -       -      I     160           -
LGA    -       -      T     161           -
LGA    -       -      P     162           -
LGA    -       -      D     163           -
LGA    -       -      R     164           -
LGA    -       -      I     165           -
LGA    -       -      Q     166           -
LGA    -       -      E     167           -
LGA    -       -      C     168           -
LGA    -       -      L     169           -
LGA    -       -      D     170           -
LGA    -       -      L     171           -
LGA    -       -      E     172           -
LGA    -       -      A     173           -
LGA    -       -      E     174           -
LGA    -       -      W     175           -
LGA    -       -      C     176           -
LGA    -       -      K     177           -
LGA    -       -      V     178           -
LGA    -       -      N     179           -
LGA    -       -      N     180           -
LGA    -       -      C     181           -
LGA    -       -      D     182           -
LGA    -       -      Q     183           -
LGA    -       -      Q     184           -
LGA    -       -      E     185           -
LGA    -       -      G     186           -
LGA    -       -      T     187           -
LGA    -       -      G     188           -
LGA    -       -      N     189           -
LGA    -       -      E     190           -
LGA    -       -      R     191           -
LGA    -       -      R     192           -
LGA    -       -      A     193           -
LGA    -       -      L     194           -
LGA    -       -      I     195           -
LGA    -       -      Y     196           -
LGA    -       -      A     197           -
LGA    -       -      L     198           -
LGA    -       -      H     199           -
LGA    -       -      N     200           -
LGA    -       -      F     201           -
LGA    -       -      E     202           -
LGA    -       -      A     203           -
LGA    -       -      L     204           -
LGA    -       -      G     205           -
LGA    -       -      L     206           -
LGA    -       -      T     207           -
LGA    -       -      G     208           -
LGA    -       -      G     209           -
LGA    -       -      I     210           -
LGA    -       -      L     211           -
LGA    -       -      H     212           -
LGA    -       -      V     213           -
LGA    -       -      N     214           -
LGA    -       -      G     215           -
LGA    -       -      K     216           -
LGA    -       -      I     217           -
LGA    -       -      V     218           -
LGA    -       -      A     219           -
LGA    -       -      F     220           -
LGA    -       -      T     221           -
LGA    -       -      F     222           -
LGA    -       -      G     223           -
LGA    -       -      M     224           -
LGA    -       -      P     225           -
LGA    -       -      I     226           -
LGA    -       -      N     227           -
LGA    -       -      H     228           -
LGA    -       -      E     229           -
LGA    -       -      T     230           -
LGA    -       -      F     231           -
LGA    -       -      G     232           -
LGA    -       -      V     233           -
LGA    -       -      H     234           -
LGA    -       -      V     235           -
LGA    -       -      E     236           -
LGA    -       -      K     237           -
LGA    -       -      A     238           -
LGA    -       -      D     239           -
LGA    -       -      T     240           -
LGA    -       -      S     241           -
LGA    -       -      I     242           -
LGA    -       -      D     243           -
LGA    -       -      G     244           -
LGA    -       -      A     245           -
LGA    -       -      Y     246           -
LGA    -       -      A     247           -
LGA    -       -      M     248           -
LGA    -       -      I     249           -
LGA    -       -      N     250           -
LGA    -       -      Y     251           -
LGA    -       -      E     252           -
LGA    -       -      F     253           -
LGA    -       -      A     254           -
LGA    -       -      N     255           -
LGA    -       -      R     256           -
LGA    -       -      I     257           -
LGA    -       -      P     258           -
LGA    -       -      E     259           -
LGA    -       -      Q     260           -
LGA    -       -      Y     261           -
LGA    -       -      I     262           -
LGA    -       -      Y     263           -
LGA    -       -      I     264           -
LGA    -       -      N     265           -
LGA    -       -      R     266           -
LGA    -       -      E     267           -
LGA    -       -      E     268           -
LGA    -       -      D     269           -
LGA    -       -      L     270           -
LGA    -       -      G     271           -
LGA    -       -      I     272           -
LGA    -       -      E     273           -
LGA    -       -      G     274           -
LGA    -       -      L     275           -
LGA    -       -      R     276           -
LGA    -       -      K     277           -
LGA    -       -      A     278           -
LGA    -       -      K     279           -
LGA    -       -      L     280           -
LGA    -       -      S     281           -
LGA    -       -      Y     282           -
LGA    -       -      Q     283           -
LGA    -       -      P     284           -
LGA    -       -      V     285           -
LGA    -       -      T     286           -
LGA    -       -      I     287           -
LGA    -       -      L     288           -
LGA    -       -      E     289           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   11  172    5.0     11    0.63    18.18      6.395     1.512

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.052885 * X  +  -0.868317 * Y  +   0.493183 * Z  +  20.870937
  Y_new =   0.813031 * X  +   0.324196 * Y  +   0.483608 * Z  +  15.531731
  Z_new =  -0.579813 * X  +   0.375398 * Y  +   0.723114 * Z  +  24.182367 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.478843   -2.662750  [ DEG:    27.4357   -152.5643 ]
  Theta =   0.618499    2.523093  [ DEG:    35.4374    144.5626 ]
  Phi   =   1.505841   -1.635751  [ DEG:    86.2784    -93.7216 ]
 
# 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: T0372AL044_1-D2                               
REMARK     2: T0372_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372AL044_1-D2.T0372_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   11  172   5.0   11   0.63   18.18   6.395
REMARK  ---------------------------------------------------------- 
MOLECULE T0372AL044_1-D2
REMARK Aligment from pdb entry: 2go8_A
ATOM    133  N   ARG   118      19.587  40.576  35.322  1.00  0.00              
ATOM    134  CA  ARG   118      19.667  39.623  36.399  1.00  0.00              
ATOM    135  C   ARG   118      20.552  38.422  36.111  1.00  0.00              
ATOM    136  O   ARG   118      21.048  37.806  37.042  1.00  0.00              
ATOM    137  N   ALA   119      20.744  38.083  34.838  1.00  0.00              
ATOM    138  CA  ALA   119      21.562  36.940  34.451  1.00  0.00              
ATOM    139  C   ALA   119      23.028  37.290  34.564  1.00  0.00              
ATOM    140  O   ALA   119      23.872  36.424  34.740  1.00  0.00              
ATOM    141  N   TYR   120      23.307  38.583  34.498  1.00  0.00              
ATOM    142  CA  TYR   120      24.657  39.113  34.564  1.00  0.00              
ATOM    143  C   TYR   120      25.100  39.228  36.010  1.00  0.00              
ATOM    144  O   TYR   120      26.291  39.231  36.291  1.00  0.00              
ATOM    145  N   ALA   121      24.141  39.334  36.925  1.00  0.00              
ATOM    146  CA  ALA   121      24.461  39.467  38.345  1.00  0.00              
ATOM    147  C   ALA   121      24.771  38.133  39.015  1.00  0.00              
ATOM    148  O   ALA   121      25.457  38.087  40.020  1.00  0.00              
ATOM    149  N   ASP   122      24.240  37.050  38.468  1.00  0.00              
ATOM    150  CA  ASP   122      24.481  35.723  39.008  1.00  0.00              
ATOM    151  C   ASP   122      25.724  35.198  38.367  1.00  0.00              
ATOM    152  O   ASP   122      26.140  34.068  38.587  1.00  0.00              
ATOM    153  N   TYR   123      26.283  36.010  37.499  1.00  0.00              
ATOM    154  CA  TYR   123      27.498  35.612  36.869  1.00  0.00              
ATOM    155  C   TYR   123      28.573  36.356  37.611  1.00  0.00              
ATOM    156  O   TYR   123      29.514  35.749  38.094  1.00  0.00              
ATOM    157  N   ILE   124      28.445  37.669  37.704  1.00  0.00              
ATOM    158  CA  ILE   124      29.421  38.419  38.446  1.00  0.00              
ATOM    159  C   ILE   124      29.408  37.824  39.851  1.00  0.00              
ATOM    160  O   ILE   124      30.416  37.878  40.545  1.00  0.00              
ATOM    161  N   TYR   125      28.278  37.233  40.247  1.00  0.00              
ATOM    162  CA  TYR   125      28.121  36.651  41.582  1.00  0.00              
ATOM    163  C   TYR   125      28.849  35.327  41.856  1.00  0.00              
ATOM    164  O   TYR   125      29.524  35.198  42.885  1.00  0.00              
ATOM    165  N   LEU   126      28.711  34.348  40.965  1.00  0.00              
ATOM    166  CA  LEU   126      29.361  33.046  41.157  1.00  0.00              
ATOM    167  C   LEU   126      30.865  33.092  40.899  1.00  0.00              
ATOM    168  O   LEU   126      31.602  32.136  41.168  1.00  0.00              
ATOM    169  N   ARG   127      31.307  34.254  40.467  1.00  0.00              
ATOM    170  CA  ARG   127      32.671  34.481  40.099  1.00  0.00              
ATOM    171  C   ARG   127      33.656  34.619  41.257  1.00  0.00              
ATOM    172  O   ARG   127      33.347  35.146  42.331  1.00  0.00              
ATOM    173  N   ARG   142      46.361  43.706  33.112  1.00  0.00              
ATOM    174  CA  ARG   142      45.862  44.782  32.273  1.00  0.00              
ATOM    175  C   ARG   142      46.453  46.139  32.546  1.00  0.00              
ATOM    176  O   ARG   142      46.381  46.644  33.658  1.00  0.00              
END
