Contacts of the strand formed by residues 203 - 207 (chain A) 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 PHE 203 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  ILE*     3.5    43.3    -      -       +      -
    109A  ALA*     5.0     2.2    -      -       +      -
    110A  LEU*     4.2     5.6    -      -       +      -
    202A  GLY*     1.3    74.6    -      -       -      +
    204A  VAL*     1.3    71.3    +      -       -      +
    205A  ALA*     4.4     4.3    -      -       +      -
    229A  VAL*     3.5    21.5    -      -       +      +
    231A  LEU*     4.2    20.0    -      -       +      -
    273A  VAL*     3.8    35.0    -      -       +      -
    276A  SER*     3.5    22.7    -      -       -      -
    278A  HIS*     3.0    16.5    +      -       +      -
    279A  LEU*     3.7    27.1    -      -       +      +
    280A  CYS*     2.9    27.6    +      -       -      -
    281A  GLY      3.6     0.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 204 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200A  LEU*     4.7     1.1    -      -       +      -
    203A  PHE*     1.3    79.8    -      -       -      +
    205A  ALA*     1.3    72.2    +      -       -      +
    206A  ALA*     4.7     0.9    -      -       -      +
    223A  PRO*     4.1    26.5    -      -       +      -
    228A  ASN*     4.0    24.9    -      -       +      -
    229A  VAL      2.9    11.4    +      -       -      +
    230A  VAL*     3.1     8.6    -      -       +      +
    231A  LEU      2.9    24.3    +      -       -      -
    280A  CYS*     3.9    14.8    -      -       -      -
    281A  GLY*     3.3    18.8    -      -       -      +
    283A  ASN*     4.4     4.5    -      -       +      +
    541A  TRP*     4.2    20.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 205 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203A  PHE*     4.1     3.2    +      -       +      -
    204A  VAL*     1.3    74.7    -      -       -      +
    206A  ALA*     1.3    59.7    +      -       -      +
    207A  ILE*     3.8     7.0    +      -       +      -
    231A  LEU      3.5     5.4    -      -       -      +
    269A  PHE*     3.9    24.0    -      -       +      -
    273A  VAL*     4.0    25.6    -      -       +      -
    279A  LEU*     4.3     4.5    -      -       +      -
    281A  GLY      2.8    13.7    +      -       -      +
    282A  ILE*     3.3     6.6    -      -       +      +
    283A  ASN      2.9    26.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 206 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204A  VAL*     3.8     2.3    +      -       +      -
    205A  ALA*     1.3    70.8    -      -       -      +
    207A  ILE*     1.3    61.2    +      -       -      +
    219A  LEU*     3.7    32.8    -      -       +      +
    220A  ALA*     3.9     7.0    -      -       -      +
    230A  VAL*     3.8    19.3    -      -       +      -
    231A  LEU      2.9     9.5    +      -       -      +
    232A  TRP*     3.6    13.0    -      -       +      -
    233A  LYS      2.9    30.7    +      -       -      +
    283A  ASN*     3.4     6.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 207 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205A  ALA*     4.2    10.8    -      -       +      +
    206A  ALA*     1.3    77.9    -      -       -      +
    208A  SER*     1.3    67.0    +      -       -      +
    209A  PRO*     5.5     0.7    -      -       +      -
    219A  LEU*     3.5     5.6    -      -       -      +
    233A  LYS*     3.9    19.7    -      -       +      -
    266A  GLY*     6.0     1.6    -      -       -      +
    269A  PHE*     3.5    33.9    -      -       +      -
    270A  GLY*     4.8     2.7    -      -       -      -
    273A  VAL*     4.7     5.8    -      -       +      -
    282A  ILE*     4.2    11.2    -      -       +      -
    283A  ASN      2.9     8.7    +      -       -      +
    284A  PHE*     3.3    26.9    -      -       +      -
    285A  THR      3.2    22.9    +      -       -      -
    290A  THR*     6.1     0.7    -      -       +      -
    294A  LEU*     4.1    28.9    -      -       +      -
----------------------------------------------------------
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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