Contacts of the strand formed by residues 528 - 535 (chain F) in PDB entry 4OMC


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 528 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    263F  VAL*     3.8    28.9    -      -       +      -
    305F  CYS*     4.6     4.9    -      -       -      -
    491F  LEU*     3.9    13.2    -      -       +      +
    492F  THR*     3.1     6.2    -      -       -      +
    493F  LEU*     2.9    56.9    +      -       +      +
    498F  ARG*     3.6    26.2    -      -       +      -
    501F  LEU*     4.7     6.1    -      -       +      -
    503F  ILE*     4.8     1.3    -      -       +      -
    516F  LEU*     3.8    32.1    -      -       +      -
    519F  ARG*     6.2     0.2    -      -       -      -
    522F  ASP*     5.4     0.9    -      -       -      -
    526F  ASP      4.7     1.6    -      -       -      -
    527F  GLY*     1.3    77.3    -      -       -      -
    529F  ASN*     1.3    60.3    +      -       -      +
    530F  ASP      3.8     0.2    -      -       -      -
    531F  TRP*     3.9    22.0    -      +       +      -
    533F  PHE*     3.8    29.8    -      +       +      -
    604F  FMT      3.6     5.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 529 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    268E  ARG*     4.7    20.1    +      -       -      +
    492F  THR*     4.3    11.8    +      -       -      +
    526F  ASP      5.1     2.2    +      -       -      +
    528F  PHE*     1.3    70.7    -      -       -      +
    530F  ASP*     1.3    75.7    +      -       -      +
    531F  TRP*     3.2     3.0    +      -       -      -
    604F  FMT      3.0    23.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 530 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233E  ASP*     4.6     6.1    -      -       -      +
    267E  ALA*     5.2     3.3    -      -       -      +
    268E  ARG*     3.8    28.3    +      -       -      +
    490F  ARG*     2.9    49.9    +      -       -      +
    491F  LEU      3.1     6.0    +      -       -      -
    492F  THR*     2.8    24.0    +      -       -      +
    529F  ASN*     1.3    77.5    -      -       -      +
    531F  TRP*     1.3    61.6    +      -       -      +
    532F  ALA      3.6     0.5    +      -       -      -
    565F  LYS*     3.1    24.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 531 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    263F  VAL*     3.7    29.1    -      -       +      +
    264F  ASP*     3.5    28.3    -      -       -      -
    265F  GLY*     4.5     2.5    -      -       -      -
    304F  ASN      2.8    29.0    +      -       -      -
    305F  CYS*     3.8    11.3    -      -       -      +
    306F  ASP      4.2     0.2    -      -       -      -
    307F  GLY*     3.8    19.1    -      -       -      -
    310F  ASN*     4.2    10.2    -      -       -      +
    489F  ALA      3.4     0.9    -      -       -      +
    490F  ARG*     3.3     1.1    -      -       -      -
    491F  LEU      2.9    26.7    +      -       -      +
    528F  PHE*     3.9    27.6    -      +       +      -
    529F  ASN      3.2     2.2    -      -       -      -
    530F  ASP*     1.3    76.4    -      -       -      +
    532F  ALA*     1.3    60.7    +      -       -      +
    533F  PHE*     3.3    41.3    +      +       +      -
    604F  FMT      4.0    11.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 532 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    310F  ASN*     2.6    28.8    +      -       -      +
    488F  GLN*     3.7    19.6    +      -       -      +
    489F  ALA      3.9     4.0    -      -       -      -
    490F  ARG*     3.4    40.4    -      -       +      +
    530F  ASP      3.6     2.2    +      -       -      -
    531F  TRP*     1.3    76.9    -      -       -      +
    533F  PHE*     1.3    59.3    +      -       -      +
    534F  MET*     3.3     3.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 533 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    304F  ASN*     4.2     9.0    -      -       +      +
    305F  CYS*     5.1     1.1    -      -       -      -
    310F  ASN*     3.9     5.4    -      -       -      +
    487F  ALA      3.9     0.2    -      -       -      +
    488F  GLN*     3.1     4.7    -      -       -      -
    489F  ALA*     2.9    43.1    +      -       -      +
    491F  LEU*     3.7    30.3    -      -       +      -
    503F  ILE*     4.5     6.3    -      -       +      -
    515F  LEU*     3.3    51.2    -      -       +      +
    516F  LEU*     4.0    15.9    -      -       +      -
    528F  PHE*     3.8    34.8    -      +       -      -
    531F  TRP*     3.6    37.7    -      +       +      -
    532F  ALA*     1.3    71.2    -      -       -      +
    534F  MET*     1.3    58.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 534 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    304F  ASN*     3.4     3.9    +      -       -      +
    310F  ASN*     3.1    46.4    +      -       -      +
    311F  SER      3.7    15.9    -      -       -      +
    312F  ILE*     4.0    16.8    -      -       +      -
    314F  THR      5.5     0.4    -      -       -      +
    334F  SER*     2.7    22.6    +      -       -      -
    335F  SER*     3.3    37.8    +      -       -      +
    486F  HIS*     4.1    17.9    -      -       +      -
    487F  ALA      3.4    11.0    -      -       -      +
    488F  GLN*     4.2     7.2    -      -       +      +
    515F  LEU*     4.7     1.3    -      -       -      -
    532F  ALA      4.0     3.4    -      -       -      +
    533F  PHE*     1.3    75.6    -      -       -      +
    535F  THR*     1.3    87.7    +      -       -      +
    536F  THR*     3.7    13.2    -      -       +      -
    608F   NA      4.1     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 535 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    334F  SER*     3.3    17.6    -      -       -      -
    485F  GLU      4.4     1.2    -      -       -      +
    486F  HIS*     3.9     2.9    -      -       -      -
    487F  ALA*     3.0    42.4    +      -       +      +
    505F  LEU*     4.6     9.9    -      -       +      -
    513F  SER*     2.7    35.1    +      -       -      +
    515F  LEU*     4.4     7.9    -      -       +      -
    534F  MET*     1.3    82.3    -      -       -      +
    536F  THR*     1.3    61.5    +      -       -      +
    537F  HIS*     3.0    11.9    +      -       -      +
    538F  SER*     5.0     8.2    +      -       -      +
    547F  TRP*     5.8     2.0    -      -       +      -
----------------------------------------------------------
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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