
#######################################################
#                                                     #
#                        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   10 (   78),  selected   10 , name T0318TS268_1_1-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected  335 , name T0318_D2.pdb
# PARAMETERS: T0318TS268_1_1-D2.T0318_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     156           -
LGA    -       -      N     157           -
LGA    -       -      E     158           -
LGA    -       -      D     159           -
LGA    -       -      A     160           -
LGA    -       -      V     161           -
LGA    -       -      F     162           -
LGA    -       -      L     163           -
LGA    -       -      T     164           -
LGA    -       -      D     165           -
LGA    -       -      L     166           -
LGA    -       -      S     167           -
LGA    -       -      E     168           -
LGA    -       -      S     169           -
LGA    -       -      V     170           -
LGA    -       -      R     171           -
LGA    -       -      E     172           -
LGA    -       -      T     173           -
LGA    -       -      A     174           -
LGA    -       -      R     175           -
LGA    -       -      L     176           -
LGA    -       -      I     177           -
LGA    -       -      D     178           -
LGA    -       -      T     179           -
LGA    -       -      P     180           -
LGA    -       -      A     181           -
LGA    -       -      N     182           -
LGA    -       -      I     183           -
LGA    -       -      L     184           -
LGA    -       -      T     185           -
LGA    -       -      T     186           -
LGA    -       -      D     187           -
LGA    -       -      A     188           -
LGA    -       -      L     189           -
LGA    -       -      V     190           -
LGA    -       -      D     191           -
LGA    -       -      E     192           -
LGA    -       -      A     193           -
LGA    -       -      V     194           -
LGA    -       -      K     195           -
LGA    -       -      V     196           -
LGA    -       -      G     197           -
LGA    -       -      N     198           -
LGA    -       -      A     199           -
LGA    -       -      T     200           -
LGA    -       -      G     201           -
LGA    -       -      S     202           -
LGA    -       -      K     203           -
LGA    -       -      I     204           -
LGA    -       -      T     205           -
LGA    -       -      V     206           -
LGA    -       -      I     207           -
LGA    -       -      R     208           -
LGA    -       -      G     209           -
LGA    -       -      E     210           -
LGA    -       -      E     211           -
LGA    -       -      L     212           -
LGA    -       -      L     213           -
LGA    -       -      K     214           -
LGA    -       -      A     215           -
LGA    -       -      G     216           -
LGA    -       -      F     217           -
LGA    -       -      G     218           -
LGA    -       -      G     219           -
LGA    -       -      I     220           -
LGA    -       -      Y     221           -
LGA    -       -      H     222           -
LGA    -       -      V     223           -
LGA    -       -      G     224           -
LGA    -       -      K     225           -
LGA    -       -      A     226           -
LGA    -       -      G     227           -
LGA    -       -      P     228           -
LGA    -       -      T     229           -
LGA    -       -      P     230           -
LGA    -       -      P     231           -
LGA    -       -      A     232           -
LGA    -       -      F     233           -
LGA    -       -      V     234           -
LGA    -       -      V     235           -
LGA    -       -      L     236           -
LGA    -       -      S     237           -
LGA    -       -      H     238           -
LGA    T     156      E     239          3.626
LGA    N     157      V     240          4.788
LGA    -       -      P     241           -
LGA    -       -      G     242           -
LGA    -       -      S     243           -
LGA    -       -      T     244           -
LGA    -       -      E     245           -
LGA    E     158      H     246          2.705
LGA    D     159      I     247          1.689
LGA    A     160      A     248          2.289
LGA    V     161      L     249          2.705
LGA    -       -      V     250           -
LGA    -       -      G     251           -
LGA    -       -      K     252           -
LGA    -       -      G     253           -
LGA    -       -      V     254           -
LGA    -       -      V     255           -
LGA    -       -      Y     256           -
LGA    -       -      D     257           -
LGA    -       -      T     258           -
LGA    -       -      G     259           -
LGA    -       -      G     260           -
LGA    -       -      L     261           -
LGA    -       -      Q     262           -
LGA    -       -      I     263           -
LGA    -       -      K     264           -
LGA    -       -      T     265           -
LGA    -       -      K     266           -
LGA    -       -      T     267           -
LGA    -       -      G     268           -
LGA    -       -      M     269           -
LGA    -       -      P     270           -
LGA    -       -      N     271           -
LGA    -       -      M     272           -
LGA    -       -      K     273           -
LGA    -       -      R     274           -
LGA    -       -      D     275           -
LGA    -       -      M     276           -
LGA    -       -      G     277           -
LGA    -       -      G     278           -
LGA    -       -      A     279           -
LGA    -       -      A     280           -
LGA    -       -      G     281           -
LGA    -       -      M     282           -
LGA    -       -      L     283           -
LGA    -       -      E     284           -
LGA    -       -      A     285           -
LGA    -       -      Y     286           -
LGA    -       -      S     287           -
LGA    -       -      A     288           -
LGA    -       -      L     289           -
LGA    -       -      V     290           -
LGA    -       -      K     291           -
LGA    -       -      H     292           -
LGA    -       -      G     293           -
LGA    -       -      F     294           -
LGA    -       -      S     295           -
LGA    -       -      Q     296           -
LGA    -       -      T     297           -
LGA    -       -      L     298           -
LGA    -       -      H     299           -
LGA    -       -      A     300           -
LGA    F     162      C     301          0.976
LGA    L     163      L     302          1.473
LGA    T     164      C     303          2.315
LGA    D     165      I     304          2.365
LGA    -       -      V     305           -
LGA    -       -      E     306           -
LGA    -       -      N     307           -
LGA    -       -      N     308           -
LGA    -       -      V     309           -
LGA    -       -      S     310           -
LGA    -       -      P     311           -
LGA    -       -      I     312           -
LGA    -       -      A     313           -
LGA    -       -      N     314           -
LGA    -       -      K     315           -
LGA    -       -      P     316           -
LGA    -       -      D     317           -
LGA    -       -      D     318           -
LGA    -       -      I     319           -
LGA    -       -      I     320           -
LGA    -       -      K     321           -
LGA    -       -      M     322           -
LGA    -       -      L     323           -
LGA    -       -      S     324           -
LGA    -       -      G     325           -
LGA    -       -      K     326           -
LGA    -       -      T     327           -
LGA    -       -      V     328           -
LGA    -       -      E     329           -
LGA    -       -      I     330           -
LGA    -       -      N     331           -
LGA    -       -      N     332           -
LGA    -       -      T     333           -
LGA    -       -      D     334           -
LGA    -       -      A     335           -
LGA    -       -      E     336           -
LGA    -       -      G     337           -
LGA    -       -      R     338           -
LGA    -       -      L     339           -
LGA    -       -      I     340           -
LGA    -       -      L     341           -
LGA    -       -      A     342           -
LGA    -       -      D     343           -
LGA    -       -      G     344           -
LGA    -       -      V     345           -
LGA    -       -      F     346           -
LGA    -       -      Y     347           -
LGA    -       -      A     348           -
LGA    -       -      K     349           -
LGA    -       -      E     350           -
LGA    -       -      T     351           -
LGA    -       -      L     352           -
LGA    -       -      K     353           -
LGA    -       -      A     354           -
LGA    -       -      T     355           -
LGA    -       -      T     356           -
LGA    -       -      I     357           -
LGA    -       -      F     358           -
LGA    -       -      D     359           -
LGA    -       -      M     360           -
LGA    -       -      A     361           -
LGA    -       -      T     362           -
LGA    -       -      L     363           -
LGA    -       -      T     364           -
LGA    -       -      G     365           -
LGA    -       -      A     366           -
LGA    -       -      Q     367           -
LGA    -       -      A     368           -
LGA    -       -      W     369           -
LGA    -       -      L     370           -
LGA    -       -      S     371           -
LGA    -       -      G     372           -
LGA    -       -      R     373           -
LGA    -       -      L     374           -
LGA    -       -      H     375           -
LGA    -       -      G     376           -
LGA    -       -      A     377           -
LGA    -       -      A     378           -
LGA    -       -      M     379           -
LGA    -       -      T     380           -
LGA    -       -      N     381           -
LGA    -       -      D     382           -
LGA    -       -      E     383           -
LGA    -       -      Q     384           -
LGA    -       -      L     385           -
LGA    -       -      E     386           -
LGA    -       -      N     387           -
LGA    -       -      E     388           -
LGA    -       -      I     389           -
LGA    -       -      I     390           -
LGA    -       -      K     391           -
LGA    -       -      A     392           -
LGA    -       -      G     393           -
LGA    -       -      K     394           -
LGA    -       -      A     395           -
LGA    -       -      S     396           -
LGA    -       -      G     397           -
LGA    -       -      D     398           -
LGA    -       -      L     399           -
LGA    -       -      V     400           -
LGA    -       -      A     401           -
LGA    -       -      P     402           -
LGA    -       -      M     403           -
LGA    -       -      L     404           -
LGA    -       -      F     405           -
LGA    -       -      A     406           -
LGA    -       -      P     407           -
LGA    -       -      D     408           -
LGA    -       -      L     409           -
LGA    -       -      F     410           -
LGA    -       -      F     411           -
LGA    -       -      G     412           -
LGA    -       -      D     413           -
LGA    -       -      L     414           -
LGA    -       -      K     415           -
LGA    -       -      S     416           -
LGA    -       -      S     417           -
LGA    -       -      I     418           -
LGA    -       -      A     419           -
LGA    -       -      D     420           -
LGA    -       -      M     421           -
LGA    -       -      K     422           -
LGA    -       -      N     423           -
LGA    -       -      S     424           -
LGA    -       -      N     425           -
LGA    -       -      L     426           -
LGA    -       -      G     427           -
LGA    -       -      K     428           -
LGA    -       -      M     429           -
LGA    -       -      D     430           -
LGA    -       -      G     431           -
LGA    -       -      P     432           -
LGA    -       -      P     433           -
LGA    -       -      S     434           -
LGA    -       -      A     435           -
LGA    -       -      V     436           -
LGA    -       -      A     437           -
LGA    -       -      G     438           -
LGA    -       -      L     439           -
LGA    -       -      L     440           -
LGA    -       -      I     441           -
LGA    -       -      G     442           -
LGA    -       -      A     443           -
LGA    -       -      H     444           -
LGA    -       -      I     445           -
LGA    -       -      G     446           -
LGA    -       -      F     447           -
LGA    -       -      G     448           -
LGA    -       -      E     449           -
LGA    -       -      G     450           -
LGA    -       -      L     451           -
LGA    -       -      R     452           -
LGA    -       -      W     453           -
LGA    -       -      L     454           -
LGA    -       -      H     455           -
LGA    -       -      L     456           -
LGA    -       -      D     457           -
LGA    -       -      I     458           -
LGA    -       -      A     459           -
LGA    -       -      A     460           -
LGA    -       -      P     461           -
LGA    -       -      A     462           -
LGA    -       -      E     463           -
LGA    -       -      V     464           -
LGA    -       -      G     465           -
LGA    -       -      D     466           -
LGA    -       -      R     467           -
LGA    -       -      G     468           -
LGA    -       -      T     469           -
LGA    -       -      G     470           -
LGA    -       -      Y     471           -
LGA    -       -      G     472           -
LGA    -       -      P     473           -
LGA    -       -      A     474           -
LGA    -       -      L     475           -
LGA    -       -      F     476           -
LGA    -       -      S     477           -
LGA    -       -      T     478           -
LGA    -       -      L     479           -
LGA    -       -      L     480           -
LGA    -       -      G     481           -
LGA    -       -      K     482           -
LGA    -       -      Y     483           -
LGA    -       -      T     484           -
LGA    -       -      S     485           -
LGA    -       -      V     486           -
LGA    -       -      P     487           -
LGA    -       -      M     488           -
LGA    -       -      L     489           -
LGA    -       -      K     490           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   10  335    5.0     10    2.70    20.00      2.279     0.357

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.547773 * X  +  -0.704759 * Y  +  -0.450842 * Z  +  41.337177
  Y_new =  -0.678938 * X  +  -0.689345 * Y  +   0.252679 * Z  +  48.887791
  Z_new =  -0.488864 * X  +   0.167683 * Y  +  -0.856093 * Z  +  75.181496 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.948172   -0.193421  [ DEG:   168.9178    -11.0822 ]
  Theta =   0.510787    2.630806  [ DEG:    29.2659    150.7341 ]
  Phi   =  -0.891917    2.249676  [ DEG:   -51.1031    128.8969 ]
 
# 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: T0318TS268_1_1-D2                             
REMARK     2: T0318_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0318TS268_1_1-D2.T0318_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   10  335   5.0   10   2.70   20.00   2.279
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS268_1_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0318
PARENT 1h3o_B
ATOM   1209  N   THR   156       5.132  32.672   0.918  1.00  0.00
ATOM   1210  CA  THR   156       4.952  32.339   2.301  1.00  0.00
ATOM   1211  C   THR   156       3.517  32.594   2.584  1.00  0.00
ATOM   1212  O   THR   156       2.844  31.811   3.252  1.00  0.00
ATOM   1213  CB  THR   156       5.844  33.204   3.210  1.00  0.00
ATOM   1214  OG1 THR   156       7.222  32.968   2.896  1.00  0.00
ATOM   1215  CG2 THR   156       5.606  32.861   4.673  1.00  0.00
ATOM   1216  N   ASN   157       3.019  33.723   2.056  1.00  0.00
ATOM   1217  CA  ASN   157       1.641  34.063   2.194  1.00  0.00
ATOM   1218  C   ASN   157       1.316  34.102   3.651  1.00  0.00
ATOM   1219  O   ASN   157       0.167  33.901   4.040  1.00  0.00
ATOM   1220  CB  ASN   157       0.759  33.024   1.499  1.00  0.00
ATOM   1221  CG  ASN   157      -0.620  33.558   1.166  1.00  0.00
ATOM   1222  OD1 ASN   157      -0.795  34.756   0.943  1.00  0.00
ATOM   1223  ND2 ASN   157      -1.605  32.669   1.132  1.00  0.00
ATOM   1224  N   GLU   158       2.325  34.382   4.500  1.00  0.00
ATOM   1225  CA  GLU   158       2.047  34.475   5.901  1.00  0.00
ATOM   1226  C   GLU   158       1.620  35.877   6.158  1.00  0.00
ATOM   1227  O   GLU   158       1.907  36.777   5.370  1.00  0.00
ATOM   1228  CB  GLU   158       3.297  34.141   6.718  1.00  0.00
ATOM   1229  CG  GLU   158       4.409  35.170   6.601  1.00  0.00
ATOM   1230  CD  GLU   158       5.599  34.845   7.482  1.00  0.00
ATOM   1231  OE1 GLU   158       5.442  34.856   8.721  1.00  0.00
ATOM   1232  OE2 GLU   158       6.689  34.579   6.934  1.00  0.00
ATOM   1233  N   ASP   159       0.897  36.098   7.271  1.00  0.00
ATOM   1234  CA  ASP   159       0.432  37.424   7.550  1.00  0.00
ATOM   1235  C   ASP   159       1.639  38.296   7.642  1.00  0.00
ATOM   1236  O   ASP   159       2.592  37.991   8.356  1.00  0.00
ATOM   1237  CB  ASP   159      -0.345  37.454   8.868  1.00  0.00
ATOM   1238  CG  ASP   159      -1.709  36.804   8.755  1.00  0.00
ATOM   1239  OD1 ASP   159      -2.133  36.504   7.619  1.00  0.00
ATOM   1240  OD2 ASP   159      -2.355  36.593   9.803  1.00  0.00
ATOM   1241  N   ALA   160       1.628  39.411   6.888  1.00  0.00
ATOM   1242  CA  ALA   160       2.742  40.306   6.892  1.00  0.00
ATOM   1243  C   ALA   160       2.185  41.680   7.038  1.00  0.00
ATOM   1244  O   ALA   160       1.011  41.919   6.766  1.00  0.00
ATOM   1245  CB  ALA   160       3.524  40.186   5.593  1.00  0.00
ATOM   1246  N   VAL   161       3.027  42.618   7.508  1.00  0.00
ATOM   1247  CA  VAL   161       2.603  43.970   7.696  1.00  0.00
ATOM   1248  C   VAL   161       2.621  44.657   6.374  1.00  0.00
ATOM   1249  O   VAL   161       3.442  44.351   5.510  1.00  0.00
ATOM   1250  CB  VAL   161       3.533  44.723   8.666  1.00  0.00
ATOM   1251  CG1 VAL   161       3.159  46.196   8.725  1.00  0.00
ATOM   1252  CG2 VAL   161       3.425  44.143  10.066  1.00  0.00
ATOM   1253  N   PHE   162       1.675  45.594   6.180  1.00  0.00
ATOM   1254  CA  PHE   162       1.639  46.384   4.985  1.00  0.00
ATOM   1255  C   PHE   162       2.439  47.597   5.321  1.00  0.00
ATOM   1256  O   PHE   162       2.745  47.825   6.492  1.00  0.00
ATOM   1257  CB  PHE   162       0.197  46.744   4.624  1.00  0.00
ATOM   1258  CG  PHE   162      -0.624  45.573   4.167  1.00  0.00
ATOM   1259  CD1 PHE   162      -1.441  44.893   5.054  1.00  0.00
ATOM   1260  CD2 PHE   162      -0.580  45.149   2.850  1.00  0.00
ATOM   1261  CE1 PHE   162      -2.197  43.815   4.633  1.00  0.00
ATOM   1262  CE2 PHE   162      -1.335  44.071   2.430  1.00  0.00
ATOM   1263  CZ  PHE   162      -2.142  43.405   3.315  1.00  0.00
ATOM   1264  N   LEU   163       2.830  48.395   4.307  1.00  0.00
ATOM   1265  CA  LEU   163       3.631  49.546   4.596  1.00  0.00
ATOM   1266  C   LEU   163       2.862  50.394   5.548  1.00  0.00
ATOM   1267  O   LEU   163       1.663  50.617   5.386  1.00  0.00
ATOM   1268  CB  LEU   163       3.923  50.330   3.315  1.00  0.00
ATOM   1269  CG  LEU   163       4.844  51.544   3.458  1.00  0.00
ATOM   1270  CD1 LEU   163       6.245  51.112   3.860  1.00  0.00
ATOM   1271  CD2 LEU   163       4.939  52.304   2.144  1.00  0.00
ATOM   1272  N   THR   164       3.563  50.879   6.589  1.00  0.00
ATOM   1273  CA  THR   164       2.948  51.675   7.604  1.00  0.00
ATOM   1274  C   THR   164       3.315  53.093   7.324  1.00  0.00
ATOM   1275  O   THR   164       4.320  53.367   6.671  1.00  0.00
ATOM   1276  CB  THR   164       3.437  51.277   9.008  1.00  0.00
ATOM   1277  OG1 THR   164       4.843  51.532   9.117  1.00  0.00
ATOM   1278  CG2 THR   164       3.184  49.799   9.261  1.00  0.00
ATOM   1279  N   ASP   165       2.482  54.034   7.805  1.00  0.00
ATOM   1280  CA  ASP   165       2.750  55.423   7.585  1.00  0.00
ATOM   1281  C   ASP   165       4.049  55.749   8.313  1.00  0.00
ATOM   1282  O   ASP   165       5.022  56.163   7.628  1.00  0.00
ATOM   1283  CB  ASP   165       1.608  56.282   8.131  1.00  0.00
ATOM   1284  CG  ASP   165       1.724  57.736   7.716  1.00  0.00
ATOM   1285  OD1 ASP   165       2.619  58.053   6.906  1.00  0.00
ATOM   1286  OD2 ASP   165       0.917  58.558   8.201  1.00  0.00
TER
END
