Contacts of the strand formed by residues 204 - 208 (chain B) in PDB entry 4OE4


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 PHE 204 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106B  VAL*     3.7    23.6    -      -       +      +
    109B  ALA*     4.6    11.4    -      -       +      -
    110B  LYS*     5.6     4.3    -      -       +      +
    113B  LYS*     5.2     1.3    -      -       -      +
    203B  GLY*     1.3    73.5    -      -       -      -
    205B  VAL*     1.3    64.3    +      -       -      +
    206B  TYR*     4.5     0.9    -      -       +      -
    230B  THR*     3.9    20.9    -      -       -      +
    232B  VAL*     3.6    34.5    -      -       +      -
    274B  VAL*     3.6    31.0    -      -       +      -
    277B  ASP*     3.6    14.8    -      -       +      -
    279B  ASP*     2.9    32.3    +      -       +      +
    280B  PHE*     3.4    34.5    -      +       -      -
    281B  GLY      2.8    27.2    +      -       -      -
    282B  ALA      3.2     4.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 205 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201B  LEU*     4.6     3.6    -      -       +      -
    203B  GLY      4.8     0.4    -      -       -      +
    204B  PHE*     1.3    77.1    -      -       -      +
    206B  TYR*     1.3    71.4    +      -       -      +
    207B  ALA*     4.5     1.1    -      -       -      +
    224B  PRO*     3.9    17.0    -      -       +      -
    229B  ASN*     3.8    33.2    -      -       +      +
    230B  THR      3.1    10.1    +      -       -      +
    231B  VAL*     3.2    12.9    -      -       +      +
    232B  VAL*     2.9    26.5    +      -       -      +
    282B  ALA*     3.5    17.0    -      -       +      +
    284B  HIS*     4.1    10.5    -      -       +      -
    552B  PHE*     4.1    25.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 206 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204B  PHE      4.0     0.8    +      -       -      -
    205B  VAL*     1.3    72.3    -      -       -      +
    207B  ALA*     1.3    60.8    +      -       -      +
    208B  VAL*     3.4    28.2    -      -       +      +
    232B  VAL*     3.3    25.1    -      -       +      -
    234B  LYS*     4.0    22.0    -      -       +      +
    263B  ILE*     5.3     1.1    -      -       +      -
    270B  VAL*     3.8     8.7    -      -       +      +
    271B  THR*     2.8    44.4    +      -       +      -
    274B  VAL*     3.6    37.2    -      -       +      -
    275B  LEU*     4.5     5.6    -      -       +      -
    280B  PHE*     3.6    24.2    -      +       +      -
    282B  ALA      2.8     8.1    +      -       -      -
    283B  LEU*     3.6    15.9    -      -       +      +
    284B  HIS      2.8    26.7    +      -       -      -
    295B  LEU*     4.9     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 207 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205B  VAL*     3.9     1.5    +      -       +      -
    206B  TYR*     1.3    73.1    -      -       -      +
    208B  VAL*     1.3    61.9    +      -       -      +
    209B  SER      4.0     0.7    -      -       -      -
    220B  LEU*     4.0    19.1    -      -       +      +
    221B  ILE*     3.9    18.8    -      -       +      -
    231B  VAL*     3.8    21.8    -      -       +      -
    232B  VAL      2.8    10.5    +      -       -      +
    233B  TRP*     3.4     6.3    -      -       +      -
    234B  LYS      3.0    26.7    +      -       -      -
    284B  HIS*     3.4     9.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 208 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206B  TYR*     3.4    46.0    +      -       +      +
    207B  ALA*     1.3    72.3    -      -       -      +
    209B  SER*     1.3    59.9    +      -       -      +
    220B  LEU*     3.5     4.0    -      -       -      +
    234B  LYS*     3.9    10.5    -      -       -      -
    271B  THR*     5.0     1.8    -      -       -      +
    283B  LEU*     4.1     9.0    -      -       +      -
    284B  HIS      2.9     9.7    +      -       -      +
    285B  PHE*     3.5    19.6    -      -       +      -
    286B  THR      3.3    25.5    +      -       -      +
    295B  LEU*     4.7     4.3    -      -       +      -
   1000B  NAD      3.3    40.2    -      -       -      +
----------------------------------------------------------
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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