Contacts of the strand formed by residues 325 - 333 (chain B) in PDB entry 6WPJ


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with LEU 325 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319B  TYR*     3.9    12.1    -      -       +      -
    323B  LYS      3.8     0.4    +      -       -      -
    324B  ASP*     1.3    72.6    -      -       -      +
    326B  ILE*     1.3    56.0    +      -       -      +
    341B  ILE*     4.2    10.8    -      -       +      -
    342B  TYR      4.0     1.3    -      -       -      -
    343B  GLN*     3.6    22.0    -      -       +      +
    349B  LEU*     3.8    25.1    -      -       +      -
    379B  SER*     4.1    16.8    -      -       -      -
    383B  TRP*     3.7    29.8    -      -       +      -
    385B  LYS*     4.1    29.2    -      -       +      +
    386B  THR      4.5     4.0    +      -       -      +
    387B  PRO*     3.0    17.3    -      -       +      +
    388B  LYS*     2.6    36.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 326 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    324B  ASP*     4.1    13.7    -      -       +      +
    325B  LEU*     1.3    74.9    -      -       -      +
    327B  ALA*     1.3    67.8    +      -       -      +
    340B  GLN      3.5     1.6    -      -       -      +
    341B  ILE*     3.3     5.5    -      -       -      +
    342B  TYR*     2.8    81.5    +      -       +      +
    343B  GLN*     4.7     7.0    -      -       -      +
    387B  PRO*     4.5     1.1    -      -       -      -
    388B  LYS*     3.5    25.4    -      -       +      +
    390B  LYS*     4.3    20.0    -      -       +      -
    415B  GLU*     5.9     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 327 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    325B  LEU      4.0     0.6    +      -       -      -
    326B  ILE*     1.3    74.9    -      -       -      +
    328B  GLU*     1.3    64.2    +      -       -      +
    329B  ILE*     5.4     1.3    -      -       +      -
    339B  TYR*     5.9     0.9    -      -       +      -
    340B  GLN      3.3     6.1    -      -       -      +
    341B  ILE*     4.6     3.6    -      -       +      +
    375B  ILE*     4.4    10.5    -      -       +      -
    387B  PRO*     3.9    14.4    -      -       +      -
    388B  LYS      2.9     7.4    +      -       -      +
    389B  PHE*     3.5    35.6    -      -       +      +
    390B  LYS*     2.9    29.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 328 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    326B  ILE*     4.2     0.6    -      -       +      -
    327B  ALA*     1.3    74.8    -      -       -      +
    329B  ILE*     1.3    63.2    +      -       -      +
    330B  GLN*     3.9    12.5    +      -       -      +
    339B  TYR*     3.0     7.4    -      -       -      +
    340B  GLN*     2.9    47.4    +      -       -      +
    342B  TYR*     2.7    35.7    +      -       +      -
    390B  LYS*     3.8    35.9    +      -       +      -
    423B  VAL*     5.1     7.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 329 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    327B  ALA      5.2     0.2    -      -       -      -
    328B  GLU*     1.3    80.2    -      -       -      +
    330B  GLN*     1.3    68.7    +      -       -      +
    337B  TRP*     4.1    31.9    -      -       +      -
    338B  THR      3.2    11.9    -      -       -      +
    339B  TYR*     4.3     1.6    -      -       +      -
    368B  LEU*     3.8    22.9    -      -       +      -
    371B  ALA*     4.5     5.8    -      -       +      -
    372B  VAL*     3.8    20.0    -      -       +      -
    375B  ILE*     3.9    26.2    -      -       +      -
    389B  PHE*     4.0    13.2    -      -       +      -
    390B  LYS      3.8     9.0    +      -       -      +
    391B  LEU*     4.3     4.3    -      -       +      -
    392B  PRO*     3.2    28.7    -      -       +      +
    417B  VAL*     5.9     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 330 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    328B  GLU*     3.9    17.6    +      -       -      +
    329B  ILE*     1.3    84.4    +      -       -      +
    331B  LYS*     1.3    64.6    +      -       -      +
    332B  GLN*     3.4    12.0    +      -       -      +
    337B  TRP*     3.5     1.9    -      -       -      -
    338B  THR*     2.3    65.6    +      -       -      +
    340B  GLN*     2.8    40.1    +      -       -      +
    392B  PRO*     4.5     2.5    -      -       -      -
    419B  THR*     5.5     9.4    -      -       -      -
    423B  VAL*     4.2    18.4    -      -       +      +
    424B  LYS*     4.4    14.1    -      -       +      +
    427B  TYR*     3.9    10.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 331 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    402A  TRP*     3.2    31.5    +      -       -      +
    403A  THR      5.2     0.9    -      -       -      -
    405A  TYR*     3.3    12.6    +      -       -      +
    406A  TRP*     3.4    27.3    +      -       -      +
    407A  GLN      2.8    33.3    +      -       -      +
    408A  ALA      4.1     1.1    -      -       -      +
    409A  THR*     4.7     1.2    -      -       -      +
    329B  ILE      4.3     0.2    -      -       -      -
    330B  GLN*     1.3    70.5    -      -       -      +
    332B  GLN*     1.3    63.3    +      -       -      +
    333B  GLY*     3.7    19.3    -      -       -      +
    336B  GLN      4.9     0.4    -      -       -      +
    337B  TRP*     3.5    34.3    -      -       +      -
    364B  ASP*     2.8    28.0    +      -       -      +
    392B  PRO*     4.5     6.2    -      -       +      +
    424B  LYS*     4.5    10.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 332 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    330B  GLN*     3.4     7.6    +      -       -      +
    331B  LYS*     1.3    74.6    -      -       -      +
    333B  GLY*     1.3    60.7    +      -       -      +
    336B  GLN*     2.9    29.6    +      -       +      +
    338B  THR*     3.5    38.1    +      -       +      -
    424B  LYS*     2.8    43.2    +      -       -      +
    427B  TYR*     4.0     2.2    -      -       -      +
    428B  GLN*     3.7    25.8    -      -       -      +
    429B  LEU*     5.2     3.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 333 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    402A  TRP*     6.3     0.4    -      -       -      -
    403A  THR*     5.6     5.6    -      -       -      -
    331B  LYS*     3.4    22.8    -      -       -      +
    332B  GLN*     1.3    82.4    -      -       -      +
    334B  GLN*     1.3    70.7    +      -       -      +
    335B  GLY      3.1     3.6    -      -       -      -
    336B  GLN*     3.0    20.4    +      -       -      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il