
#######################################################
#                                                     #
#                        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_2_1-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected  335 , name T0318_D2.pdb
# PARAMETERS: T0318TS268_2_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    -       -      P     241           -
LGA    -       -      G     242           -
LGA    -       -      S     243           -
LGA    -       -      T     244           -
LGA    -       -      E     245           -
LGA    T     156      H     246          1.910
LGA    N     157      I     247          0.569
LGA    E     158      A     248          1.356
LGA    -       -      L     249           -
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    D     159      H     299          1.591
LGA    A     160      A     300          0.275
LGA    V     161      C     301          1.957
LGA    F     162      L     302          1.266
LGA    L     163      C     303          1.433
LGA    T     164      I     304          1.850
LGA    D     165      V     305          0.111
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    1.39    10.00      2.848     0.671

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.237554 * X  +   0.283959 * Y  +  -0.928943 * Z  + -16.464615
  Y_new =   0.922528 * X  +  -0.233490 * Y  +  -0.307287 * Z  +  92.288681
  Z_new =  -0.304156 * X  +  -0.929973 * Y  +  -0.206493 * Z  +  47.034023 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.789294    1.352299  [ DEG:  -102.5190     77.4810 ]
  Theta =   0.309052    2.832541  [ DEG:    17.7074    162.2926 ]
  Phi   =   1.822824   -1.318768  [ DEG:   104.4401    -75.5599 ]
 
# 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_2_1-D2                             
REMARK     2: T0318_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0318TS268_2_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   1.39   10.00   2.848
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS268_2_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0318
PARENT 1g6o_A
ATOM   1209  N   THR   156      -1.345  34.148   5.980  1.00  0.00
ATOM   1210  CA  THR   156      -2.064  35.065   6.817  1.00  0.00
ATOM   1211  C   THR   156      -1.191  35.578   7.916  1.00  0.00
ATOM   1212  O   THR   156      -1.632  35.848   9.033  1.00  0.00
ATOM   1213  CB  THR   156      -3.289  34.396   7.466  1.00  0.00
ATOM   1214  OG1 THR   156      -2.866  33.264   8.236  1.00  0.00
ATOM   1215  CG2 THR   156      -4.268  33.928   6.400  1.00  0.00
ATOM   1216  N   ASN   157       0.108  35.731   7.606  1.00  0.00
ATOM   1217  CA  ASN   157       1.017  36.373   8.510  1.00  0.00
ATOM   1218  C   ASN   157       1.529  37.567   7.756  1.00  0.00
ATOM   1219  O   ASN   157       1.780  37.481   6.556  1.00  0.00
ATOM   1220  CB  ASN   157       2.156  35.425   8.889  1.00  0.00
ATOM   1221  CG  ASN   157       1.668  34.197   9.634  1.00  0.00
ATOM   1222  OD1 ASN   157       1.182  34.296  10.760  1.00  0.00
ATOM   1223  ND2 ASN   157       1.798  33.035   9.005  1.00  0.00
ATOM   1224  N   GLU   158       1.678  38.729   8.426  1.00  0.00
ATOM   1225  CA  GLU   158       2.012  39.917   7.685  1.00  0.00
ATOM   1226  C   GLU   158       3.438  39.945   7.261  1.00  0.00
ATOM   1227  O   GLU   158       4.362  39.844   8.067  1.00  0.00
ATOM   1228  CB  GLU   158       1.764  41.166   8.535  1.00  0.00
ATOM   1229  CG  GLU   158       0.311  41.367   8.933  1.00  0.00
ATOM   1230  CD  GLU   158      -0.087  40.526  10.129  1.00  0.00
ATOM   1231  OE1 GLU   158       0.800  39.878  10.722  1.00  0.00
ATOM   1232  OE2 GLU   158      -1.287  40.515  10.474  1.00  0.00
ATOM   1233  N   ASP   159       3.633  40.040   5.934  1.00  0.00
ATOM   1234  CA  ASP   159       4.930  40.217   5.372  1.00  0.00
ATOM   1235  C   ASP   159       5.389  41.641   5.506  1.00  0.00
ATOM   1236  O   ASP   159       6.565  41.879   5.773  1.00  0.00
ATOM   1237  CB  ASP   159       4.923  39.858   3.885  1.00  0.00
ATOM   1238  CG  ASP   159       4.800  38.366   3.646  1.00  0.00
ATOM   1239  OD1 ASP   159       4.994  37.593   4.608  1.00  0.00
ATOM   1240  OD2 ASP   159       4.511  37.970   2.497  1.00  0.00
ATOM   1241  N   ALA   160       4.485  42.636   5.349  1.00  0.00
ATOM   1242  CA  ALA   160       4.950  43.996   5.438  1.00  0.00
ATOM   1243  C   ALA   160       3.882  44.887   6.003  1.00  0.00
ATOM   1244  O   ALA   160       2.689  44.600   5.927  1.00  0.00
ATOM   1245  CB  ALA   160       5.329  44.517   4.060  1.00  0.00
ATOM   1246  N   VAL   161       4.308  46.009   6.619  1.00  0.00
ATOM   1247  CA  VAL   161       3.390  46.982   7.141  1.00  0.00
ATOM   1248  C   VAL   161       3.708  48.249   6.426  1.00  0.00
ATOM   1249  O   VAL   161       4.785  48.811   6.617  1.00  0.00
ATOM   1250  CB  VAL   161       3.561  47.161   8.661  1.00  0.00
ATOM   1251  CG1 VAL   161       2.598  48.214   9.186  1.00  0.00
ATOM   1252  CG2 VAL   161       3.284  45.852   9.386  1.00  0.00
ATOM   1253  N   PHE   162       2.783  48.757   5.595  1.00  0.00
ATOM   1254  CA  PHE   162       3.127  49.965   4.912  1.00  0.00
ATOM   1255  C   PHE   162       2.522  51.103   5.659  1.00  0.00
ATOM   1256  O   PHE   162       1.306  51.185   5.820  1.00  0.00
ATOM   1257  CB  PHE   162       2.589  49.943   3.480  1.00  0.00
ATOM   1258  CG  PHE   162       3.249  48.920   2.600  1.00  0.00
ATOM   1259  CD1 PHE   162       2.723  47.646   2.480  1.00  0.00
ATOM   1260  CD2 PHE   162       4.397  49.233   1.892  1.00  0.00
ATOM   1261  CE1 PHE   162       3.331  46.704   1.671  1.00  0.00
ATOM   1262  CE2 PHE   162       5.004  48.292   1.082  1.00  0.00
ATOM   1263  CZ  PHE   162       4.476  47.032   0.969  1.00  0.00
ATOM   1264  N   LEU   163       3.388  52.017   6.133  1.00  0.00
ATOM   1265  CA  LEU   163       2.945  53.184   6.833  1.00  0.00
ATOM   1266  C   LEU   163       2.969  54.290   5.841  1.00  0.00
ATOM   1267  O   LEU   163       3.900  54.407   5.047  1.00  0.00
ATOM   1268  CB  LEU   163       3.877  53.490   8.007  1.00  0.00
ATOM   1269  CG  LEU   163       3.986  52.410   9.086  1.00  0.00
ATOM   1270  CD1 LEU   163       5.003  52.808  10.144  1.00  0.00
ATOM   1271  CD2 LEU   163       2.644  52.200   9.772  1.00  0.00
ATOM   1272  N   THR   164       1.918  55.128   5.844  1.00  0.00
ATOM   1273  CA  THR   164       1.917  56.247   4.953  1.00  0.00
ATOM   1274  C   THR   164       1.821  57.461   5.805  1.00  0.00
ATOM   1275  O   THR   164       1.189  57.442   6.859  1.00  0.00
ATOM   1276  CB  THR   164       0.726  56.191   3.978  1.00  0.00
ATOM   1277  OG1 THR   164       0.769  54.964   3.238  1.00  0.00
ATOM   1278  CG2 THR   164       0.781  57.357   3.002  1.00  0.00
ATOM   1279  N   ASP   165       2.483  58.550   5.377  1.00  0.00
ATOM   1280  CA  ASP   165       2.422  59.755   6.141  1.00  0.00
ATOM   1281  C   ASP   165       0.968  60.204   6.079  1.00  0.00
ATOM   1282  O   ASP   165       0.465  60.742   7.101  1.00  0.00
ATOM   1283  CB  ASP   165       3.347  60.816   5.543  1.00  0.00
ATOM   1284  CG  ASP   165       3.543  62.005   6.463  1.00  0.00
ATOM   1285  OD1 ASP   165       3.132  61.919   7.639  1.00  0.00
ATOM   1286  OD2 ASP   165       4.109  63.022   6.009  1.00  0.00
TER
END
