Contacts of the strand formed by residues 259 - 261 (chain B) in PDB entry 4OE5


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 ILE 259 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128B  PHE*     5.4     1.1    -      -       +      -
    220B  ALA*     3.9    23.1    -      -       +      +
    221B  GLY*     4.7     0.9    -      -       -      +
    224B  ALA*     4.0    23.3    -      -       +      -
    230B  VAL*     3.4     9.6    -      -       +      +
    232B  TRP*     3.9    30.3    -      -       +      -
    246B  TYR*     2.9    48.4    +      -       +      -
    249B  LEU*     4.3    19.1    -      -       +      -
    250B  ARG*     5.1     1.2    +      -       -      -
    254B  LEU*     3.8    25.2    -      -       +      +
    255B  PRO      4.9     0.6    +      -       -      -
    257B  ASN      4.9     1.7    +      -       -      -
    258B  ILE*     1.3    82.8    +      -       -      +
    260B  GLN*     1.3    66.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 260 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67B  VAL      3.6     4.0    -      -       -      +
     68B  VAL*     3.4     8.2    -      -       -      +
     69B  GLY      3.0    23.2    +      -       -      +
    105B  ALA*     2.9    38.7    +      -       +      +
    108B  ALA*     3.9     3.4    -      -       -      +
    109B  ALA*     3.6    14.2    -      -       +      +
    230B  VAL      2.7    19.0    +      -       -      +
    231B  LEU*     3.9    19.5    -      -       +      -
    232B  TRP*     2.9    30.7    +      -       -      +
    257B  ASN*     3.0    35.1    +      -       -      +
    259B  ILE*     1.3    76.8    -      -       -      +
    261B  PHE*     1.3    58.4    +      -       -      +
    262B  VAL*     3.4     5.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 261 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64B  ILE*     3.8    13.9    -      -       +      -
     65B  PRO      3.8    12.6    -      -       -      -
     66B  CYS*     3.2     8.1    -      -       -      -
     67B  VAL*     2.8    49.3    +      -       +      -
    232B  TRP*     3.9    22.7    -      +       -      -
    234B  PRO*     3.6    24.9    -      -       +      -
    239B  MET*     3.6    12.1    -      -       -      -
    242B  SER      4.1     1.3    -      -       -      -
    243B  TYR*     3.6    47.3    -      +       +      -
    246B  TYR*     3.8    26.2    -      +       +      -
    259B  ILE      3.8     2.8    +      -       -      -
    260B  GLN*     1.3    68.1    -      -       -      +
    262B  VAL*     1.3    60.4    +      -       -      +
    263B  PRO*     3.8    19.7    -      -       +      -
----------------------------------------------------------
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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