Contacts of the strand formed by residues 234 - 239 (chain X) in PDB entry 2AE0


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 VAL 234 (chain X).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121X  TYR      4.5     1.6    +      -       -      +
    133X  ARG*     5.5     0.4    -      -       -      +
    160X  ASP*     3.6    43.6    +      -       +      +
    163X  GLY*     5.1     1.3    -      -       -      -
    180X  TYR*     3.9    17.9    -      -       +      -
    182X  GLY      3.8     7.4    -      -       -      +
    183X  LYS*     4.5    13.5    -      -       +      -
    232X  SER*     5.2     2.2    -      -       -      +
    233X  PHE*     1.3   100.6    -      -       -      +
    235X  PHE*     1.3    76.2    +      -       -      +
    236X  PHE*     3.6    33.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 235 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121X  TYR*     3.5    11.7    -      -       +      -
    122X  ARG      3.4    15.3    -      -       -      -
    123X  MET*     3.8    37.9    -      -       +      +
    124X  PRO*     3.7    17.0    -      -       +      -
    129X  ARG*     3.6    24.7    -      -       +      -
    136X  ILE*     4.3     7.9    -      -       +      -
    141X  LEU*     3.7    28.0    -      -       +      -
    181X  ALA*     3.0    20.8    +      -       -      -
    182X  GLY      2.9    18.8    +      -       -      +
    183X  LYS      4.0     4.7    -      -       -      -
    184X  ASN*     3.8    20.4    -      -       +      -
    233X  PHE*     3.8    21.5    -      +       -      -
    234X  VAL*     1.3    82.0    -      -       -      +
    236X  PHE*     1.3    64.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 236 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120X  ILE*     3.8    25.6    -      -       +      -
    121X  TYR      2.9    14.3    +      -       -      +
    122X  ARG*     3.1    26.2    -      -       -      +
    123X  MET      3.9     0.3    +      -       -      -
    147X  LEU*     3.6     8.2    -      -       +      +
    156X  ASN      5.4     0.2    -      -       -      -
    159X  MET*     3.7    38.6    -      -       +      -
    160X  ASP*     3.5    21.3    -      -       -      -
    163X  GLY      3.5    34.8    -      -       -      -
    164X  SER*     4.5     1.3    -      -       -      -
    178X  PHE*     4.1    13.7    -      -       +      -
    179X  SER      3.2    11.9    -      -       -      +
    180X  TYR      4.4     0.2    -      -       -      -
    181X  ALA*     3.5     8.0    -      -       -      +
    234X  VAL*     3.6    29.8    -      -       +      -
    235X  PHE*     1.3    75.7    -      -       -      +
    237X  LYS*     1.3    63.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 237 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122X  ARG*     5.3     0.7    -      -       +      -
    147X  LEU*     4.6     1.1    -      -       -      -
    178X  PHE*     3.3     6.3    -      -       -      -
    179X  SER*     2.9    46.6    +      -       -      +
    180X  TYR      3.6    20.0    +      -       -      -
    181X  ALA*     3.9    15.4    +      -       +      +
    236X  PHE*     1.3    76.6    -      -       -      +
    238X  PRO*     1.3    82.7    -      -       +      +
    239X  GLN*     4.6     5.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 238 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122X  ARG*     5.8     1.6    -      -       +      -
    147X  LEU*     4.6    13.9    -      -       +      -
    177X  PHE      3.8     1.3    -      -       -      +
    178X  PHE*     3.8    25.1    -      -       +      -
    237X  LYS*     1.3    99.1    -      -       +      +
    239X  GLN*     1.3    60.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 239 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177X  PHE*     2.9    52.0    +      -       +      +
    179X  SER*     2.7    35.2    +      -       -      +
    237X  LYS*     4.6     6.9    -      -       -      -
    238X  PRO*     1.3    77.5    -      -       -      +
    240X  SER*     1.3    81.2    +      -       -      +
    241X  PHE      3.4     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