
#######################################################
#                                                     #
#                        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   15 (   60),  selected   15 , name T0298AL242_4-D2
# Molecule2: number of CA atoms  186 ( 1394),  selected  186 , name T0298_D2.pdb
# PARAMETERS: T0298AL242_4-D2.T0298_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      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    -       -      E     138           -
LGA    -       -      V     139           -
LGA    -       -      L     140           -
LGA    -       -      A     141           -
LGA    -       -      P     142           -
LGA    -       -      L     143           -
LGA    -       -      L     144           -
LGA    -       -      A     145           -
LGA    -       -      T     146           -
LGA    -       -      L     147           -
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    C     130      S     159          4.384
LGA    A     131      V     160          2.706
LGA    -       -      S     161           -
LGA    -       -      S     162           -
LGA    -       -      L     163           -
LGA    -       -      G     164           -
LGA    -       -      R     165           -
LGA    -       -      E     166           -
LGA    V     132      G     167          2.917
LGA    A     133      V     168          2.539
LGA    A     134      K     169          2.920
LGA    -       -      E     170           -
LGA    E     135      L     171          1.575
LGA    L     136      A     172          1.424
LGA    C     137      R     173          1.072
LGA    E     138      Q     174          1.011
LGA    V     139      T     175          1.000
LGA    L     140      A     176          1.207
LGA    A     141      E     177          0.956
LGA    P     142      L     178          0.407
LGA    L     143      L     179          0.720
LGA    L     144      N     180          1.374
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)   15  186    5.0     15    2.04     6.67      7.071     0.700

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.983977 * X  +  -0.162512 * Y  +  -0.073340 * Z  +  52.930721
  Y_new =   0.102465 * X  +  -0.852061 * Y  +   0.513316 * Z  +  78.980370
  Z_new =  -0.145910 * X  +   0.497577 * Y  +   0.855060 * Z  + -22.465277 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.527020   -2.614573  [ DEG:    30.1960   -149.8040 ]
  Theta =   0.146433    2.995160  [ DEG:     8.3900    171.6100 ]
  Phi   =   3.037833   -0.103759  [ DEG:   174.0550     -5.9450 ]
 
# 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: T0298AL242_4-D2                               
REMARK     2: T0298_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0298AL242_4-D2.T0298_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   15  186   5.0   15   2.04    6.67   7.071
REMARK  ---------------------------------------------------------- 
MOLECULE T0298AL242_4-D2
REMARK Aligment from pdb entry: 1brm_A
ATOM    505  N   CYS   130      -3.569  60.168   9.817  1.00  0.00              
ATOM    506  CA  CYS   130      -3.187  60.566   8.477  1.00  0.00              
ATOM    507  C   CYS   130      -3.672  61.988   8.266  1.00  0.00              
ATOM    508  O   CYS   130      -4.661  62.401   8.874  1.00  0.00              
ATOM    509  N   ALA   131      -2.999  62.743   7.405  1.00  0.00              
ATOM    510  CA  ALA   131      -3.407  64.118   7.181  1.00  0.00              
ATOM    511  C   ALA   131      -4.280  64.394   5.969  1.00  0.00              
ATOM    512  O   ALA   131      -4.817  63.484   5.339  1.00  0.00              
ATOM    513  N   VAL   132      -4.355  58.867   1.496  1.00  0.00              
ATOM    514  CA  VAL   132      -5.222  58.239   2.486  1.00  0.00              
ATOM    515  C   VAL   132      -4.629  57.052   3.259  1.00  0.00              
ATOM    516  O   VAL   132      -4.174  57.203   4.393  1.00  0.00              
ATOM    517  N   ALA   133      -4.627  55.882   2.628  1.00  0.00              
ATOM    518  CA  ALA   133      -4.160  54.650   3.254  1.00  0.00              
ATOM    519  C   ALA   133      -2.665  54.395   3.404  1.00  0.00              
ATOM    520  O   ALA   133      -2.215  54.014   4.480  1.00  0.00              
ATOM    521  N   ALA   134      -1.895  54.586   2.344  1.00  0.00              
ATOM    522  CA  ALA   134      -0.466  54.320   2.411  1.00  0.00              
ATOM    523  C   ALA   134       0.198  54.719   3.723  1.00  0.00              
ATOM    524  O   ALA   134       0.885  53.912   4.328  1.00  0.00              
ATOM    525  N   GLU   135      -0.009  55.964   4.185  1.00  0.00              
ATOM    526  CA  GLU   135       0.626  56.372   5.448  1.00  0.00              
ATOM    527  C   GLU   135       0.252  55.476   6.638  1.00  0.00              
ATOM    528  O   GLU   135       1.075  55.230   7.520  1.00  0.00              
ATOM    529  N   LEU   136      -0.988  55.001   6.662  1.00  0.00              
ATOM    530  CA  LEU   136      -1.452  54.122   7.732  1.00  0.00              
ATOM    531  C   LEU   136      -0.715  52.782   7.643  1.00  0.00              
ATOM    532  O   LEU   136      -0.080  52.337   8.602  1.00  0.00              
ATOM    533  N   CYS   137      -0.801  52.157   6.474  1.00  0.00              
ATOM    534  CA  CYS   137      -0.162  50.874   6.208  1.00  0.00              
ATOM    535  C   CYS   137       1.283  50.824   6.699  1.00  0.00              
ATOM    536  O   CYS   137       1.714  49.824   7.270  1.00  0.00              
ATOM    537  N   GLU   138       2.020  51.910   6.481  1.00  0.00              
ATOM    538  CA  GLU   138       3.421  51.990   6.881  1.00  0.00              
ATOM    539  C   GLU   138       3.612  52.275   8.365  1.00  0.00              
ATOM    540  O   GLU   138       4.596  51.839   8.963  1.00  0.00              
ATOM    541  N   VAL   139       2.689  53.019   8.964  1.00  0.00              
ATOM    542  CA  VAL   139       2.803  53.310  10.387  1.00  0.00              
ATOM    543  C   VAL   139       2.643  51.980  11.109  1.00  0.00              
ATOM    544  O   VAL   139       3.385  51.670  12.038  1.00  0.00              
ATOM    545  N   LEU   140       1.668  51.196  10.660  1.00  0.00              
ATOM    546  CA  LEU   140       1.402  49.888  11.241  1.00  0.00              
ATOM    547  C   LEU   140       2.646  49.009  11.151  1.00  0.00              
ATOM    548  O   LEU   140       2.985  48.305  12.098  1.00  0.00              
ATOM    549  N   ALA   141       3.327  49.052  10.012  1.00  0.00              
ATOM    550  CA  ALA   141       4.529  48.254   9.832  1.00  0.00              
ATOM    551  C   ALA   141       5.584  48.598  10.881  1.00  0.00              
ATOM    552  O   ALA   141       6.259  47.714  11.410  1.00  0.00              
ATOM    553  N   PRO   142       5.718  49.886  11.180  1.00  0.00              
ATOM    554  CA  PRO   142       6.682  50.365  12.165  1.00  0.00              
ATOM    555  C   PRO   142       6.415  49.799  13.556  1.00  0.00              
ATOM    556  O   PRO   142       7.338  49.392  14.264  1.00  0.00              
ATOM    557  N   LEU   143       5.143  49.784  13.942  1.00  0.00              
ATOM    558  CA  LEU   143       4.732  49.303  15.256  1.00  0.00              
ATOM    559  C   LEU   143       4.614  47.783  15.369  1.00  0.00              
ATOM    560  O   LEU   143       4.618  47.241  16.476  1.00  0.00              
ATOM    561  N   LEU   144       4.519  47.098  14.234  1.00  0.00              
ATOM    562  CA  LEU   144       4.384  45.643  14.233  1.00  0.00              
ATOM    563  C   LEU   144       5.509  44.949  14.991  1.00  0.00              
ATOM    564  O   LEU   144       5.306  43.775  15.369  1.00  0.00              
END
