
#######################################################
#                                                     #
#                        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   41 (  164),  selected   41 , name T0316AL242_5-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316AL242_5-D3.T0316_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M     284           -
LGA    M     284      S     285          4.984
LGA    S     285      T     286          2.224
LGA    T     286      S     287          4.073
LGA    -       -      L     288           -
LGA    -       -      E     289           -
LGA    -       -      A     290           -
LGA    -       -      S     291           -
LGA    -       -      Q     292           -
LGA    -       -      V     293           -
LGA    -       -      H     294           -
LGA    -       -      F     295           -
LGA    -       -      T     296           -
LGA    -       -      R     297           -
LGA    -       -      E     298           -
LGA    -       -      M     299           -
LGA    -       -      P     300           -
LGA    -       -      E     301           -
LGA    -       -      E     302           -
LGA    -       -      F     303           -
LGA    -       -      T     304           -
LGA    -       -      L     305           -
LGA    -       -      E     306           -
LGA    -       -      C     307           -
LGA    -       -      T     308           -
LGA    -       -      A     309           -
LGA    -       -      K     310           -
LGA    -       -      F     311           -
LGA    -       -      R     312           -
LGA    -       -      Y     313           -
LGA    -       -      R     314           -
LGA    -       -      Q     315           -
LGA    -       -      P     316           -
LGA    -       -      D     317           -
LGA    -       -      S     318           -
LGA    -       -      K     319           -
LGA    -       -      V     320           -
LGA    -       -      T     321           -
LGA    -       -      V     322           -
LGA    -       -      H     323           -
LGA    -       -      V     324           -
LGA    -       -      K     325           -
LGA    -       -      G     326           -
LGA    -       -      E     327           -
LGA    -       -      K     328           -
LGA    -       -      T     329           -
LGA    S     287      E     330          3.760
LGA    L     288      V     331          1.368
LGA    E     289      I     332          1.826
LGA    A     290      F     333          1.359
LGA    S     291      A     334          2.765
LGA    Q     292      E     335          2.315
LGA    V     293      P     336          3.246
LGA    H     294      -       -           -
LGA    F     295      -       -           -
LGA    T     296      Q     337          2.271
LGA    R     297      R     338          2.104
LGA    E     298      A     339          4.811
LGA    M     299      I     340          2.784
LGA    P     300      -       -           -
LGA    E     301      T     341          2.100
LGA    E     302      P     342          2.367
LGA    F     303      -       -           -
LGA    T     304      -       -           -
LGA    P     336      -       -           -
LGA    Q     337      G     343          2.281
LGA    R     338      Q     344          2.201
LGA    A     339      A     345          0.727
LGA    I     340      V     346          2.231
LGA    T     341      V     347          1.829
LGA    P     342      F     348          3.857
LGA    G     343      Y     349          2.593
LGA    -       -      D     350           -
LGA    -       -      G     351           -
LGA    -       -      E     352           -
LGA    -       -      E     353           -
LGA    -       -      C     354           -
LGA    -       -      L     355           -
LGA    Q     344      G     356           #
LGA    A     345      G     357          2.347
LGA    V     346      G     358          3.570
LGA    V     347      L     359          0.168
LGA    F     348      I     360          4.007
LGA    Y     349      -       -           -
LGA    D     350      -       -           -
LGA    G     351      -       -           -
LGA    E     352      D     361          3.923
LGA    E     353      N     362           #
LGA    C     354      A     363           -
LGA    L     355      Y     364           -
LGA    -       -      R     365           -
LGA    -       -      D     366           -
LGA    -       -      G     367           -
LGA    -       -      Q     368           -
LGA    -       -      V     369           -
LGA    -       -      C     370           -
LGA    -       -      Q     371           -
LGA    -       -      Y     372           -
LGA    -       -      I     373           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   41   90    5.0     28    2.88     7.14     20.399     0.940

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.752346 * X  +  -0.519248 * Y  +   0.405410 * Z  + -38.284973
  Y_new =   0.015200 * X  +   0.601559 * Y  +   0.798683 * Z  + -46.140633
  Z_new =  -0.658593 * X  +   0.607048 * Y  +  -0.444688 * Z  +  -9.391047 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.203030   -0.938562  [ DEG:   126.2243    -53.7757 ]
  Theta =   0.718947    2.422645  [ DEG:    41.1926    138.8074 ]
  Phi   =   3.121392   -0.020200  [ DEG:   178.8426     -1.1574 ]
 
# 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: T0316AL242_5-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316AL242_5-D3.T0316_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   41   90   5.0   28   2.88    7.14  20.399
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL242_5-D3
REMARK Aligment from pdb entry: 1wy5_A
ATOM   1001  N   MET   284      26.788   5.527  -9.392  1.00  0.00              
ATOM   1002  CA  MET   284      26.348   6.408  -8.331  1.00  0.00              
ATOM   1003  C   MET   284      24.959   6.030  -7.817  1.00  0.00              
ATOM   1004  O   MET   284      24.731   6.065  -6.605  1.00  0.00              
ATOM   1005  N   SER   285      24.042   5.661  -8.715  1.00  0.00              
ATOM   1006  CA  SER   285      22.692   5.258  -8.297  1.00  0.00              
ATOM   1007  C   SER   285      22.797   4.149  -7.265  1.00  0.00              
ATOM   1008  O   SER   285      22.136   4.183  -6.230  1.00  0.00              
ATOM   1009  N   THR   286      23.631   3.158  -7.564  1.00  0.00              
ATOM   1010  CA  THR   286      23.812   2.022  -6.673  1.00  0.00              
ATOM   1011  C   THR   286      24.515   2.406  -5.378  1.00  0.00              
ATOM   1012  O   THR   286      24.016   2.141  -4.288  1.00  0.00              
ATOM   1013  N   SER   287      25.670   3.041  -5.507  1.00  0.00              
ATOM   1014  CA  SER   287      26.451   3.454  -4.351  1.00  0.00              
ATOM   1015  C   SER   287      25.659   4.275  -3.326  1.00  0.00              
ATOM   1016  O   SER   287      26.027   4.322  -2.152  1.00  0.00              
ATOM   1017  N   LEU   288      24.573   4.910  -3.754  1.00  0.00              
ATOM   1018  CA  LEU   288      23.792   5.731  -2.835  1.00  0.00              
ATOM   1019  C   LEU   288      22.329   5.321  -2.697  1.00  0.00              
ATOM   1020  O   LEU   288      21.568   5.972  -1.980  1.00  0.00              
ATOM   1021  N   GLU   289      21.938   4.247  -3.378  1.00  0.00              
ATOM   1022  CA  GLU   289      20.562   3.778  -3.304  1.00  0.00              
ATOM   1023  C   GLU   289      19.531   4.865  -3.553  1.00  0.00              
ATOM   1024  O   GLU   289      18.716   5.168  -2.682  1.00  0.00              
ATOM   1025  N   ALA   290      19.563   5.448  -4.747  1.00  0.00              
ATOM   1026  CA  ALA   290      18.634   6.508  -5.118  1.00  0.00              
ATOM   1027  C   ALA   290      18.558   6.633  -6.637  1.00  0.00              
ATOM   1028  O   ALA   290      19.582   6.605  -7.318  1.00  0.00              
ATOM   1029  N   SER   291      17.344   6.774  -7.162  1.00  0.00              
ATOM   1030  CA  SER   291      17.146   6.910  -8.603  1.00  0.00              
ATOM   1031  C   SER   291      16.876   8.351  -9.042  1.00  0.00              
ATOM   1032  O   SER   291      17.004   8.673 -10.223  1.00  0.00              
ATOM   1033  N   GLN   292      16.516   9.212  -8.093  1.00  0.00              
ATOM   1034  CA  GLN   292      16.225  10.621  -8.382  1.00  0.00              
ATOM   1035  C   GLN   292      17.281  11.290  -9.252  1.00  0.00              
ATOM   1036  O   GLN   292      18.434  11.440  -8.846  1.00  0.00              
ATOM   1037  N   VAL   293      16.869  11.701 -10.448  1.00  0.00              
ATOM   1038  CA  VAL   293      17.765  12.360 -11.392  1.00  0.00              
ATOM   1039  C   VAL   293      18.522  13.491 -10.709  1.00  0.00              
ATOM   1040  O   VAL   293      19.707  13.720 -10.969  1.00  0.00              
ATOM   1041  N   HIS   294      17.818  14.195  -9.834  1.00  0.00              
ATOM   1042  CA  HIS   294      18.389  15.318  -9.114  1.00  0.00              
ATOM   1043  C   HIS   294      19.504  14.901  -8.158  1.00  0.00              
ATOM   1044  O   HIS   294      20.612  15.445  -8.209  1.00  0.00              
ATOM   1045  N   PHE   295      19.217  13.931  -7.295  1.00  0.00              
ATOM   1046  CA  PHE   295      20.208  13.463  -6.330  1.00  0.00              
ATOM   1047  C   PHE   295      21.455  12.869  -6.975  1.00  0.00              
ATOM   1048  O   PHE   295      22.569  13.151  -6.541  1.00  0.00              
ATOM   1049  N   THR   296      21.268  12.059  -8.014  1.00  0.00              
ATOM   1050  CA  THR   296      22.390  11.440  -8.710  1.00  0.00              
ATOM   1051  C   THR   296      23.398  12.465  -9.242  1.00  0.00              
ATOM   1052  O   THR   296      24.595  12.372  -8.963  1.00  0.00              
ATOM   1053  N   ARG   297      22.911  13.439 -10.008  1.00  0.00              
ATOM   1054  CA  ARG   297      23.772  14.472 -10.584  1.00  0.00              
ATOM   1055  C   ARG   297      24.414  15.369  -9.520  1.00  0.00              
ATOM   1056  O   ARG   297      25.565  15.793  -9.663  1.00  0.00              
ATOM   1057  N   GLU   298      23.667  15.662  -8.461  1.00  0.00              
ATOM   1058  CA  GLU   298      24.176  16.507  -7.385  1.00  0.00              
ATOM   1059  C   GLU   298      25.386  15.807  -6.759  1.00  0.00              
ATOM   1060  O   GLU   298      26.381  16.441  -6.411  1.00  0.00              
ATOM   1061  N   MET   299      25.286  14.488  -6.640  1.00  0.00              
ATOM   1062  CA  MET   299      26.348  13.666  -6.084  1.00  0.00              
ATOM   1063  C   MET   299      27.441  13.489  -7.140  1.00  0.00              
ATOM   1064  O   MET   299      28.631  13.517  -6.832  1.00  0.00              
ATOM   1065  N   PRO   300      27.039  13.330  -8.394  1.00  0.00              
ATOM   1066  CA  PRO   300      28.002  13.146  -9.471  1.00  0.00              
ATOM   1067  C   PRO   300      28.987  14.310  -9.575  1.00  0.00              
ATOM   1068  O   PRO   300      30.159  14.110  -9.898  1.00  0.00              
ATOM   1069  N   GLU   301      28.512  15.520  -9.295  1.00  0.00              
ATOM   1070  CA  GLU   301      29.358  16.707  -9.377  1.00  0.00              
ATOM   1071  C   GLU   301      30.556  16.670  -8.434  1.00  0.00              
ATOM   1072  O   GLU   301      31.569  17.324  -8.690  1.00  0.00              
ATOM   1073  N   GLU   302      30.455  15.906  -7.350  1.00  0.00              
ATOM   1074  CA  GLU   302      31.562  15.817  -6.403  1.00  0.00              
ATOM   1075  C   GLU   302      32.716  15.020  -6.993  1.00  0.00              
ATOM   1076  O   GLU   302      33.733  14.792  -6.336  1.00  0.00              
ATOM   1077  N   PHE   303      32.555  14.602  -8.243  1.00  0.00              
ATOM   1078  CA  PHE   303      33.591  13.850  -8.935  1.00  0.00              
ATOM   1079  C   PHE   303      34.567  14.824  -9.597  1.00  0.00              
ATOM   1080  O   PHE   303      35.647  14.428 -10.043  1.00  0.00              
ATOM   1081  N   THR   304      34.187  16.100  -9.652  1.00  0.00              
ATOM   1082  CA  THR   304      35.034  17.109 -10.280  1.00  0.00              
ATOM   1083  C   THR   304      35.451  18.238  -9.338  1.00  0.00              
ATOM   1084  O   THR   304      36.384  18.985  -9.640  1.00  0.00              
ATOM   1085  N   PRO   336      34.758  18.366  -8.207  1.00  0.00              
ATOM   1086  CA  PRO   336      35.069  19.405  -7.227  1.00  0.00              
ATOM   1087  C   PRO   336      34.716  18.949  -5.811  1.00  0.00              
ATOM   1088  O   PRO   336      33.584  18.546  -5.548  1.00  0.00              
ATOM   1089  N   GLN   337      35.687  19.018  -4.904  1.00  0.00              
ATOM   1090  CA  GLN   337      35.454  18.611  -3.528  1.00  0.00              
ATOM   1091  C   GLN   337      34.215  19.232  -2.904  1.00  0.00              
ATOM   1092  O   GLN   337      33.688  20.226  -3.406  1.00  0.00              
ATOM   1093  N   ARG   338      33.746  18.644  -1.806  1.00  0.00              
ATOM   1094  CA  ARG   338      32.567  19.165  -1.137  1.00  0.00              
ATOM   1095  C   ARG   338      31.780  18.094  -0.405  1.00  0.00              
ATOM   1096  O   ARG   338      32.288  17.002  -0.156  1.00  0.00              
ATOM   1097  N   ALA   339      30.535  18.408  -0.059  1.00  0.00              
ATOM   1098  CA  ALA   339      29.677  17.464   0.649  1.00  0.00              
ATOM   1099  C   ALA   339      28.241  17.534   0.129  1.00  0.00              
ATOM   1100  O   ALA   339      27.824  18.549  -0.429  1.00  0.00              
ATOM   1101  N   ILE   340      27.488  16.453   0.316  1.00  0.00              
ATOM   1102  CA  ILE   340      26.100  16.385  -0.135  1.00  0.00              
ATOM   1103  C   ILE   340      25.228  15.665   0.891  1.00  0.00              
ATOM   1104  O   ILE   340      25.573  14.576   1.349  1.00  0.00              
ATOM   1105  N   THR   341      24.093  16.266   1.236  1.00  0.00              
ATOM   1106  CA  THR   341      23.192  15.679   2.223  1.00  0.00              
ATOM   1107  C   THR   341      21.817  15.321   1.654  1.00  0.00              
ATOM   1108  O   THR   341      21.156  16.145   1.019  1.00  0.00              
ATOM   1109  N   PRO   342      21.403  14.081   1.896  1.00  0.00              
ATOM   1110  CA  PRO   342      20.111  13.568   1.447  1.00  0.00              
ATOM   1111  C   PRO   342      19.481  12.894   2.667  1.00  0.00              
ATOM   1112  O   PRO   342      18.357  12.394   2.617  1.00  0.00              
ATOM   1113  N   GLY   343      20.236  12.899   3.762  1.00  0.00              
ATOM   1114  CA  GLY   343      19.826  12.269   5.004  1.00  0.00              
ATOM   1115  C   GLY   343      21.010  11.394   5.380  1.00  0.00              
ATOM   1116  O   GLY   343      21.020  10.698   6.397  1.00  0.00              
ATOM   1117  N   GLN   344      22.018  11.458   4.512  1.00  0.00              
ATOM   1118  CA  GLN   344      23.273  10.723   4.624  1.00  0.00              
ATOM   1119  C   GLN   344      24.349  11.617   3.995  1.00  0.00              
ATOM   1120  O   GLN   344      24.060  12.371   3.068  1.00  0.00              
ATOM   1121  N   ALA   345      25.582  11.538   4.485  1.00  0.00              
ATOM   1122  CA  ALA   345      26.626  12.398   3.950  1.00  0.00              
ATOM   1123  C   ALA   345      27.623  11.816   2.963  1.00  0.00              
ATOM   1124  O   ALA   345      28.112  10.703   3.139  1.00  0.00              
ATOM   1125  N   VAL   346      27.926  12.589   1.922  1.00  0.00              
ATOM   1126  CA  VAL   346      28.883  12.190   0.893  1.00  0.00              
ATOM   1127  C   VAL   346      29.990  13.229   0.813  1.00  0.00              
ATOM   1128  O   VAL   346      29.787  14.316   0.278  1.00  0.00              
ATOM   1129  N   VAL   347      31.160  12.888   1.342  1.00  0.00              
ATOM   1130  CA  VAL   347      32.294  13.807   1.348  1.00  0.00              
ATOM   1131  C   VAL   347      33.357  13.410   0.324  1.00  0.00              
ATOM   1132  O   VAL   347      33.575  12.224   0.074  1.00  0.00              
ATOM   1133  N   PHE   348      34.009  14.407  -0.271  1.00  0.00              
ATOM   1134  CA  PHE   348      35.069  14.142  -1.236  1.00  0.00              
ATOM   1135  C   PHE   348      36.392  14.323  -0.496  1.00  0.00              
ATOM   1136  O   PHE   348      36.811  15.445  -0.207  1.00  0.00              
ATOM   1137  N   TYR   349      37.035  13.207  -0.173  1.00  0.00              
ATOM   1138  CA  TYR   349      38.305  13.226   0.536  1.00  0.00              
ATOM   1139  C   TYR   349      39.428  12.888  -0.437  1.00  0.00              
ATOM   1140  O   TYR   349      39.961  11.780  -0.409  1.00  0.00              
ATOM   1141  N   ASP   350      39.774  13.847  -1.293  1.00  0.00              
ATOM   1142  CA  ASP   350      40.832  13.674  -2.288  1.00  0.00              
ATOM   1143  C   ASP   350      40.885  12.269  -2.897  1.00  0.00              
ATOM   1144  O   ASP   350      41.464  11.352  -2.319  1.00  0.00              
ATOM   1145  N   GLY   351      40.272  12.109  -4.065  1.00  0.00              
ATOM   1146  CA  GLY   351      40.259  10.828  -4.768  1.00  0.00              
ATOM   1147  C   GLY   351      39.239   9.813  -4.253  1.00  0.00              
ATOM   1148  O   GLY   351      38.772   8.970  -5.017  1.00  0.00              
ATOM   1149  N   GLU   352      38.892   9.880  -2.971  1.00  0.00              
ATOM   1150  CA  GLU   352      37.922   8.940  -2.411  1.00  0.00              
ATOM   1151  C   GLU   352      36.586   9.639  -2.156  1.00  0.00              
ATOM   1152  O   GLU   352      36.438  10.823  -2.455  1.00  0.00              
ATOM   1153  N   GLU   353      35.619   8.906  -1.608  1.00  0.00              
ATOM   1154  CA  GLU   353      34.296   9.465  -1.328  1.00  0.00              
ATOM   1155  C   GLU   353      33.416   8.530  -0.486  1.00  0.00              
ATOM   1156  O   GLU   353      33.136   7.410  -0.903  1.00  0.00              
ATOM   1157  N   CYS   354      32.954   9.005   0.674  1.00  0.00              
ATOM   1158  CA  CYS   354      32.135   8.184   1.574  1.00  0.00              
ATOM   1159  C   CYS   354      30.613   8.322   1.510  1.00  0.00              
ATOM   1160  O   CYS   354      30.077   9.318   1.031  1.00  0.00              
ATOM   1161  N   LEU   355      29.959   7.286   2.038  1.00  0.00              
ATOM   1162  CA  LEU   355      28.510   7.115   2.172  1.00  0.00              
ATOM   1163  C   LEU   355      28.117   5.716   1.732  1.00  0.00              
ATOM   1164  O   LEU   355      27.598   5.570   0.605  1.00  0.00              
END
