Contacts of the strand formed by residues 558 - 561 (chain B) in PDB entry 3KCZ


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 GLU 558 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  3AB      4.0    20.1    +      -       +      -
    456B  MET*     4.2    12.2    -      -       -      +
    457B  PHE*     3.5    36.1    -      -       +      -
    462B  TYR*     3.6    18.9    -      -       -      -
    463B  PHE      3.3    13.0    -      -       -      +
    469B  LYS*     2.8    28.8    +      -       -      +
    515B  THR      3.9     0.2    -      -       -      +
    516B  LYS*     3.3     5.0    -      -       -      +
    517B  GLY      2.8    32.0    +      -       -      +
    554B  LEU*     3.9    16.8    -      -       +      +
    557B  ASN*     1.3    74.9    -      -       -      +
    559B  TYR*     1.3    66.4    +      -       -      +
    560B  ILE*     3.9     5.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 559 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    422B  ASN*     5.9     0.2    -      -       -      -
    424B  MET*     4.2    19.0    -      -       -      +
    426B  LEU*     3.8    21.5    -      -       +      -
    461B  ILE      3.6     2.1    -      -       -      +
    462B  TYR*     3.6     2.4    -      -       -      -
    463B  PHE*     2.9    45.4    +      -       +      +
    465B  ASP*     2.9    43.8    +      -       +      +
    492B  LEU*     3.5    45.3    -      -       +      -
    495B  CYS*     4.9     1.8    -      -       -      -
    515B  THR      3.4     5.2    -      -       -      -
    516B  LYS*     3.5    40.9    +      -       +      -
    557B  ASN*     3.5    16.1    +      -       +      -
    558B  GLU*     1.3    76.6    -      -       -      +
    560B  ILE*     1.3    63.0    -      -       -      +
    561B  VAL      4.3     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 560 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    457B  PHE*     3.7    32.5    -      -       +      +
    460B  GLY*     3.5    30.7    -      -       -      +
    461B  ILE      3.3     5.4    -      -       -      +
    462B  TYR*     3.5    30.3    -      -       +      -
    514B  SER*     3.3     5.6    -      -       -      -
    515B  THR*     2.8    43.1    +      -       +      +
    558B  GLU*     3.9    11.4    -      -       +      +
    559B  TYR*     1.3    87.0    -      -       -      +
    561B  VAL*     1.3    64.2    +      -       -      +
    562B  TYR*     3.6    26.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 561 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    460B  GLY*     3.2     0.7    -      -       -      -
    461B  ILE*     2.7    39.5    +      -       +      +
    463B  PHE*     4.2    11.2    -      -       +      -
    490B  VAL*     3.6    24.2    -      -       +      -
    491B  ALA      4.2     2.9    -      -       -      +
    492B  LEU*     4.2     2.5    -      -       +      -
    513B  HIS      4.5     2.5    -      -       -      -
    514B  SER*     4.0    11.4    -      -       -      -
    560B  ILE*     1.3    78.2    -      -       -      +
    562B  TYR*     1.3    63.5    +      -       -      +
    563B  ASN      3.9     9.6    +      -       -      +
    566B  GLN*     3.7    31.6    -      -       +      +
    567B  VAL*     3.8    29.2    -      -       +      -
----------------------------------------------------------
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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