Contacts of the strand formed by residues 664 - 669 (chain D) in PDB entry 2OX8


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 HIS 664 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    621D  PHE*     3.7    31.6    -      +       +      -
    622D  SER      4.1     5.4    -      -       -      -
    658D  MET*     5.0     6.4    -      -       +      +
    662D  GLU*     2.4    39.6    +      -       -      -
    663D  SER*     1.3    73.9    -      -       -      +
    665D  TRP*     1.3    66.8    +      -       -      +
    666D  ILE*     5.6     0.2    -      -       +      -
    710D  GLY*     4.4     0.9    -      -       -      -
    711D  LEU*     2.7    40.3    +      -       +      +
    727D  ASN*     3.0    28.8    +      -       +      +
    728D  PHE*     3.1    24.8    +      -       -      -
    729D  ILE*     2.9    30.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 665 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    626D  GLU      3.0    22.6    +      -       -      -
    627D  ILE      4.3     0.7    -      -       -      -
    628D  PHE*     3.7    37.0    -      +       +      +
    631D  ALA*     4.3     2.0    -      -       +      -
    642D  LEU*     4.7     7.6    -      -       +      -
    643D  VAL*     4.3     2.8    -      -       -      +
    663D  SER      4.1     0.2    +      -       -      -
    664D  HIS*     1.3    83.4    -      -       -      +
    666D  ILE*     1.3    68.5    +      -       -      +
    708D  CYS*     3.0    33.0    -      -       +      -
    709D  ALA      3.4    22.9    -      -       -      +
    710D  GLY*     4.2     2.7    -      -       -      -
    720D  PHE*     3.5    16.2    -      +       +      -
    721D  GLN      3.6    22.0    -      -       -      -
    722D  CYS*     4.1     3.8    -      -       -      -
    724D  ASP*     3.4    22.7    -      -       +      -
    726D  ASN*     3.4    28.7    +      -       +      +
    727D  ASN      2.9    26.9    +      -       -      -
    728D  PHE*     3.6    15.9    -      -       +      +
    729D  ILE      4.0     9.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 666 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    628D  PHE*     3.8     5.9    -      -       -      -
    642D  LEU*     3.9     6.3    -      -       -      -
    643D  VAL*     3.8    26.7    -      -       +      +
    645D  ILE*     4.3    10.3    -      -       +      -
    664D  HIS*     4.1     6.5    -      -       +      +
    665D  TRP*     1.3    85.8    -      -       -      +
    667D  GLY*     1.3    52.4    +      -       -      +
    668D  LEU*     2.4    29.9    +      -       +      +
    679D  TRP*     4.6     6.7    -      -       +      -
    709D  ALA*     3.3    33.2    +      -       +      +
    710D  GLY      4.0     6.1    -      -       -      +
    711D  LEU*     4.1    14.4    -      -       +      -
    717D  TRP*     3.7    46.9    -      -       +      +
    729D  ILE*     5.8     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 667 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    642D  LEU*     3.2    25.9    -      -       -      +
    643D  VAL      3.3     7.5    +      -       -      -
    644D  PHE*     3.7     9.7    -      -       -      -
    666D  ILE*     1.3    67.4    -      -       -      +
    668D  LEU*     1.3    57.0    +      -       -      -
    679D  TRP*     2.9    16.3    -      -       -      +
    680D  LEU*     2.8    43.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 668 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    666D  ILE*     2.4    22.8    +      -       +      +
    667D  GLY      1.3    70.5    -      -       -      +
    669D  THR*     1.3    70.3    +      -       -      +
    677D  TRP*     3.4    22.9    -      -       +      +
    678D  LYS      3.3    39.0    -      -       -      +
    679D  TRP*     3.7    19.5    -      -       +      +
    685D  PRO*     4.4    12.6    -      -       +      -
    690D  TRP*     3.9    14.6    -      -       +      -
    709D  ALA*     2.9    38.3    +      -       +      +
    717D  TRP*     3.7    36.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 669 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    628D  PHE*     3.2    37.5    -      -       +      -
    668D  LEU*     1.3    82.6    -      -       -      +
    670D  ASP*     1.3    58.9    +      -       -      +
    671D  SER*     3.1    22.3    +      -       -      +
    676D  GLU      3.2     0.9    -      -       -      +
    677D  TRP*     3.3     8.5    -      -       -      -
    678D  LYS*     2.9    35.9    +      -       -      +
    680D  LEU*     4.5    10.4    -      -       +      +
    707D  ASP      2.8    22.0    -      -       -      +
    708D  CYS*     4.2     3.1    -      -       -      -
----------------------------------------------------------
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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