Contacts of the strand formed by residues 535 - 539 (chain B) in PDB entry 6RKU


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 TYR 535 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    533B  PRO*     4.0     2.3    -      -       -      +
    534B  LEU*     1.3    97.4    +      -       +      +
    536B  LYS*     1.3    60.5    +      -       -      +
    537B  VAL*     4.1     5.6    -      -       +      -
    545B  TYR*     3.7     5.4    -      -       -      +
    546B  ILE*     2.3    74.6    +      -       +      +
    548B  ASP      4.6     4.5    -      -       -      -
    549B  ASP*     5.1     8.2    +      -       +      -
    552B  MET*     4.2    30.3    -      -       +      -
    736B  ILE*     4.0    20.6    -      -       +      -
    737B  GLN      3.7     2.2    -      -       -      -
    738B  ARG*     3.6    49.0    +      -       +      -
    739B  TYR*     5.4     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 536 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    535B  TYR*     1.3    73.7    -      -       -      +
    537B  VAL*     1.3    62.5    +      -       -      +
    538B  LYS*     4.0    33.5    -      -       +      +
    543B  GLU*     5.3    11.8    +      -       +      -
    544B  GLN      3.5     8.3    -      -       -      +
    545B  TYR*     4.7    20.6    +      -       +      +
    735B  SER      3.9     0.5    -      -       -      +
    736B  ILE*     3.3     2.1    -      -       -      +
    737B  GLN*     2.7    63.4    +      -       +      +
    739B  TYR*     3.8    29.9    +      -       +      +
    749B  GLN*     4.6    12.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 537 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    535B  TYR*     4.7     1.8    -      -       +      -
    536B  LYS*     1.3    76.6    -      -       -      +
    538B  LYS*     1.3    63.1    +      -       -      +
    539B  LYS*     3.3    35.0    -      -       +      +
    542B  GLN      3.8     0.9    -      -       -      +
    543B  GLU*     3.3     3.3    -      -       -      +
    544B  GLN*     2.8    42.2    +      -       +      +
    546B  ILE*     3.7    24.5    -      -       +      -
    552B  MET*     3.9    13.5    -      -       +      -
    555B  TYR*     3.6    13.9    -      -       +      +
    734B  LEU*     5.2     1.3    -      -       +      -
    735B  SER      3.3     9.4    -      -       -      +
    736B  ILE*     3.7    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 538 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    536B  LYS*     4.0    25.7    +      -       +      +
    537B  VAL*     1.3    74.1    -      -       -      +
    539B  LYS*     1.3    61.4    +      -       -      +
    540B  GLY*     2.9    33.1    +      -       -      +
    541B  LYS*     4.6     7.3    +      -       -      +
    542B  GLN      3.2     7.0    -      -       -      +
    543B  GLU*     4.3     8.8    +      -       +      +
    734B  LEU*     4.6     0.2    -      -       -      -
    735B  SER*     2.2    50.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 539 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    537B  VAL*     3.3    12.3    -      -       +      +
    538B  LYS*     1.3    73.0    -      -       -      +
    540B  GLY*     1.3    59.7    +      -       -      +
    541B  LYS      3.0     1.0    +      -       -      -
    542B  GLN*     2.6    49.7    +      -       +      +
    555B  TYR*     3.2    38.1    +      -       -      +
    559B  ILE*     3.7    32.3    -      -       +      +
    730B  SER      5.0     2.2    -      -       -      -
    733B  GLY      5.2     6.3    -      -       -      +
    734B  LEU*     3.7    38.0    -      -       +      +
----------------------------------------------------------
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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