
#######################################################
#                                                     #
#                        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 T0318TS022_1_1-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected  335 , name T0318_D2.pdb
# PARAMETERS: T0318TS022_1_1-D2.T0318_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      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    -       -      H     246           -
LGA    -       -      I     247           -
LGA    -       -      A     248           -
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    -       -      H     299           -
LGA    -       -      A     300           -
LGA    -       -      C     301           -
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    T     156      A     366          2.234
LGA    N     157      Q     367          2.561
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    E     158      P     432          2.964
LGA    D     159      P     433          1.592
LGA    A     160      S     434          1.279
LGA    V     161      A     435          0.408
LGA    F     162      V     436          0.272
LGA    L     163      A     437          1.106
LGA    T     164      G     438          1.268
LGA    D     165      L     439          0.978
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    1.69     0.00      2.853     0.559

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.263033 * X  +  -0.066522 * Y  +  -0.962491 * Z  + -37.374851
  Y_new =   0.865109 * X  +   0.457880 * Y  +   0.204774 * Z  +  22.697142
  Z_new =   0.427084 * X  +  -0.886521 * Y  +   0.177986 * Z  +  43.391045 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.372661    1.768932  [ DEG:   -78.6477    101.3523 ]
  Theta =  -0.441265   -2.700327  [ DEG:   -25.2826   -154.7174 ]
  Phi   =   1.275632   -1.865961  [ DEG:    73.0883   -106.9117 ]
 
# 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: T0318TS022_1_1-D2                             
REMARK     2: T0318_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0318TS022_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   1.69    0.00   2.853
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS022_1_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0318
PARENT 1gyt_A
ATOM   1209  N   THR   156       0.867  58.613  29.299  1.00  0.00
ATOM   1210  CA  THR   156       0.179  57.556  29.968  1.00  0.00
ATOM   1211  C   THR   156       0.217  56.371  29.052  1.00  0.00
ATOM   1212  O   THR   156      -0.168  56.453  27.886  1.00  0.00
ATOM   1213  CB  THR   156      -1.282  57.937  30.271  1.00  0.00
ATOM   1214  OG1 THR   156      -1.312  59.094  31.117  1.00  0.00
ATOM   1215  CG2 THR   156      -1.995  56.794  30.977  1.00  0.00
ATOM   1216  N   ASN   157       0.713  55.233  29.574  1.00  0.00
ATOM   1217  CA  ASN   157       0.835  54.002  28.844  1.00  0.00
ATOM   1218  C   ASN   157      -0.542  53.500  28.563  1.00  0.00
ATOM   1219  O   ASN   157      -0.804  52.892  27.527  1.00  0.00
ATOM   1220  CB  ASN   157       1.607  52.967  29.665  1.00  0.00
ATOM   1221  CG  ASN   157       3.087  53.280  29.754  1.00  0.00
ATOM   1222  OD1 ASN   157       3.626  54.017  28.929  1.00  0.00
ATOM   1223  ND2 ASN   157       3.750  52.719  30.759  1.00  0.00
ATOM   1224  N   GLU   158      -1.467  53.774  29.497  1.00  0.00
ATOM   1225  CA  GLU   158      -2.803  53.260  29.460  1.00  0.00
ATOM   1226  C   GLU   158      -3.478  53.720  28.213  1.00  0.00
ATOM   1227  O   GLU   158      -4.373  53.053  27.702  1.00  0.00
ATOM   1228  CB  GLU   158      -3.602  53.754  30.668  1.00  0.00
ATOM   1229  CG  GLU   158      -3.176  53.134  31.989  1.00  0.00
ATOM   1230  CD  GLU   158      -3.922  53.716  33.173  1.00  0.00
ATOM   1231  OE1 GLU   158      -4.723  54.652  32.969  1.00  0.00
ATOM   1232  OE2 GLU   158      -3.707  53.235  34.305  1.00  0.00
ATOM   1233  N   ASP   159      -3.069  54.878  27.677  1.00  0.00
ATOM   1234  CA  ASP   159      -3.723  55.419  26.524  1.00  0.00
ATOM   1235  C   ASP   159      -3.615  54.448  25.386  1.00  0.00
ATOM   1236  O   ASP   159      -4.501  54.374  24.537  1.00  0.00
ATOM   1237  CB  ASP   159      -3.074  56.742  26.112  1.00  0.00
ATOM   1238  CG  ASP   159      -3.411  57.876  27.060  1.00  0.00
ATOM   1239  OD1 ASP   159      -4.323  57.701  27.896  1.00  0.00
ATOM   1240  OD2 ASP   159      -2.762  58.939  26.969  1.00  0.00
ATOM   1241  N   ALA   160      -2.528  53.658  25.344  1.00  0.00
ATOM   1242  CA  ALA   160      -2.270  52.786  24.233  1.00  0.00
ATOM   1243  C   ALA   160      -3.406  51.828  24.043  1.00  0.00
ATOM   1244  O   ALA   160      -3.766  51.510  22.911  1.00  0.00
ATOM   1245  CB  ALA   160      -1.000  51.986  24.471  1.00  0.00
ATOM   1246  N   VAL   161      -3.999  51.326  25.139  1.00  0.00
ATOM   1247  CA  VAL   161      -5.054  50.363  25.008  1.00  0.00
ATOM   1248  C   VAL   161      -6.215  50.961  24.272  1.00  0.00
ATOM   1249  O   VAL   161      -6.825  50.300  23.433  1.00  0.00
ATOM   1250  CB  VAL   161      -5.557  49.885  26.383  1.00  0.00
ATOM   1251  CG1 VAL   161      -6.799  49.022  26.227  1.00  0.00
ATOM   1252  CG2 VAL   161      -4.486  49.064  27.086  1.00  0.00
ATOM   1253  N   PHE   162      -6.545  52.238  24.548  1.00  0.00
ATOM   1254  CA  PHE   162      -7.706  52.851  23.965  1.00  0.00
ATOM   1255  C   PHE   162      -7.566  52.884  22.476  1.00  0.00
ATOM   1256  O   PHE   162      -8.527  52.623  21.752  1.00  0.00
ATOM   1257  CB  PHE   162      -7.869  54.284  24.477  1.00  0.00
ATOM   1258  CG  PHE   162      -8.452  54.371  25.858  1.00  0.00
ATOM   1259  CD1 PHE   162      -7.638  54.603  26.955  1.00  0.00
ATOM   1260  CD2 PHE   162      -9.812  54.221  26.062  1.00  0.00
ATOM   1261  CE1 PHE   162      -8.175  54.683  28.225  1.00  0.00
ATOM   1262  CE2 PHE   162     -10.348  54.302  27.334  1.00  0.00
ATOM   1263  CZ  PHE   162      -9.536  54.532  28.413  1.00  0.00
ATOM   1264  N   LEU   163      -6.367  53.224  21.973  1.00  0.00
ATOM   1265  CA  LEU   163      -6.196  53.345  20.555  1.00  0.00
ATOM   1266  C   LEU   163      -6.415  52.025  19.889  1.00  0.00
ATOM   1267  O   LEU   163      -7.012  51.975  18.815  1.00  0.00
ATOM   1268  CB  LEU   163      -4.781  53.826  20.224  1.00  0.00
ATOM   1269  CG  LEU   163      -4.450  55.270  20.605  1.00  0.00
ATOM   1270  CD1 LEU   163      -2.972  55.558  20.390  1.00  0.00
ATOM   1271  CD2 LEU   163      -5.252  56.247  19.757  1.00  0.00
ATOM   1272  N   THR   164      -5.950  50.917  20.496  1.00  0.00
ATOM   1273  CA  THR   164      -6.159  49.654  19.849  1.00  0.00
ATOM   1274  C   THR   164      -7.633  49.464  19.722  1.00  0.00
ATOM   1275  O   THR   164      -8.128  49.049  18.675  1.00  0.00
ATOM   1276  CB  THR   164      -5.555  48.495  20.665  1.00  0.00
ATOM   1277  OG1 THR   164      -4.140  48.679  20.784  1.00  0.00
ATOM   1278  CG2 THR   164      -5.824  47.165  19.979  1.00  0.00
ATOM   1279  N   ASP   165      -8.384  49.781  20.792  1.00  0.00
ATOM   1280  CA  ASP   165      -9.805  49.630  20.732  1.00  0.00
ATOM   1281  C   ASP   165     -10.352  50.903  20.114  1.00  0.00
ATOM   1282  O   ASP   165     -10.084  51.133  18.904  1.00  0.00
ATOM   1283  CB  ASP   165     -10.382  49.427  22.134  1.00  0.00
ATOM   1284  CG  ASP   165     -11.832  48.985  22.108  1.00  0.00
ATOM   1285  OD1 ASP   165     -12.332  48.650  21.014  1.00  0.00
ATOM   1286  OD2 ASP   165     -12.469  48.974  23.184  1.00  0.00
TER
END
