Contacts of the strand formed by residues 554 - 560 (chain F) in PDB entry 4OQB


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 SER 554 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    531F  ALA*     4.9    15.0    -      -       -      +
    532F  ALA      5.3     0.7    +      -       -      -
    545F  VAL*     4.2     7.9    -      -       -      -
    552F  VAL*     2.7    29.3    +      -       -      +
    553F  PHE*     1.3    76.5    -      -       -      +
    555F  ALA*     1.3    63.1    +      -       -      +
    556F  THR*     5.4     2.4    +      -       -      -
    571F  LYS*     5.4     2.1    -      -       -      +
    572F  LEU      3.4     7.9    -      -       -      -
    573F  GLN*     3.5    24.6    +      -       -      +
    614F  PHE*     3.9     4.4    -      -       -      -
    626F  TRP*     4.4     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 555 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    554F  SER*     1.3    75.6    +      -       -      +
    556F  THR*     1.3    64.3    +      -       -      +
    557F  LEU*     4.0    10.9    -      -       +      +
    570F  TYR      3.8     1.4    -      -       -      +
    571F  LYS*     3.5     1.7    -      -       -      +
    572F  LEU*     2.8    42.4    +      -       +      +
    614F  PHE*     4.9     1.3    -      -       +      -
    618F  TYR*     4.0    28.5    -      -       +      -
    626F  TRP*     4.3    10.1    -      -       +      -
    640F  PRO*     5.2     4.7    -      -       +      -
    641F  LEU      5.7     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 556 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    554F  SER*     5.4     1.7    +      -       -      -
    555F  ALA*     1.3    73.2    -      -       -      +
    557F  LEU*     1.3    69.6    +      -       -      +
    569F  TYR*     5.5     4.7    -      -       +      -
    570F  TYR      3.8     2.5    -      -       -      +
    571F  LYS*     3.6    34.6    -      -       +      +
    641F  LEU*     2.9    43.4    +      -       +      +
    643F  ILE*     3.2    32.3    -      -       +      +
    695F  LYS*     5.0    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 557 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    555F  ALA*     4.1    18.2    -      -       +      +
    556F  THR*     1.3    80.7    -      -       -      +
    558F  GLY*     1.3    60.3    +      -       -      +
    569F  TYR*     3.5     6.9    -      -       -      +
    570F  TYR*     2.8    58.6    +      -       +      +
    572F  LEU*     5.8     2.5    -      -       +      +
    618F  TYR*     4.3    14.4    -      -       +      +
    621F  LYS*     4.1    13.9    -      -       +      -
    622F  THR*     4.2    11.4    -      -       -      +
    638F  PHE*     3.7    30.7    -      -       +      -
    639F  TYR      3.4     5.2    -      -       -      +
    640F  PRO*     3.5    31.4    -      -       +      -
    641F  LEU*     4.6     4.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 558 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    557F  LEU*     1.3    76.8    -      -       -      +
    559F  LEU*     1.3    62.1    +      -       -      +
    568F  SER      3.5    11.0    -      -       -      -
    633F  LYS*     4.9     0.3    +      -       -      -
    638F  PHE*     3.7     4.2    -      -       -      -
    639F  TYR*     2.9    31.8    +      -       -      +
    641F  LEU*     4.5     8.4    -      -       -      +
    738F  THR*     3.3    21.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 559 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318D  TRP      5.7     2.9    -      -       -      +
    558F  GLY*     1.3    75.9    -      -       -      +
    560F  VAL*     1.3    78.8    +      -       -      +
    561F  ASP*     5.5     0.2    -      -       +      -
    566F  THR*     4.2     6.7    -      -       +      +
    567F  ASN*     3.5     1.3    +      -       -      -
    568F  SER*     2.8    39.4    +      -       -      +
    633F  LYS*     3.6    22.0    -      -       -      +
    636F  LYS*     3.6    52.9    -      -       +      +
    637F  LYS      4.1     4.0    -      -       -      +
    638F  PHE*     3.7    34.9    -      -       +      -
    738F  THR*     3.9     5.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 560 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318D  TRP      4.7     5.7    -      -       -      +
    559F  LEU*     1.3    85.4    -      -       -      +
    561F  ASP*     1.3    69.6    +      -       -      +
    562F  ILE*     4.2     4.0    -      -       +      +
    566F  THR      3.3    13.9    -      -       -      +
    567F  ASN*     4.1    11.9    -      -       +      +
    734F  ASN*     3.2    28.0    -      -       -      +
    737F  TYR*     3.8    11.2    -      -       +      -
    738F  THR*     2.9    45.1    +      -       -      +
    749F  PRO*     3.9    24.9    -      -       +      -
----------------------------------------------------------
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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