
#######################################################
#                                                     #
#                        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_3_1-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected  335 , name T0318_D2.pdb
# PARAMETERS: T0318TS268_3_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    -       -      E     239           -
LGA    -       -      V     240           -
LGA    T     156      P     241          2.161
LGA    N     157      G     242          1.264
LGA    E     158      S     243          0.308
LGA    D     159      T     244          1.925
LGA    A     160      E     245          2.381
LGA    -       -      H     246           -
LGA    V     161      I     247          1.531
LGA    F     162      A     248          1.215
LGA    L     163      L     249          1.454
LGA    T     164      V     250          1.323
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    D     165      C     301          2.018
LGA    -       -      L     302           -
LGA    -       -      C     303           -
LGA    -       -      I     304           -
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    1.66    10.00      2.736     0.569

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.518876 * X  +   0.835889 * Y  +  -0.179046 * Z  + -119.637085
  Y_new =   0.847349 * X  +  -0.475230 * Y  +   0.236972 * Z  + -32.124077
  Z_new =   0.112995 * X  +  -0.274674 * Y  +  -0.954875 * Z  +  66.794991 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.861501    0.280092  [ DEG:  -163.9519     16.0481 ]
  Theta =  -0.113236   -3.028356  [ DEG:    -6.4880   -173.5120 ]
  Phi   =   1.021344   -2.120249  [ DEG:    58.5187   -121.4813 ]
 
# 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_3_1-D2                             
REMARK     2: T0318_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0318TS268_3_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   1.66   10.00   2.736
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS268_3_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0318
PARENT 1tf7_A
ATOM   1209  N   THR   156       1.849  27.145  -2.462  1.00  0.00
ATOM   1210  CA  THR   156       2.503  26.541  -1.327  1.00  0.00
ATOM   1211  C   THR   156       1.534  26.398  -0.189  1.00  0.00
ATOM   1212  O   THR   156       1.485  25.360   0.467  1.00  0.00
ATOM   1213  CB  THR   156       3.690  27.393  -0.840  1.00  0.00
ATOM   1214  OG1 THR   156       4.667  27.496  -1.884  1.00  0.00
ATOM   1215  CG2 THR   156       4.338  26.756   0.380  1.00  0.00
ATOM   1216  N   ASN   157       0.720  27.444   0.057  1.00  0.00
ATOM   1217  CA  ASN   157      -0.297  27.434   1.073  1.00  0.00
ATOM   1218  C   ASN   157       0.237  27.180   2.450  1.00  0.00
ATOM   1219  O   ASN   157      -0.276  26.313   3.154  1.00  0.00
ATOM   1220  CB  ASN   157      -1.330  26.341   0.788  1.00  0.00
ATOM   1221  CG  ASN   157      -2.609  26.529   1.578  1.00  0.00
ATOM   1222  OD1 ASN   157      -2.964  27.648   1.948  1.00  0.00
ATOM   1223  ND2 ASN   157      -3.309  25.430   1.837  1.00  0.00
ATOM   1224  N   GLU   158       1.278  27.912   2.887  1.00  0.00
ATOM   1225  CA  GLU   158       1.734  27.741   4.241  1.00  0.00
ATOM   1226  C   GLU   158       0.844  28.582   5.117  1.00  0.00
ATOM   1227  O   GLU   158       0.223  29.532   4.642  1.00  0.00
ATOM   1228  CB  GLU   158       3.189  28.194   4.378  1.00  0.00
ATOM   1229  CG  GLU   158       4.179  27.348   3.594  1.00  0.00
ATOM   1230  CD  GLU   158       5.617  27.772   3.822  1.00  0.00
ATOM   1231  OE1 GLU   158       5.832  28.799   4.498  1.00  0.00
ATOM   1232  OE2 GLU   158       6.527  27.076   3.325  1.00  0.00
ATOM   1233  N   ASP   159       0.720  28.232   6.419  1.00  0.00
ATOM   1234  CA  ASP   159      -0.081  29.041   7.305  1.00  0.00
ATOM   1235  C   ASP   159       0.686  30.303   7.507  1.00  0.00
ATOM   1236  O   ASP   159       1.771  30.292   8.084  1.00  0.00
ATOM   1237  CB  ASP   159      -0.302  28.320   8.637  1.00  0.00
ATOM   1238  CG  ASP   159      -1.220  29.086   9.569  1.00  0.00
ATOM   1239  OD1 ASP   159      -1.625  30.213   9.211  1.00  0.00
ATOM   1240  OD2 ASP   159      -1.533  28.561  10.657  1.00  0.00
ATOM   1241  N   ALA   160       0.144  31.441   7.051  1.00  0.00
ATOM   1242  CA  ALA   160       0.923  32.620   7.253  1.00  0.00
ATOM   1243  C   ALA   160       0.036  33.656   7.833  1.00  0.00
ATOM   1244  O   ALA   160      -1.184  33.512   7.829  1.00  0.00
ATOM   1245  CB  ALA   160       1.494  33.111   5.931  1.00  0.00
ATOM   1246  N   VAL   161       0.661  34.719   8.369  1.00  0.00
ATOM   1247  CA  VAL   161       0.030  35.832   9.013  1.00  0.00
ATOM   1248  C   VAL   161       0.476  37.039   8.254  1.00  0.00
ATOM   1249  O   VAL   161       0.773  36.938   7.067  1.00  0.00
ATOM   1250  CB  VAL   161       0.449  35.939  10.491  1.00  0.00
ATOM   1251  CG1 VAL   161      -0.018  34.718  11.268  1.00  0.00
ATOM   1252  CG2 VAL   161       1.963  36.035  10.611  1.00  0.00
ATOM   1253  N   PHE   162       0.474  38.229   8.888  1.00  0.00
ATOM   1254  CA  PHE   162       0.931  39.371   8.147  1.00  0.00
ATOM   1255  C   PHE   162       1.821  40.226   8.995  1.00  0.00
ATOM   1256  O   PHE   162       1.916  40.051  10.209  1.00  0.00
ATOM   1257  CB  PHE   162      -0.256  40.219   7.684  1.00  0.00
ATOM   1258  CG  PHE   162      -1.037  40.833   8.809  1.00  0.00
ATOM   1259  CD1 PHE   162      -0.733  42.102   9.271  1.00  0.00
ATOM   1260  CD2 PHE   162      -2.076  40.141   9.407  1.00  0.00
ATOM   1261  CE1 PHE   162      -1.454  42.667  10.307  1.00  0.00
ATOM   1262  CE2 PHE   162      -2.796  40.707  10.444  1.00  0.00
ATOM   1263  CZ  PHE   162      -2.489  41.964  10.893  1.00  0.00
ATOM   1264  N   LEU   163       2.531  41.159   8.327  1.00  0.00
ATOM   1265  CA  LEU   163       3.451  42.079   8.939  1.00  0.00
ATOM   1266  C   LEU   163       2.746  43.380   9.115  1.00  0.00
ATOM   1267  O   LEU   163       1.572  43.516   8.775  1.00  0.00
ATOM   1268  CB  LEU   163       4.683  42.274   8.052  1.00  0.00
ATOM   1269  CG  LEU   163       5.483  41.013   7.718  1.00  0.00
ATOM   1270  CD1 LEU   163       6.640  41.342   6.786  1.00  0.00
ATOM   1271  CD2 LEU   163       6.052  40.385   8.980  1.00  0.00
ATOM   1272  N   THR   164       3.451  44.369   9.700  1.00  0.00
ATOM   1273  CA  THR   164       2.851  45.653   9.871  1.00  0.00
ATOM   1274  C   THR   164       2.775  46.282   8.522  1.00  0.00
ATOM   1275  O   THR   164       3.692  46.169   7.710  1.00  0.00
ATOM   1276  CB  THR   164       3.683  46.543  10.813  1.00  0.00
ATOM   1277  OG1 THR   164       3.792  45.916  12.097  1.00  0.00
ATOM   1278  CG2 THR   164       3.023  47.903  10.984  1.00  0.00
ATOM   1279  N   ASP   165       1.640  46.951   8.244  1.00  0.00
ATOM   1280  CA  ASP   165       1.454  47.563   6.963  1.00  0.00
ATOM   1281  C   ASP   165       1.755  49.048   7.081  1.00  0.00
ATOM   1282  O   ASP   165       2.378  49.452   8.100  1.00  0.00
ATOM   1283  CB  ASP   165       0.012  47.376   6.485  1.00  0.00
ATOM   1284  CG  ASP   165      -0.282  45.950   6.066  1.00  0.00
ATOM   1285  OD1 ASP   165       0.675  45.155   5.949  1.00  0.00
ATOM   1286  OD2 ASP   165      -1.469  45.625   5.855  1.00  0.00
TER
END
