
#######################################################
#                                                     #
#                        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 (   32),  selected    8 , name T0356AL333_1-D2
# Molecule2: number of CA atoms  192 ( 1487),  selected  192 , name T0356_D2.pdb
# PARAMETERS: T0356AL333_1-D2.T0356_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     122           -
LGA    -       -      K     123           -
LGA    -       -      R     124           -
LGA    -       -      L     125           -
LGA    -       -      R     126           -
LGA    -       -      G     127           -
LGA    -       -      A     128           -
LGA    -       -      P     129           -
LGA    -       -      C     130           -
LGA    -       -      Q     131           -
LGA    -       -      Q     132           -
LGA    -       -      K     133           -
LGA    -       -      I     134           -
LGA    -       -      V     135           -
LGA    -       -      S     136           -
LGA    -       -      G     137           -
LGA    -       -      D     138           -
LGA    -       -      D     139           -
LGA    -       -      V     140           -
LGA    -       -      D     141           -
LGA    -       -      L     142           -
LGA    -       -      N     143           -
LGA    -       -      R     144           -
LGA    -       -      I     145           -
LGA    -       -      P     146           -
LGA    -       -      I     147           -
LGA    -       -      M     148           -
LGA    -       -      T     149           -
LGA    -       -      C     150           -
LGA    -       -      W     151           -
LGA    -       -      P     152           -
LGA    -       -      E     153           -
LGA    -       -      D     154           -
LGA    -       -      A     155           -
LGA    -       -      A     156           -
LGA    -       -      P     157           -
LGA    -       -      L     158           -
LGA    -       -      I     159           -
LGA    -       -      T     160           -
LGA    -       -      W     161           -
LGA    -       -      G     162           -
LGA    -       -      L     163           -
LGA    -       -      T     164           -
LGA    -       -      V     165           -
LGA    -       -      T     166           -
LGA    -       -      R     167           -
LGA    -       -      G     168           -
LGA    -       -      P     169           -
LGA    -       -      H     170           -
LGA    -       -      K     171           -
LGA    -       -      E     172           -
LGA    -       -      R     173           -
LGA    -       -      Q     174           -
LGA    -       -      N     175           -
LGA    -       -      L     176           -
LGA    -       -      G     177           -
LGA    -       -      I     178           -
LGA    -       -      Y     179           -
LGA    -       -      R     180           -
LGA    -       -      Q     181           -
LGA    -       -      Q     182           -
LGA    -       -      L     183           -
LGA    -       -      I     184           -
LGA    -       -      G     185           -
LGA    -       -      K     186           -
LGA    -       -      N     187           -
LGA    -       -      K     188           -
LGA    -       -      L     189           -
LGA    -       -      I     190           -
LGA    -       -      M     191           -
LGA    -       -      R     192           -
LGA    -       -      W     193           -
LGA    -       -      L     194           -
LGA    -       -      S     195           -
LGA    -       -      H     196           -
LGA    -       -      R     197           -
LGA    -       -      G     198           -
LGA    -       -      G     199           -
LGA    -       -      A     200           -
LGA    -       -      L     201           -
LGA    -       -      D     202           -
LGA    -       -      Y     203           -
LGA    -       -      Q     204           -
LGA    -       -      E     205           -
LGA    -       -      W     206           -
LGA    -       -      C     207           -
LGA    -       -      A     208           -
LGA    -       -      A     209           -
LGA    -       -      H     210           -
LGA    -       -      P     211           -
LGA    -       -      G     212           -
LGA    A     269      E     213          1.056
LGA    E     270      R     214          0.688
LGA    I     271      F     215          1.340
LGA    V     272      P     216          0.962
LGA    L     273      V     217          0.507
LGA    E     274      S     218          0.742
LGA    -       -      V     219           -
LGA    -       -      A     220           -
LGA    -       -      L     221           -
LGA    -       -      G     222           -
LGA    -       -      A     223           -
LGA    -       -      D     224           -
LGA    -       -      P     225           -
LGA    -       -      A     226           -
LGA    -       -      T     227           -
LGA    -       -      I     228           -
LGA    -       -      L     229           -
LGA    -       -      G     230           -
LGA    -       -      A     231           -
LGA    -       -      V     232           -
LGA    -       -      T     233           -
LGA    -       -      P     234           -
LGA    -       -      V     235           -
LGA    -       -      P     236           -
LGA    -       -      D     237           -
LGA    -       -      T     238           -
LGA    -       -      L     239           -
LGA    -       -      S     240           -
LGA    -       -      E     241           -
LGA    -       -      Y     242           -
LGA    -       -      A     243           -
LGA    -       -      F     244           -
LGA    -       -      A     245           -
LGA    -       -      G     246           -
LGA    -       -      L     247           -
LGA    -       -      L     248           -
LGA    -       -      R     249           -
LGA    -       -      G     250           -
LGA    -       -      T     251           -
LGA    -       -      K     252           -
LGA    -       -      T     253           -
LGA    -       -      E     254           -
LGA    -       -      V     255           -
LGA    -       -      V     256           -
LGA    -       -      K     257           -
LGA    -       -      C     258           -
LGA    -       -      I     259           -
LGA    -       -      S     260           -
LGA    -       -      N     261           -
LGA    -       -      D     262           -
LGA    -       -      L     263           -
LGA    -       -      E     264           -
LGA    -       -      V     265           -
LGA    -       -      P     266           -
LGA    -       -      A     267           -
LGA    -       -      S     268           -
LGA    -       -      A     269           -
LGA    -       -      E     270           -
LGA    -       -      I     271           -
LGA    -       -      V     272           -
LGA    -       -      L     273           -
LGA    G     275      E     274          1.537
LGA    Y     276      G     275          0.740
LGA    -       -      Y     276           -
LGA    -       -      I     277           -
LGA    -       -      E     278           -
LGA    -       -      Q     279           -
LGA    -       -      G     280           -
LGA    -       -      E     281           -
LGA    -       -      T     282           -
LGA    -       -      A     283           -
LGA    -       -      P     284           -
LGA    -       -      E     285           -
LGA    -       -      G     286           -
LGA    -       -      P     287           -
LGA    -       -      Y     288           -
LGA    -       -      G     289           -
LGA    -       -      D     290           -
LGA    -       -      H     291           -
LGA    -       -      T     292           -
LGA    -       -      G     293           -
LGA    -       -      Y     294           -
LGA    -       -      Y     295           -
LGA    -       -      N     296           -
LGA    -       -      E     297           -
LGA    -       -      V     298           -
LGA    -       -      D     299           -
LGA    -       -      S     300           -
LGA    -       -      F     301           -
LGA    -       -      P     302           -
LGA    -       -      V     303           -
LGA    -       -      F     304           -
LGA    -       -      T     305           -
LGA    -       -      V     306           -
LGA    -       -      T     307           -
LGA    -       -      H     308           -
LGA    -       -      I     309           -
LGA    -       -      T     310           -
LGA    -       -      Q     311           -
LGA    -       -      R     312           -
LGA    -       -      E     313           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    8  192    5.0      8    1.00     0.00      4.084     0.726

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.239240 * X  +   0.967561 * Y  +  -0.081176 * Z  + -74.465225
  Y_new =   0.204263 * X  +  -0.131886 * Y  +  -0.969991 * Z  + 113.887032
  Z_new =  -0.949232 * X  +   0.215479 * Y  +  -0.229190 * Z  + 195.526733 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.387017   -0.754575  [ DEG:   136.7660    -43.2340 ]
  Theta =   1.250784    1.890808  [ DEG:    71.6647    108.3353 ]
  Phi   =   0.706697   -2.434896  [ DEG:    40.4907   -139.5093 ]
 
# 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: T0356AL333_1-D2                               
REMARK     2: T0356_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356AL333_1-D2.T0356_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    8  192   5.0    8   1.00    0.00   4.084
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL333_1-D2
REMARK Aligment from pdb entry: 1lwh_A
ATOM    129  N   ALA   269      89.337  46.073  78.947  1.00  0.00              
ATOM    130  CA  ALA   269      90.209  47.259  79.014  1.00  0.00              
ATOM    131  C   ALA   269      89.368  48.493  79.371  1.00  0.00              
ATOM    132  O   ALA   269      88.376  48.798  78.713  1.00  0.00              
ATOM    133  N   GLU   270      89.779  49.188  80.428  1.00  0.00              
ATOM    134  CA  GLU   270      89.073  50.360  80.934  1.00  0.00              
ATOM    135  C   GLU   270      88.671  51.377  79.894  1.00  0.00              
ATOM    136  O   GLU   270      89.090  51.307  78.749  1.00  0.00              
ATOM    137  N   ILE   271      87.838  52.318  80.312  1.00  0.00              
ATOM    138  CA  ILE   271      87.351  53.375  79.443  1.00  0.00              
ATOM    139  C   ILE   271      86.600  54.314  80.371  1.00  0.00              
ATOM    140  O   ILE   271      85.798  53.864  81.178  1.00  0.00              
ATOM    141  N   VAL   272      86.858  55.614  80.271  1.00  0.00              
ATOM    142  CA  VAL   272      86.199  56.571  81.164  1.00  0.00              
ATOM    143  C   VAL   272      84.926  57.241  80.655  1.00  0.00              
ATOM    144  O   VAL   272      84.842  57.642  79.500  1.00  0.00              
ATOM    145  N   LEU   273      83.930  57.333  81.532  1.00  0.00              
ATOM    146  CA  LEU   273      82.675  58.016  81.216  1.00  0.00              
ATOM    147  C   LEU   273      82.346  58.856  82.443  1.00  0.00              
ATOM    148  O   LEU   273      82.399  58.362  83.572  1.00  0.00              
ATOM    149  N   GLU   274      82.013  60.124  82.204  1.00  0.00              
ATOM    150  CA  GLU   274      81.698  61.062  83.259  1.00  0.00              
ATOM    151  C   GLU   274      82.653  60.927  84.451  1.00  0.00              
ATOM    152  O   GLU   274      82.245  60.951  85.618  1.00  0.00              
ATOM    153  N   GLY   275      83.937  60.781  84.133  1.00  0.00              
ATOM    154  CA  GLY   275      84.959  60.684  85.156  1.00  0.00              
ATOM    155  C   GLY   275      85.088  59.343  85.830  1.00  0.00              
ATOM    156  O   GLY   275      85.992  59.144  86.651  1.00  0.00              
ATOM    157  N   TYR   276      84.200  58.415  85.475  1.00  0.00              
ATOM    158  CA  TYR   276      84.193  57.067  86.056  1.00  0.00              
ATOM    159  C   TYR   276      85.012  56.026  85.270  1.00  0.00              
ATOM    160  O   TYR   276      84.903  55.924  84.043  1.00  0.00              
END
