Contacts of the strand formed by residues 518 - 523 (chain B) in PDB entry 3HO5


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 518 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219B  ILE*     5.7     1.1    -      -       +      -
    495B  PHE*     5.1     1.3    -      +       -      -
    510B  VAL*     4.0    17.5    -      -       +      -
    511B  PHE      3.5     4.0    -      -       -      -
    512B  GLY*     3.6    21.8    -      -       -      -
    516B  GLY*     3.1    30.5    +      -       -      -
    517B  ASN*     1.3    74.5    -      -       -      +
    519B  LEU*     1.3    65.3    +      -       -      +
    534B  PRO*     3.8     6.4    -      -       -      +
    535B  LEU*     3.2    47.6    +      -       +      +
    537B  LEU*     3.9    30.7    -      -       +      -
    547B  PHE*     4.7     2.7    -      +       -      -
    551B  ILE*     3.7    20.9    -      -       +      -
    554B  PHE*     4.1    17.5    -      +       -      -
    564B  ILE*     3.8    17.9    -      -       +      -
    582B  ILE*     4.7    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 519 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    486B  PHE*     3.5    36.8    -      -       +      -
    488B  ASN*     4.3    25.4    -      -       +      +
    491B  LEU*     4.2     8.5    -      -       +      -
    510B  VAL*     3.3     9.4    -      -       -      +
    511B  PHE*     2.7    43.9    +      -       +      +
    517B  ASN*     4.9     4.0    -      -       +      +
    518B  PHE*     1.3    80.4    -      -       -      +
    520B  THR*     1.3    68.3    +      -       -      +
    521B  LEU*     4.1     1.6    -      -       +      +
    532B  GLU*     3.2    26.7    -      -       +      +
    533B  LYS      3.6     6.3    -      -       -      +
    534B  PRO*     5.3     6.1    -      -       +      -
    535B  LEU*     4.6     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 520 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    505B  LEU*     4.4     5.9    -      -       +      +
    508B  SER*     3.7    31.2    -      -       -      +
    509B  TYR      3.2     4.9    +      -       -      -
    510B  VAL*     4.5     0.3    -      -       -      +
    519B  LEU*     1.3    76.8    +      -       -      +
    521B  LEU*     1.3    60.3    +      -       -      +
    522B  GLN*     3.1    22.6    +      -       +      +
    531B  GLN      3.6     0.2    -      -       -      +
    532B  GLU*     3.4     2.4    -      -       -      -
    533B  LYS*     2.7    46.5    +      -       +      +
    534B  PRO      5.1     1.1    -      -       -      -
    535B  LEU*     3.5    25.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 521 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    451B  LEU*     4.2    18.4    -      -       +      -
    483B  PHE*     4.8     1.8    -      -       +      -
    485B  PRO*     3.9    27.1    -      -       +      -
    486B  PHE*     3.8    31.4    -      -       +      -
    508B  SER*     4.7     0.7    -      -       -      -
    509B  TYR*     3.1    36.2    +      -       +      +
    511B  PHE*     4.1    18.8    -      -       +      -
    519B  LEU*     4.1     2.4    -      -       +      +
    520B  THR*     1.3    70.0    -      -       -      +
    522B  GLN*     1.3    62.1    +      -       -      +
    523B  GLN      3.6     2.4    +      -       -      -
    530B  TRP*     4.0    27.0    -      -       +      +
    531B  GLN      4.0     2.5    -      -       -      -
    532B  GLU*     3.8    28.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 522 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    504B  ARG      5.2     2.1    -      -       -      +
    506B  TYR      5.4     1.6    +      -       -      +
    507B  GLY      5.1     4.6    +      -       -      -
    508B  SER*     2.8    34.4    +      -       -      +
    520B  THR*     3.1    17.1    +      -       +      +
    521B  LEU*     1.3    70.5    -      -       -      +
    523B  GLN*     1.3    81.0    +      -       -      +
    524B  SER*     3.1    10.4    +      -       -      +
    525B  PRO*     6.1     0.6    -      -       +      +
    529B  GLN      3.8     0.2    -      -       -      +
    530B  TRP*     4.7     1.6    -      -       -      -
    531B  GLN*     3.2    31.7    +      -       +      +
    533B  LYS*     5.1    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 523 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    438B  ASP*     5.4     2.4    -      -       -      +
    509B  TYR*     4.8     7.5    +      -       +      -
    521B  LEU      3.6     4.0    +      -       -      +
    522B  GLN*     1.3    82.6    +      -       -      +
    524B  SER*     1.3    70.1    +      -       -      +
    525B  PRO*     3.2    11.7    -      -       +      +
    528B  LYS*     5.6     6.7    -      -       -      +
    529B  GLN      4.3     6.1    -      -       -      +
    530B  TRP*     3.3    40.6    -      -       +      -
----------------------------------------------------------
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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