
#######################################################
#                                                     #
#                        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    8 (   59),  selected    8 , name T0298TS268_3_1-D2
# Molecule2: number of CA atoms  186 ( 1394),  selected  186 , name T0298_D2.pdb
# PARAMETERS: T0298TS268_3_1-D2.T0298_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    -       -      C     130           -
LGA    -       -      A     131           -
LGA    -       -      V     132           -
LGA    -       -      A     133           -
LGA    -       -      A     134           -
LGA    -       -      E     135           -
LGA    -       -      L     136           -
LGA    -       -      C     137           -
LGA    C     130      E     138          0.464
LGA    A     131      V     139          0.406
LGA    V     132      L     140          1.729
LGA    A     133      A     141          1.112
LGA    A     134      P     142          1.117
LGA    E     135      L     143          2.945
LGA    L     136      L     144          3.621
LGA    -       -      A     145           -
LGA    -       -      T     146           -
LGA    C     137      L     147          1.493
LGA    -       -      D     148           -
LGA    -       -      C     149           -
LGA    -       -      R     150           -
LGA    -       -      Q     151           -
LGA    -       -      L     152           -
LGA    -       -      N     153           -
LGA    -       -      L     154           -
LGA    -       -      T     155           -
LGA    -       -      A     156           -
LGA    -       -      C     157           -
LGA    -       -      L     158           -
LGA    -       -      S     159           -
LGA    -       -      V     160           -
LGA    -       -      S     161           -
LGA    -       -      S     162           -
LGA    -       -      L     163           -
LGA    -       -      G     164           -
LGA    -       -      R     165           -
LGA    -       -      E     166           -
LGA    -       -      G     167           -
LGA    -       -      V     168           -
LGA    -       -      K     169           -
LGA    -       -      E     170           -
LGA    -       -      L     171           -
LGA    -       -      A     172           -
LGA    -       -      R     173           -
LGA    -       -      Q     174           -
LGA    -       -      T     175           -
LGA    -       -      A     176           -
LGA    -       -      E     177           -
LGA    -       -      L     178           -
LGA    -       -      L     179           -
LGA    -       -      N     180           -
LGA    -       -      A     181           -
LGA    -       -      R     182           -
LGA    -       -      P     183           -
LGA    -       -      L     184           -
LGA    -       -      E     185           -
LGA    -       -      P     186           -
LGA    -       -      R     187           -
LGA    -       -      L     188           -
LGA    -       -      F     189           -
LGA    -       -      D     190           -
LGA    -       -      R     191           -
LGA    -       -      Q     192           -
LGA    -       -      I     193           -
LGA    -       -      A     194           -
LGA    -       -      F     195           -
LGA    -       -      N     196           -
LGA    -       -      L     197           -
LGA    -       -      L     198           -
LGA    -       -      A     199           -
LGA    -       -      Q     200           -
LGA    -       -      V     201           -
LGA    -       -      G     202           -
LGA    -       -      A     203           -
LGA    -       -      V     204           -
LGA    -       -      D     205           -
LGA    -       -      A     206           -
LGA    -       -      E     207           -
LGA    -       -      G     208           -
LGA    -       -      H     209           -
LGA    -       -      S     210           -
LGA    -       -      A     211           -
LGA    -       -      I     212           -
LGA    -       -      E     213           -
LGA    -       -      R     214           -
LGA    -       -      R     215           -
LGA    -       -      I     216           -
LGA    -       -      F     217           -
LGA    -       -      A     218           -
LGA    -       -      E     219           -
LGA    -       -      V     220           -
LGA    -       -      Q     221           -
LGA    -       -      A     222           -
LGA    -       -      L     223           -
LGA    -       -      L     224           -
LGA    -       -      G     225           -
LGA    -       -      E     226           -
LGA    -       -      R     227           -
LGA    -       -      I     228           -
LGA    -       -      G     229           -
LGA    -       -      P     230           -
LGA    -       -      L     231           -
LGA    -       -      N     232           -
LGA    -       -      V     233           -
LGA    -       -      T     234           -
LGA    -       -      C     235           -
LGA    -       -      I     236           -
LGA    -       -      Q     237           -
LGA    -       -      A     238           -
LGA    -       -      P     239           -
LGA    -       -      V     240           -
LGA    -       -      F     241           -
LGA    -       -      F     242           -
LGA    -       -      G     243           -
LGA    -       -      D     244           -
LGA    -       -      S     245           -
LGA    -       -      L     246           -
LGA    -       -      S     247           -
LGA    -       -      V     248           -
LGA    -       -      T     249           -
LGA    -       -      L     250           -
LGA    -       -      Q     251           -
LGA    -       -      C     252           -
LGA    -       -      A     253           -
LGA    -       -      E     254           -
LGA    -       -      P     255           -
LGA    -       -      V     256           -
LGA    -       -      D     257           -
LGA    -       -      L     258           -
LGA    -       -      A     259           -
LGA    -       -      A     260           -
LGA    -       -      V     261           -
LGA    -       -      T     262           -
LGA    -       -      R     263           -
LGA    -       -      V     264           -
LGA    -       -      L     265           -
LGA    -       -      D     266           -
LGA    -       -      A     267           -
LGA    -       -      T     268           -
LGA    -       -      K     269           -
LGA    -       -      G     270           -
LGA    -       -      I     271           -
LGA    -       -      E     272           -
LGA    -       -      W     273           -
LGA    -       -      V     274           -
LGA    -       -      G     275           -
LGA    -       -      E     276           -
LGA    -       -      G     277           -
LGA    -       -      D     278           -
LGA    -       -      Y     279           -
LGA    -       -      P     280           -
LGA    -       -      T     281           -
LGA    -       -      V     282           -
LGA    -       -      V     283           -
LGA    -       -      G     284           -
LGA    -       -      D     285           -
LGA    -       -      A     286           -
LGA    -       -      L     287           -
LGA    -       -      G     288           -
LGA    -       -      Q     289           -
LGA    -       -      D     290           -
LGA    -       -      E     291           -
LGA    -       -      T     292           -
LGA    -       -      Y     293           -
LGA    -       -      V     294           -
LGA    -       -      G     295           -
LGA    -       -      R     296           -
LGA    -       -      V     297           -
LGA    -       -      R     298           -
LGA    -       -      A     299           -
LGA    -       -      G     300           -
LGA    -       -      Q     301           -
LGA    -       -      A     302           -
LGA    -       -      D     303           -
LGA    -       -      P     304           -
LGA    -       -      C     305           -
LGA    -       -      Q     306           -
LGA    -       -      V     307           -
LGA    -       -      N     308           -
LGA    -       -      L     309           -
LGA    -       -      W     310           -
LGA    -       -      I     311           -
LGA    -       -      V     312           -
LGA    -       -      S     313           -
LGA    -       -      D     314           -
LGA    -       -      N     315           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    8  186    5.0      8    1.93    25.00      3.957     0.394

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.906909 * X  +   0.323732 * Y  +   0.269656 * Z  + -19.720423
  Y_new =  -0.193878 * X  +   0.247574 * Y  +  -0.949273 * Z  + 117.262138
  Z_new =  -0.374070 * X  +  -0.913184 * Y  +  -0.161762 * Z  +  67.208092 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.746118    1.395475  [ DEG:  -100.0452     79.9548 ]
  Theta =   0.383393    2.758199  [ DEG:    21.9668    158.0332 ]
  Phi   =  -2.930984    0.210609  [ DEG:  -167.9330     12.0670 ]
 
# 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: T0298TS268_3_1-D2                             
REMARK     2: T0298_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0298TS268_3_1-D2.T0298_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    8  186   5.0    8   1.93   25.00   3.957
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS268_3_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0298
PARENT 1p5f_A
ATOM   1050  N   CYS   130     -17.851  79.892   6.553  1.00  0.00
ATOM   1051  CA  CYS   130     -17.632  79.047   7.693  1.00  0.00
ATOM   1052  C   CYS   130     -17.324  79.867   8.906  1.00  0.00
ATOM   1053  O   CYS   130     -17.798  80.989   9.054  1.00  0.00
ATOM   1054  CB  CYS   130     -16.456  78.101   7.441  1.00  0.00
ATOM   1055  SG  CYS   130     -16.722  76.920   6.099  1.00  0.00
ATOM   1056  HN  CYS   130     -17.061  80.104   5.816  1.00  0.00
ATOM   1057  N   ALA   131     -16.515  79.284   9.818  1.00  0.00
ATOM   1058  CA  ALA   131     -16.197  79.846  11.099  1.00  0.00
ATOM   1059  C   ALA   131     -15.511  81.162  10.934  1.00  0.00
ATOM   1060  O   ALA   131     -15.748  82.087  11.711  1.00  0.00
ATOM   1061  CB  ALA   131     -15.275  78.914  11.872  1.00  0.00
ATOM   1062  HN  ALA   131     -16.099  78.315   9.505  1.00  0.00
ATOM   1063  N   VAL   132     -14.633  81.278   9.923  1.00  0.00
ATOM   1064  CA  VAL   132     -13.943  82.519   9.725  1.00  0.00
ATOM   1065  C   VAL   132     -15.000  83.545   9.521  1.00  0.00
ATOM   1066  O   VAL   132     -14.954  84.623  10.109  1.00  0.00
ATOM   1067  CB  VAL   132     -13.012  82.458   8.500  1.00  0.00
ATOM   1068  CG1 VAL   132     -12.447  83.837   8.193  1.00  0.00
ATOM   1069  CG2 VAL   132     -11.853  81.509   8.757  1.00  0.00
ATOM   1070  HN  VAL   132     -14.485  80.395   9.284  1.00  0.00
ATOM   1071  N   ALA   133     -16.007  83.224   8.694  1.00  0.00
ATOM   1072  CA  ALA   133     -17.099  84.140   8.581  1.00  0.00
ATOM   1073  C   ALA   133     -17.819  84.051   9.885  1.00  0.00
ATOM   1074  O   ALA   133     -17.800  83.028  10.563  1.00  0.00
ATOM   1075  CB  ALA   133     -18.005  83.743   7.424  1.00  0.00
ATOM   1076  HN  ALA   133     -15.944  82.272   8.147  1.00  0.00
ATOM   1077  N   ALA   134     -18.467  85.144  10.291  1.00  0.00
ATOM   1078  CA  ALA   134     -19.134  85.145  11.553  1.00  0.00
ATOM   1079  C   ALA   134     -19.499  86.565  11.733  1.00  0.00
ATOM   1080  O   ALA   134     -19.896  87.223  10.775  1.00  0.00
ATOM   1081  CB  ALA   134     -18.202  84.646  12.646  1.00  0.00
ATOM   1082  HN  ALA   134     -18.452  86.010   9.614  1.00  0.00
ATOM   1083  N   GLU   135     -19.448  87.077  12.970  1.00  0.00
ATOM   1084  CA  GLU   135     -19.728  88.474  13.044  1.00  0.00
ATOM   1085  C   GLU   135     -18.722  89.112  13.940  1.00  0.00
ATOM   1086  O   GLU   135     -18.196  88.482  14.854  1.00  0.00
ATOM   1087  CB  GLU   135     -21.131  88.712  13.605  1.00  0.00
ATOM   1088  CG  GLU   135     -22.245  88.106  12.767  1.00  0.00
ATOM   1089  CD  GLU   135     -22.473  88.857  11.471  1.00  0.00
ATOM   1090  OE1 GLU   135     -21.965  89.991  11.343  1.00  0.00
ATOM   1091  OE2 GLU   135     -23.158  88.313  10.580  1.00  0.00
ATOM   1092  HN  GLU   135     -19.207  86.427  13.825  1.00  0.00
ATOM   1093  N   LEU   136     -18.409  90.393  13.660  1.00  0.00
ATOM   1094  CA  LEU   136     -17.520  91.137  14.496  1.00  0.00
ATOM   1095  C   LEU   136     -16.113  90.740  14.209  1.00  0.00
ATOM   1096  O   LEU   136     -15.842  89.642  13.722  1.00  0.00
ATOM   1097  CB  LEU   136     -17.819  90.866  15.973  1.00  0.00
ATOM   1098  CG  LEU   136     -19.230  91.212  16.452  1.00  0.00
ATOM   1099  CD1 LEU   136     -19.409  90.831  17.914  1.00  0.00
ATOM   1100  CD2 LEU   136     -19.494  92.703  16.314  1.00  0.00
ATOM   1101  HN  LEU   136     -18.874  90.825  12.761  1.00  0.00
ATOM   1102  N   CYS   137     -15.178  91.668  14.483  1.00  0.00
ATOM   1103  CA  CYS   137     -13.791  91.396  14.264  1.00  0.00
ATOM   1104  C   CYS   137     -13.575  89.910  14.531  1.00  0.00
ATOM   1105  O   CYS   137     -13.002  89.221  13.642  1.00  0.00
ATOM   1106  CB  CYS   137     -12.925  92.232  15.210  1.00  0.00
ATOM   1107  SG  CYS   137     -12.996  94.013  14.909  1.00  0.00
ATOM   1108  HN  CYS   137     -15.540  92.629  14.877  1.00  0.00
TER
END
