Contacts of the strand formed by residues 227 - 231 (chain A) in PDB entry 4AOR


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 GLY 227 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185A  CYS*     3.2     5.9    -      -       -      +
    186A  ALA      3.1    30.1    +      -       -      -
    194A  ASP*     3.4    13.4    +      -       -      -
    216A  TRP      3.9     1.6    -      -       -      -
    226A  PRO*     1.3    75.6    -      -       -      +
    228A  VAL*     1.3    58.1    +      -       -      -
    229A  TYR*     3.3    12.6    -      -       -      -
     32D  ARG*     3.4    28.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 228 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175A  TYR*     3.6    39.0    -      -       +      -
    179A  ILE*     4.0     6.3    -      -       +      -
    183A  MET*     3.8    23.3    -      -       +      -
    184A  PHE      3.6     6.1    -      -       -      +
    185A  CYS*     4.0     5.4    -      -       -      -
    215A  SER*     3.4     8.2    +      -       -      -
    216A  TRP*     2.8    80.0    +      -       +      +
    226A  PRO      3.9     1.1    -      -       -      +
    227A  GLY*     1.3    74.4    -      -       -      +
    229A  TYR*     1.3    66.4    +      -       -      +
     32D  ARG*     4.7     0.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 229 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141A  ILE*     3.5    19.7    -      -       +      +
    183A  MET*     3.2     7.3    -      -       -      -
    184A  PHE*     2.9    55.0    +      +       +      +
    186A  ALA*     3.7    30.6    +      -       +      -
    194A  ASP*     3.7     9.7    +      -       -      -
    195A  SER*     2.8    31.2    +      -       -      -
    204A  VAL*     3.3    26.7    -      -       +      -
    213A  ILE      3.3     9.6    -      -       -      +
    214A  VAL*     3.5    28.3    -      -       +      -
    215A  SER*     4.2     1.8    -      -       -      -
    227A  GLY*     3.3    27.6    -      -       -      -
    228A  VAL*     1.3    78.4    -      -       -      +
    230A  THR*     1.3    63.5    +      -       -      +
     32D  ARG*     4.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 230 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107A  ASP*     2.9    50.7    +      -       -      +
    108A  ILE*     4.2     7.9    -      -       +      -
    182A  ASN      3.5     9.0    -      -       -      +
    183A  MET*     4.7     2.2    -      -       -      +
    184A  PHE*     3.8     0.4    -      -       -      -
    212A  GLY*     3.2    21.3    -      -       -      -
    213A  ILE*     3.1    22.6    +      -       +      +
    215A  SER*     3.8    10.9    -      -       -      -
    229A  TYR*     1.3    69.2    -      -       -      +
    231A  LYS*     1.3    61.9    +      -       -      +
    232A  VAL*     3.2     7.3    +      -       -      +
    235A  TYR*     3.9    24.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 231 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  CYS*     3.7    16.6    -      -       -      +
    133A  ALA      5.6     3.7    +      -       -      +
    181A  SER      3.8    19.3    +      -       -      +
    182A  ASN*     2.8    24.5    +      -       -      +
    183A  MET      4.0     9.7    +      -       -      +
    184A  PHE*     3.9    23.4    -      -       +      +
    211A  GLN      3.8     4.3    -      -       -      +
    229A  TYR      3.4     1.0    +      -       -      -
    230A  THR*     1.3    69.9    -      -       -      +
    232A  VAL*     1.3    63.5    +      -       -      +
    233A  CYS*     3.6    28.9    -      -       -      -
    234A  ASN*     3.1    19.5    +      -       -      +
    235A  TYR*     3.2    15.0    -      -       -      -
----------------------------------------------------------
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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