Contacts of the strand formed by residues 758 - 761 (chain P) in PDB entry 1O18


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 TYR 758 (chain P).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    711P  PHE*     4.5     3.6    -      -       -      -
    748P  LEU*     3.5    36.0    -      -       +      +
    753P  VAL*     5.2     4.5    -      -       +      -
    754P  ASP      3.0    25.6    -      -       -      -
    755P  HIS*     2.8    54.6    +      +       +      +
    756P  THR      2.5    26.2    +      -       -      +
    757P  GLN*     1.3    78.6    -      -       +      +
    759P  ALA*     1.3    68.5    +      -       -      +
    760P  PHE*     3.5    43.7    -      +       -      -
    765P  VAL*     3.8     4.7    -      -       +      -
    766P  PHE      2.9    13.9    -      -       -      +
    767P  PHE*     3.6    19.7    -      +       +      -
    771P  LEU*     5.4     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 759 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    508P  ILE*     2.9    34.6    -      -       +      +
    711P  PHE*     4.9     9.6    -      -       +      -
    758P  TYR*     1.3    82.1    -      -       -      +
    760P  PHE*     1.3    67.5    +      -       -      +
    765P  VAL*     3.1     2.1    -      -       -      -
    766P  PHE*     2.3    48.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 760 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    507P  GLY      3.4     4.3    -      -       -      +
    508P  ILE*     3.2    24.8    -      -       -      +
    717P  TYR*     3.1    21.8    -      +       -      +
    741P  LYS*     5.5     4.5    -      -       -      -
    744P  SER      4.4     3.6    -      -       -      -
    745P  GLU*     3.6    58.3    -      -       +      +
    748P  LEU*     4.5     3.8    -      -       +      -
    758P  TYR*     3.5    36.1    -      +       -      -
    759P  ALA*     1.3    80.8    -      -       -      +
    761P  GLY*     1.3    59.1    +      -       -      +
    764P  MLY      3.8     2.7    -      -       -      -
    765P  VAL*     3.8    16.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 761 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    506P  GLU*     2.3    32.3    -      -       -      -
    507P  GLY*     3.5     2.9    -      -       -      -
    717P  TYR*     3.3    11.1    -      -       -      -
    741P  LYS*     4.8     6.1    -      -       -      -
    760P  PHE*     1.3    79.5    -      -       -      +
    762P  HIS*     1.3    51.5    +      -       -      -
    763P  THR      2.7    16.2    +      -       -      -
    764P  MLY      2.9    16.6    +      -       -      +
----------------------------------------------------------
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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