Contacts of the strand formed by residues 432 - 436 (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 CYS 432 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341B  PHE*     3.5     5.2    -      -       -      -
    404B  LEU*     3.6    33.4    -      -       +      -
    415B  ILE*     4.0     8.7    -      -       -      -
    417B  ALA      3.4    11.9    -      -       -      +
    419B  GLY*     3.8    15.9    -      -       -      +
    430B  GLU      3.3     2.9    +      -       -      +
    431B  PRO*     1.3    74.1    -      -       -      +
    433B  ILE*     1.3    60.8    +      -       -      +
    434B  VAL*     3.7    22.7    -      -       -      -
    451B  PRO      2.8    15.9    +      -       -      +
    452B  VAL*     3.4     5.1    -      -       +      +
    453B  LEU      2.8    31.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 433 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    337B  LEU*     4.1    20.2    -      -       +      -
    341B  PHE*     3.9    14.8    -      -       +      -
    368B  LEU*     4.3    29.2    -      -       +      +
    369B  LEU*     4.5     3.6    -      -       +      -
    372B  HIS*     4.0    22.2    -      -       +      -
    415B  ILE*     3.7     2.8    -      -       -      -
    416B  LEU*     2.8    46.1    +      -       +      -
    417B  ALA*     3.1    23.1    +      -       +      +
    432B  CYS*     1.3    75.6    -      -       -      +
    434B  VAL*     1.3    60.7    +      -       -      +
    453B  LEU*     3.5    11.9    -      -       +      +
    455B  VAL*     4.1    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 434 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    407B  ALA*     3.8    31.2    -      -       +      -
    413B  LEU*     4.1    17.9    -      -       +      -
    414B  THR      3.4    10.5    -      -       -      +
    415B  ILE*     4.3     3.6    -      -       +      -
    416B  LEU*     4.8     0.9    -      -       -      -
    432B  CYS*     3.7    22.2    -      -       -      -
    433B  ILE*     1.3    80.0    -      -       -      +
    435B  GLU*     1.3    70.6    +      -       -      +
    436B  SER      4.9     0.2    -      -       -      +
    443B  ILE*     4.3    12.3    -      -       +      -
    452B  VAL*     4.4    12.1    -      -       +      -
    453B  LEU      2.8    14.6    +      -       -      +
    454B  SER*     3.2     5.2    -      -       -      -
    455B  VAL*     2.8    28.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 435 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    361B  TRP*     3.9    17.9    +      -       +      -
    365B  LYS*     5.3     2.8    +      -       -      -
    412B  SER      3.5     1.2    -      -       -      +
    413B  LEU*     3.3     5.2    -      -       -      +
    414B  THR*     2.8    43.3    +      -       -      +
    416B  LEU*     3.8    26.2    -      -       +      +
    434B  VAL*     1.3    73.5    -      -       -      +
    436B  SER*     1.3    71.6    +      -       -      +
    437B  LYS*     5.6     1.7    -      -       -      -
    455B  VAL*     3.5    17.0    -      -       +      +
    457B  VAL*     3.4    30.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 436 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    412B  SER      3.4     3.8    +      -       -      -
    413B  LEU*     3.4    21.5    -      -       -      +
    434B  VAL      3.8     1.9    +      -       -      -
    435B  GLU*     1.3    81.4    -      -       -      +
    437B  LYS*     1.3    59.7    +      -       -      +
    438B  ASP      2.8    31.4    +      -       -      -
    441B  GLU*     3.5     6.4    -      -       -      +
    443B  ILE*     4.6     2.2    -      -       -      -
    444B  MET*     4.2    18.8    -      -       -      -
    454B  SER*     5.4     0.4    -      -       -      -
    455B  VAL      2.8    21.5    +      -       -      +
    456B  TYR*     3.4    15.0    -      -       -      -
    457B  VAL      4.5     1.4    +      -       -      -
----------------------------------------------------------
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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