
#######################################################
#                                                     #
#                        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   13 (  114),  selected   13 , name T0372TS022_4_1-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected  172 , name T0372_D2.pdb
# PARAMETERS: T0372TS022_4_1-D2.T0372_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    -       -      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    -       -      Q     139           -
LGA    -       -      A     140           -
LGA    -       -      K     141           -
LGA    -       -      R     142           -
LGA    -       -      N     143           -
LGA    -       -      H     144           -
LGA    -       -      I     145           -
LGA    -       -      N     146           -
LGA    R     118      R     147          3.886
LGA    A     119      F     148          3.656
LGA    Y     120      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    -       -      P     159           -
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    A     121      G     244          2.446
LGA    D     122      A     245          1.426
LGA    -       -      Y     246           -
LGA    -       -      A     247           -
LGA    -       -      M     248           -
LGA    Y     123      I     249          1.084
LGA    I     124      N     250          2.679
LGA    -       -      Y     251           -
LGA    -       -      E     252           -
LGA    Y     125      F     253          1.495
LGA    L     126      A     254          1.312
LGA    -       -      N     255           -
LGA    -       -      R     256           -
LGA    R     127      I     257          1.819
LGA    S     128      P     258          1.884
LGA    D     129      E     259          0.867
LGA    L     130      Q     260          1.651
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)   13  172    5.0     12    2.22     8.33      5.883     0.517

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.457167 * X  +  -0.832120 * Y  +  -0.313965 * Z  + 143.606506
  Y_new =  -0.311796 * X  +  -0.180658 * Y  +   0.932816 * Z  +  84.696014
  Z_new =  -0.832936 * X  +   0.524346 * Y  +  -0.176861 * Z  +  65.095375 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.896111   -1.245481  [ DEG:   108.6392    -71.3608 ]
  Theta =   0.984392    2.157201  [ DEG:    56.4015    123.5985 ]
  Phi   =  -2.543037    0.598555  [ DEG:  -145.7053     34.2947 ]
 
# 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: T0372TS022_4_1-D2                             
REMARK     2: T0372_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS022_4_1-D2.T0372_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   13  172   5.0   12   2.22    8.33   5.883
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS022_4_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0372
PARENT 1mk4_A
ATOM    953  N   ARG   118      32.175  35.790  39.725  1.00  0.00
ATOM    954  CA  ARG   118      32.405  34.401  39.966  1.00  0.00
ATOM    955  C   ARG   118      31.325  33.532  39.385  1.00  0.00
ATOM    956  O   ARG   118      31.631  32.514  38.765  1.00  0.00
ATOM    957  CB  ARG   118      32.460  34.119  41.468  1.00  0.00
ATOM    958  CG  ARG   118      33.706  34.656  42.155  1.00  0.00
ATOM    959  CD  ARG   118      33.659  34.410  43.655  1.00  0.00
ATOM    960  NE  ARG   118      34.848  34.924  44.330  1.00  0.00
ATOM    961  CZ  ARG   118      35.023  34.909  45.648  1.00  0.00
ATOM    962  NH1 ARG   118      36.137  35.399  46.174  1.00  0.00
ATOM    963  NH2 ARG   118      34.083  34.405  46.436  1.00  0.00
ATOM    964  N   ALA   119      30.036  33.915  39.529  1.00  0.00
ATOM    965  CA  ALA   119      29.003  32.990  39.145  1.00  0.00
ATOM    966  C   ALA   119      29.106  32.642  37.693  1.00  0.00
ATOM    967  O   ALA   119      29.278  31.474  37.346  1.00  0.00
ATOM    968  CB  ALA   119      27.630  33.595  39.392  1.00  0.00
ATOM    969  N   TYR   120      29.025  33.639  36.792  1.00  0.00
ATOM    970  CA  TYR   120      29.237  33.316  35.411  1.00  0.00
ATOM    971  C   TYR   120      30.143  34.356  34.874  1.00  0.00
ATOM    972  O   TYR   120      29.664  35.396  34.425  1.00  0.00
ATOM    973  CB  TYR   120      27.909  33.316  34.651  1.00  0.00
ATOM    974  CG  TYR   120      26.918  32.287  35.148  1.00  0.00
ATOM    975  CD1 TYR   120      25.906  32.643  36.030  1.00  0.00
ATOM    976  CD2 TYR   120      26.998  30.964  34.734  1.00  0.00
ATOM    977  CE1 TYR   120      24.996  31.711  36.490  1.00  0.00
ATOM    978  CE2 TYR   120      26.098  30.017  35.183  1.00  0.00
ATOM    979  CZ  TYR   120      25.091  30.402  36.068  1.00  0.00
ATOM    980  OH  TYR   120      24.186  29.471  36.525  1.00  0.00
ATOM    981  N   ALA   121      31.467  34.133  34.868  1.00  0.00
ATOM    982  CA  ALA   121      32.203  35.190  34.253  1.00  0.00
ATOM    983  C   ALA   121      33.648  34.853  34.210  1.00  0.00
ATOM    984  O   ALA   121      34.169  34.097  35.028  1.00  0.00
ATOM    985  CB  ALA   121      32.030  36.482  35.036  1.00  0.00
ATOM    986  N   ASP   122      34.322  35.435  33.207  1.00  0.00
ATOM    987  CA  ASP   122      35.723  35.271  33.017  1.00  0.00
ATOM    988  C   ASP   122      36.318  36.610  33.294  1.00  0.00
ATOM    989  O   ASP   122      36.784  36.874  34.402  1.00  0.00
ATOM    990  CB  ASP   122      36.021  34.824  31.585  1.00  0.00
ATOM    991  CG  ASP   122      35.509  33.427  31.292  1.00  0.00
ATOM    992  OD1 ASP   122      35.804  32.508  32.084  1.00  0.00
ATOM    993  OD2 ASP   122      34.811  33.253  30.271  1.00  0.00
ATOM    994  N   TYR   123      36.309  37.502  32.284  1.00  0.00
ATOM    995  CA  TYR   123      36.861  38.811  32.470  1.00  0.00
ATOM    996  C   TYR   123      35.829  39.826  32.079  1.00  0.00
ATOM    997  O   TYR   123      35.069  39.634  31.130  1.00  0.00
ATOM    998  CB  TYR   123      38.109  38.995  31.604  1.00  0.00
ATOM    999  CG  TYR   123      39.244  38.062  31.960  1.00  0.00
ATOM   1000  CD1 TYR   123      39.356  36.815  31.358  1.00  0.00
ATOM   1001  CD2 TYR   123      40.201  38.431  32.897  1.00  0.00
ATOM   1002  CE1 TYR   123      40.391  35.956  31.678  1.00  0.00
ATOM   1003  CE2 TYR   123      41.242  37.586  33.229  1.00  0.00
ATOM   1004  CZ  TYR   123      41.331  36.340  32.610  1.00  0.00
ATOM   1005  OH  TYR   123      42.362  35.487  32.929  1.00  0.00
ATOM   1006  N   ILE   124      35.774  40.940  32.838  1.00  0.00
ATOM   1007  CA  ILE   124      34.846  42.000  32.566  1.00  0.00
ATOM   1008  C   ILE   124      35.677  43.184  32.206  1.00  0.00
ATOM   1009  O   ILE   124      36.648  43.503  32.892  1.00  0.00
ATOM   1010  CB  ILE   124      33.971  42.313  33.795  1.00  0.00
ATOM   1011  CG1 ILE   124      33.152  41.084  34.193  1.00  0.00
ATOM   1012  CG2 ILE   124      33.012  43.454  33.489  1.00  0.00
ATOM   1013  CD1 ILE   124      32.440  41.229  35.520  1.00  0.00
ATOM   1014  N   TYR   125      35.332  43.864  31.097  1.00  0.00
ATOM   1015  CA  TYR   125      36.135  44.976  30.685  1.00  0.00
ATOM   1016  C   TYR   125      35.255  46.176  30.566  1.00  0.00
ATOM   1017  O   TYR   125      34.155  46.108  30.019  1.00  0.00
ATOM   1018  CB  TYR   125      36.792  44.690  29.333  1.00  0.00
ATOM   1019  CG  TYR   125      37.798  43.561  29.367  1.00  0.00
ATOM   1020  CD1 TYR   125      37.410  42.254  29.106  1.00  0.00
ATOM   1021  CD2 TYR   125      39.133  43.807  29.662  1.00  0.00
ATOM   1022  CE1 TYR   125      38.322  41.216  29.135  1.00  0.00
ATOM   1023  CE2 TYR   125      40.059  42.782  29.697  1.00  0.00
ATOM   1024  CZ  TYR   125      39.642  41.479  29.429  1.00  0.00
ATOM   1025  OH  TYR   125      40.552  40.447  29.460  1.00  0.00
ATOM   1026  N   LEU   126      35.718  47.316  31.107  1.00  0.00
ATOM   1027  CA  LEU   126      34.945  48.510  30.987  1.00  0.00
ATOM   1028  C   LEU   126      35.684  49.459  30.119  1.00  0.00
ATOM   1029  O   LEU   126      36.892  49.652  30.245  1.00  0.00
ATOM   1030  CB  LEU   126      34.721  49.143  32.362  1.00  0.00
ATOM   1031  CG  LEU   126      33.586  48.553  33.202  1.00  0.00
ATOM   1032  CD1 LEU   126      33.835  47.080  33.486  1.00  0.00
ATOM   1033  CD2 LEU   126      33.470  49.280  34.533  1.00  0.00
ATOM   1034  N   ARG   127      34.942  50.056  29.173  1.00  0.00
ATOM   1035  CA  ARG   127      35.497  51.095  28.382  1.00  0.00
ATOM   1036  C   ARG   127      35.436  52.249  29.311  1.00  0.00
ATOM   1037  O   ARG   127      34.407  52.473  29.949  1.00  0.00
ATOM   1038  CB  ARG   127      34.662  51.308  27.117  1.00  0.00
ATOM   1039  CG  ARG   127      34.687  50.135  26.152  1.00  0.00
ATOM   1040  CD  ARG   127      33.825  50.406  24.930  1.00  0.00
ATOM   1041  NE  ARG   127      33.834  49.284  23.994  1.00  0.00
ATOM   1042  CZ  ARG   127      33.122  49.242  22.871  1.00  0.00
ATOM   1043  NH1 ARG   127      33.194  48.180  22.081  1.00  0.00
ATOM   1044  NH2 ARG   127      32.341  50.262  22.544  1.00  0.00
ATOM   1045  N   SER   128      36.518  53.042  29.396  1.00  0.00
ATOM   1046  CA  SER   128      36.476  54.111  30.346  1.00  0.00
ATOM   1047  C   SER   128      35.489  55.111  29.842  1.00  0.00
ATOM   1048  O   SER   128      34.778  54.858  28.869  1.00  0.00
ATOM   1049  CB  SER   128      37.855  54.758  30.486  1.00  0.00
ATOM   1050  OG  SER   128      38.224  55.438  29.298  1.00  0.00
ATOM   1051  N   ASP   129      35.403  56.271  30.520  1.00  0.00
ATOM   1052  CA  ASP   129      34.451  57.289  30.188  1.00  0.00
ATOM   1053  C   ASP   129      34.560  57.566  28.724  1.00  0.00
ATOM   1054  O   ASP   129      35.639  57.853  28.210  1.00  0.00
ATOM   1055  CB  ASP   129      34.739  58.569  30.976  1.00  0.00
ATOM   1056  CG  ASP   129      33.674  59.629  30.774  1.00  0.00
ATOM   1057  OD1 ASP   129      32.783  59.422  29.923  1.00  0.00
ATOM   1058  OD2 ASP   129      33.732  60.668  31.465  1.00  0.00
ATOM   1059  N   LEU   130      33.428  57.435  28.006  1.00  0.00
ATOM   1060  CA  LEU   130      33.428  57.702  26.597  1.00  0.00
ATOM   1061  C   LEU   130      32.812  59.090  26.454  1.00  0.00
ATOM   1062  O   LEU   130      32.214  59.553  27.462  1.00  0.00
ATOM   1063  CB  LEU   130      32.601  56.653  25.852  1.00  0.00
ATOM   1064  CG  LEU   130      33.050  55.199  26.010  1.00  0.00
ATOM   1065  CD1 LEU   130      32.106  54.262  25.272  1.00  0.00
ATOM   1066  CD2 LEU   130      34.449  55.004  25.446  1.00  0.00
TER
END
