Contacts of the strand formed by residues 230 - 233 (chain C) 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 VAL 230 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109C  ALA*     4.9     1.0    -      -       -      +
    204C  VAL*     3.2    14.4    -      -       +      +
    206C  ALA*     3.8    20.2    -      -       +      -
    220C  ALA*     3.9    31.0    -      -       +      +
    223C  PRO*     4.1    12.1    -      -       +      -
    224C  ALA*     4.1    16.6    -      -       +      +
    228C  ASN      4.5     0.7    -      -       -      +
    229C  VAL*     1.3    83.5    -      -       -      +
    231C  LEU*     1.3    78.4    +      -       -      +
    232C  TRP*     3.9     3.1    -      -       +      +
    258C  ILE      2.8    14.7    +      -       -      +
    259C  ILE*     3.4     7.4    -      -       +      -
    260C  GLN*     2.8    30.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 231 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102C  LEU*     3.8    29.2    -      -       +      +
    105C  ALA*     3.9    22.2    -      -       +      +
    106C  ILE*     3.6    33.7    -      -       +      +
    109C  ALA*     4.3     6.1    -      -       +      -
    203C  PHE*     4.1    13.4    -      -       +      -
    204C  VAL      2.9    11.2    +      -       -      +
    205C  ALA*     3.5     2.4    -      -       -      -
    206C  ALA      2.8    26.2    +      -       -      +
    230C  VAL*     1.3    74.6    -      -       -      +
    232C  TRP*     1.3    59.7    +      -       -      +
    233C  LYS      3.8     0.9    +      -       -      -
    260C  GLN*     3.8    21.3    -      -       +      -
    262C  VAL*     4.1     9.0    -      -       +      -
    269C  PHE*     3.8    12.3    -      -       +      -
    273C  VAL*     4.4    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 232 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206C  ALA*     3.5    21.1    -      -       +      -
    208C  SER*     4.7     3.6    +      -       -      +
    215C  ILE*     3.7    36.4    +      -       +      -
    216C  GLY      4.7     5.9    +      -       -      -
    217C  GLY*     4.6    11.7    -      -       -      -
    219C  LEU*     5.3     2.6    -      -       +      +
    220C  ALA*     3.9    19.3    -      -       +      +
    230C  VAL      3.8     0.8    +      -       -      -
    231C  LEU*     1.3    71.1    -      -       -      +
    233C  LYS*     1.3    66.6    +      -       -      +
    234C  PRO*     3.1    22.7    -      -       +      +
    242C  SER*     3.7    39.5    -      -       -      -
    245C  VAL*     5.0     6.1    -      -       +      -
    246C  TYR*     4.3    11.9    -      +       +      -
    249C  LEU*     5.6     4.3    -      -       +      -
    259C  ILE*     3.9    24.5    -      -       +      -
    260C  GLN      2.9    17.2    +      -       -      +
    261C  PHE*     3.9    21.2    -      +       -      -
    262C  VAL*     2.9    31.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 233 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206C  ALA      2.9    12.8    +      -       -      +
    207C  ILE*     4.0    14.6    -      -       +      -
    208C  SER*     2.9    51.0    +      -       -      -
    209C  PRO*     4.8     1.8    -      -       -      -
    210C  PHE*     3.9    17.4    -      -       -      +
    231C  LEU      3.8     1.4    +      -       -      -
    232C  TRP*     1.3    74.5    -      -       -      +
    234C  PRO*     1.3    77.6    +      -       -      +
    236C  ASP*     4.3     2.6    +      -       -      -
    262C  VAL      3.5    15.9    -      -       -      +
    264C  ALA      3.6    31.1    +      -       -      +
    266C  GLY*     4.3    13.9    -      -       -      -
    269C  PHE*     3.8    42.4    -      -       +      -
----------------------------------------------------------
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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