
#######################################################
#                                                     #
#                        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   18 (  148),  selected   18 , name T0372TS021_1_1-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected  172 , name T0372_D2.pdb
# PARAMETERS: T0372TS021_1_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     147           -
LGA    -       -      F     148           -
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    -       -      P     159           -
LGA    -       -      I     160           -
LGA    R     118      T     161          2.768
LGA    A     119      P     162          3.219
LGA    Y     120      D     163          4.553
LGA    A     121      R     164          2.828
LGA    D     122      I     165          2.180
LGA    Y     123      Q     166          2.306
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    I     124      L     198          2.655
LGA    Y     125      H     199          1.641
LGA    L     126      N     200          3.137
LGA    R     127      F     201          2.310
LGA    -       -      E     202           -
LGA    -       -      A     203           -
LGA    -       -      L     204           -
LGA    S     128      G     205           #
LGA    D     129      L     206          1.196
LGA    L     130      T     207          2.710
LGA    A     131      G     208          4.558
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    T     132      F     253          3.613
LGA    L     133      A     254          2.942
LGA    K     134      N     255          1.797
LGA    G     135      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)   18  172    5.0     16    2.92     0.00      6.060     0.530

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.783678 * X  +  -0.136758 * Y  +   0.605926 * Z  +  67.218521
  Y_new =  -0.370622 * X  +   0.885753 * Y  +  -0.279430 * Z  +  37.634098
  Z_new =  -0.498486 * X  +  -0.443552 * Y  +  -0.744831 * Z  +  52.374687 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.604483    0.537110  [ DEG:  -149.2259     30.7741 ]
  Theta =   0.521852    2.619741  [ DEG:    29.8999    150.1001 ]
  Phi   =  -2.699838    0.441755  [ DEG:  -154.6893     25.3107 ]
 
# 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: T0372TS021_1_1-D2                             
REMARK     2: T0372_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS021_1_1-D2.T0372_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   18  172   5.0   16   2.92    0.00   6.060
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS021_1_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0372
PARENT N/A
ATOM    953  N   ARG   118      53.823  46.356  30.260  1.00218.80       1SG 954
ATOM    954  CA  ARG   118      53.920  44.947  30.126  1.00218.80       1SG 955
ATOM    955  CB  ARG   118      53.428  44.171  31.358  1.00218.80       1SG 956
ATOM    956  CG  ARG   118      54.413  44.261  32.527  1.00218.80       1SG 957
ATOM    957  CD  ARG   118      54.207  43.195  33.606  1.00218.80       1SG 958
ATOM    958  NE  ARG   118      55.251  43.410  34.649  1.00218.80       1SG 959
ATOM    959  CZ  ARG   118      56.480  42.828  34.528  1.00218.80       1SG 960
ATOM    960  NH1 ARG   118      56.765  42.042  33.448  1.00218.80       1SG 961
ATOM    961  NH2 ARG   118      57.428  43.034  35.488  1.00218.80       1SG 962
ATOM    962  C   ARG   118      53.116  44.537  28.949  1.00218.80       1SG 963
ATOM    963  O   ARG   118      53.607  43.791  28.105  1.00218.80       1SG 964
ATOM    964  N   ALA   119      51.880  45.057  28.816  1.00292.80       1SG 965
ATOM    965  CA  ALA   119      51.053  44.533  27.773  1.00292.80       1SG 966
ATOM    966  CB  ALA   119      51.667  44.688  26.370  1.00292.80       1SG 967
ATOM    967  C   ALA   119      50.977  43.089  28.107  1.00292.80       1SG 968
ATOM    968  O   ALA   119      50.974  42.216  27.239  1.00292.80       1SG 969
ATOM    969  N   TYR   120      50.926  42.831  29.427  1.00206.78       1SG 970
ATOM    970  CA  TYR   120      50.917  41.507  29.948  1.00206.78       1SG 971
ATOM    971  CB  TYR   120      49.626  40.754  29.597  1.00206.78       1SG 972
ATOM    972  CG  TYR   120      48.537  41.559  30.221  1.00206.78       1SG 973
ATOM    973  CD1 TYR   120      48.046  42.674  29.578  1.00206.78       1SG 974
ATOM    974  CD2 TYR   120      48.014  41.214  31.446  1.00206.78       1SG 975
ATOM    975  CE1 TYR   120      47.046  43.430  30.143  1.00206.78       1SG 976
ATOM    976  CE2 TYR   120      47.014  41.966  32.016  1.00206.78       1SG 977
ATOM    977  CZ  TYR   120      46.528  43.074  31.365  1.00206.78       1SG 978
ATOM    978  OH  TYR   120      45.501  43.847  31.948  1.00206.78       1SG 979
ATOM    979  C   TYR   120      52.101  40.799  29.395  1.00206.78       1SG 980
ATOM    980  O   TYR   120      51.995  39.693  28.870  1.00206.78       1SG 981
ATOM    981  N   ALA   121      53.278  41.448  29.512  1.00100.12       1SG 982
ATOM    982  CA  ALA   121      54.495  40.878  29.020  1.00100.12       1SG 983
ATOM    983  CB  ALA   121      54.897  39.582  29.744  1.00100.12       1SG 984
ATOM    984  C   ALA   121      54.259  40.566  27.591  1.00100.12       1SG 985
ATOM    985  O   ALA   121      54.729  39.556  27.069  1.00100.12       1SG 986
ATOM    986  N   ASP   122      53.536  41.466  26.907  1.00186.82       1SG 987
ATOM    987  CA  ASP   122      53.226  41.189  25.550  1.00186.82       1SG 988
ATOM    988  CB  ASP   122      54.465  40.924  24.678  1.00186.82       1SG 989
ATOM    989  CG  ASP   122      55.214  42.237  24.516  1.00186.82       1SG 990
ATOM    990  OD1 ASP   122      54.664  43.288  24.942  1.00186.82       1SG 991
ATOM    991  OD2 ASP   122      56.344  42.209  23.958  1.00186.82       1SG 992
ATOM    992  C   ASP   122      52.392  39.961  25.566  1.00186.82       1SG 993
ATOM    993  O   ASP   122      51.252  39.978  26.027  1.00186.82       1SG 994
ATOM    994  N   TYR   123      52.950  38.856  25.040  1.00250.31       1SG 995
ATOM    995  CA  TYR   123      52.227  37.625  24.897  1.00250.31       1SG 996
ATOM    996  CB  TYR   123      51.596  37.100  26.202  1.00250.31       1SG 997
ATOM    997  CG  TYR   123      52.681  36.552  27.068  1.00250.31       1SG 998
ATOM    998  CD1 TYR   123      53.359  37.354  27.957  1.00250.31       1SG 999
ATOM    999  CD2 TYR   123      53.022  35.222  26.984  1.00250.31       1SG1000
ATOM   1000  CE1 TYR   123      54.359  36.836  28.748  1.00250.31       1SG1001
ATOM   1001  CE2 TYR   123      54.019  34.698  27.771  1.00250.31       1SG1002
ATOM   1002  CZ  TYR   123      54.691  35.506  28.655  1.00250.31       1SG1003
ATOM   1003  OH  TYR   123      55.716  34.971  29.465  1.00250.31       1SG1004
ATOM   1004  C   TYR   123      51.139  37.873  23.906  1.00250.31       1SG1005
ATOM   1005  O   TYR   123      50.224  37.067  23.745  1.00250.31       1SG1006
ATOM   1006  N   ILE   124      51.248  39.011  23.199  1.00154.32       1SG1007
ATOM   1007  CA  ILE   124      50.346  39.438  22.182  1.00154.32       1SG1008
ATOM   1008  CB  ILE   124      49.218  40.296  22.683  1.00154.32       1SG1009
ATOM   1009  CG2 ILE   124      49.810  41.606  23.230  1.00154.32       1SG1010
ATOM   1010  CG1 ILE   124      48.165  40.495  21.580  1.00154.32       1SG1011
ATOM   1011  CD1 ILE   124      46.903  41.208  22.057  1.00154.32       1SG1012
ATOM   1012  C   ILE   124      51.176  40.283  21.273  1.00154.32       1SG1013
ATOM   1013  O   ILE   124      52.355  40.504  21.546  1.00154.32       1SG1014
ATOM   1014  N   TYR   125      50.586  40.750  20.156  1.00104.12       1SG1015
ATOM   1015  CA  TYR   125      51.269  41.626  19.251  1.00104.12       1SG1016
ATOM   1016  CB  TYR   125      50.344  42.209  18.170  1.00104.12       1SG1017
ATOM   1017  CG  TYR   125      49.894  41.068  17.324  1.00104.12       1SG1018
ATOM   1018  CD1 TYR   125      48.998  40.148  17.817  1.00104.12       1SG1019
ATOM   1019  CD2 TYR   125      50.354  40.925  16.034  1.00104.12       1SG1020
ATOM   1020  CE1 TYR   125      48.576  39.094  17.042  1.00104.12       1SG1021
ATOM   1021  CE2 TYR   125      49.935  39.873  15.254  1.00104.12       1SG1022
ATOM   1022  CZ  TYR   125      49.045  38.955  15.758  1.00104.12       1SG1023
ATOM   1023  OH  TYR   125      48.614  37.874  14.960  1.00104.12       1SG1024
ATOM   1024  C   TYR   125      51.795  42.749  20.084  1.00104.12       1SG1025
ATOM   1025  O   TYR   125      51.156  43.182  21.041  1.00104.12       1SG1026
ATOM   1026  N   LEU   126      53.005  43.232  19.758  1.00117.10       1SG1027
ATOM   1027  CA  LEU   126      53.615  44.241  20.569  1.00117.10       1SG1028
ATOM   1028  CB  LEU   126      54.996  44.671  20.017  1.00117.10       1SG1029
ATOM   1029  CG  LEU   126      55.847  45.652  20.863  1.00117.10       1SG1030
ATOM   1030  CD1 LEU   126      57.177  45.946  20.151  1.00117.10       1SG1031
ATOM   1031  CD2 LEU   126      55.118  46.960  21.211  1.00117.10       1SG1032
ATOM   1032  C   LEU   126      52.693  45.416  20.596  1.00117.10       1SG1033
ATOM   1033  O   LEU   126      52.110  45.797  19.583  1.00117.10       1SG1034
ATOM   1034  N   ARG   127      52.532  46.002  21.798  1.00120.69       1SG1035
ATOM   1035  CA  ARG   127      51.732  47.175  21.980  1.00120.69       1SG1036
ATOM   1036  CB  ARG   127      52.306  48.405  21.254  1.00120.69       1SG1037
ATOM   1037  CG  ARG   127      51.544  49.703  21.530  1.00120.69       1SG1038
ATOM   1038  CD  ARG   127      52.083  50.902  20.745  1.00120.69       1SG1039
ATOM   1039  NE  ARG   127      51.799  50.646  19.305  1.00120.69       1SG1040
ATOM   1040  CZ  ARG   127      52.100  51.590  18.367  1.00120.69       1SG1041
ATOM   1041  NH1 ARG   127      52.664  52.774  18.743  1.00120.69       1SG1042
ATOM   1042  NH2 ARG   127      51.838  51.345  17.049  1.00120.69       1SG1043
ATOM   1043  C   ARG   127      50.350  46.929  21.471  1.00120.69       1SG1044
ATOM   1044  O   ARG   127      49.802  47.741  20.728  1.00120.69       1SG1045
ATOM   1045  N   SER   128      49.740  45.792  21.854  1.00140.05       1SG1046
ATOM   1046  CA  SER   128      48.396  45.564  21.414  1.00140.05       1SG1047
ATOM   1047  CB  SER   128      47.907  44.117  21.602  1.00140.05       1SG1048
ATOM   1048  OG  SER   128      48.599  43.248  20.718  1.00140.05       1SG1049
ATOM   1049  C   SER   128      47.497  46.455  22.213  1.00140.05       1SG1050
ATOM   1050  O   SER   128      47.773  46.746  23.377  1.00140.05       1SG1051
ATOM   1051  N   ASP   129      46.401  46.924  21.579  1.00242.92       1SG1052
ATOM   1052  CA  ASP   129      45.431  47.779  22.208  1.00242.92       1SG1053
ATOM   1053  CB  ASP   129      44.644  48.649  21.213  1.00242.92       1SG1054
ATOM   1054  CG  ASP   129      45.599  49.687  20.639  1.00242.92       1SG1055
ATOM   1055  OD1 ASP   129      46.641  49.963  21.293  1.00242.92       1SG1056
ATOM   1056  OD2 ASP   129      45.301  50.218  19.536  1.00242.92       1SG1057
ATOM   1057  C   ASP   129      44.449  46.908  22.927  1.00242.92       1SG1058
ATOM   1058  O   ASP   129      44.475  45.688  22.774  1.00242.92       1SG1059
ATOM   1059  N   LEU   130      43.567  47.509  23.758  1.00212.10       1SG1060
ATOM   1060  CA  LEU   130      42.648  46.697  24.514  1.00212.10       1SG1061
ATOM   1061  CB  LEU   130      43.193  46.207  25.869  1.00212.10       1SG1062
ATOM   1062  CG  LEU   130      44.462  45.335  25.826  1.00212.10       1SG1063
ATOM   1063  CD1 LEU   130      45.714  46.157  25.478  1.00212.10       1SG1064
ATOM   1064  CD2 LEU   130      44.623  44.532  27.126  1.00212.10       1SG1065
ATOM   1065  C   LEU   130      41.417  47.484  24.883  1.00212.10       1SG1066
ATOM   1066  O   LEU   130      41.119  48.523  24.292  1.00212.10       1SG1067
ATOM   1067  N   ALA   131      40.657  46.932  25.870  1.00 66.69       1SG1068
ATOM   1068  CA  ALA   131      39.468  47.507  26.453  1.00 66.69       1SG1069
ATOM   1069  CB  ALA   131      38.168  46.789  26.056  1.00 66.69       1SG1070
ATOM   1070  C   ALA   131      39.595  47.406  27.955  1.00 66.69       1SG1071
ATOM   1071  O   ALA   131      40.191  46.464  28.478  1.00 66.69       1SG1072
ATOM   1072  N   THR   132      39.014  48.395  28.675  1.00207.67       1SG1073
ATOM   1073  CA  THR   132      39.120  48.580  30.104  1.00207.67       1SG1074
ATOM   1074  CB  THR   132      38.629  49.916  30.578  1.00207.67       1SG1075
ATOM   1075  OG1 THR   132      39.040  50.132  31.921  1.00207.67       1SG1076
ATOM   1076  CG2 THR   132      37.096  49.949  30.484  1.00207.67       1SG1077
ATOM   1077  C   THR   132      38.436  47.540  30.935  1.00207.67       1SG1078
ATOM   1078  O   THR   132      38.961  47.207  31.993  1.00207.67       1SG1079
ATOM   1079  N   LEU   133      37.250  47.037  30.521  1.00187.13       1SG1080
ATOM   1080  CA  LEU   133      36.533  46.030  31.265  1.00187.13       1SG1081
ATOM   1081  CB  LEU   133      37.188  44.641  31.176  1.00187.13       1SG1082
ATOM   1082  CG  LEU   133      37.192  44.036  29.762  1.00187.13       1SG1083
ATOM   1083  CD1 LEU   133      37.929  44.936  28.759  1.00187.13       1SG1084
ATOM   1084  CD2 LEU   133      37.747  42.602  29.780  1.00187.13       1SG1085
ATOM   1085  C   LEU   133      36.459  46.409  32.711  1.00187.13       1SG1086
ATOM   1086  O   LEU   133      37.095  45.763  33.544  1.00187.13       1SG1087
ATOM   1087  N   LYS   134      35.704  47.479  33.049  1.00205.93       1SG1088
ATOM   1088  CA  LYS   134      35.641  47.908  34.420  1.00205.93       1SG1089
ATOM   1089  CB  LYS   134      34.633  49.038  34.700  1.00205.93       1SG1090
ATOM   1090  CG  LYS   134      35.031  50.415  34.168  1.00205.93       1SG1091
ATOM   1091  CD  LYS   134      33.914  51.451  34.325  1.00205.93       1SG1092
ATOM   1092  CE  LYS   134      34.338  52.883  33.995  1.00205.93       1SG1093
ATOM   1093  NZ  LYS   134      33.206  53.809  34.224  1.00205.93       1SG1094
ATOM   1094  C   LYS   134      35.214  46.754  35.256  1.00205.93       1SG1095
ATOM   1095  O   LYS   134      34.195  46.117  34.995  1.00205.93       1SG1096
ATOM   1096  N   GLY   135      36.013  46.465  36.298  1.00 36.72       1SG1097
ATOM   1097  CA  GLY   135      35.723  45.371  37.170  1.00 36.72       1SG1098
ATOM   1098  C   GLY   135      36.838  45.345  38.206  1.00 36.72       1SG1099
ATOM   1099  O   GLY   135      37.717  46.246  38.150  1.00 36.72       1SG1100
ATOM   1100  OXT GLY   135      36.826  44.424  39.067  1.00 36.72       1SG1101
TER
END
