Contacts of the strand formed by residues 265 - 268 (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 ILE 265 (chain P).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225P  ALA*     4.1    24.9    -      -       +      -
    229P  LEU*     4.2    18.6    -      -       +      -
    246P  PHE*     6.3     0.2    -      -       +      -
    248P  MLY      4.5    20.4    -      -       +      -
    249P  PHE      3.5     4.3    -      -       -      +
    250P  ILE*     4.3    19.1    -      -       +      -
    264P  ASP*     1.3    82.5    -      -       -      +
    266P  GLU*     1.3    85.9    +      -       -      +
    267P  THR*     4.5     4.7    -      -       -      +
    442P  VAL*     3.9    17.7    -      -       +      +
    445P  ILE*     4.2    15.0    -      -       +      -
    446P  ASN*     2.6    36.2    +      -       -      +
    449P  LEU*     4.7     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 266 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248P  MLY      3.3     9.4    -      -       -      +
    249P  PHE*     3.1    36.1    +      -       +      +
    264P  ASP*     5.4     4.3    -      -       -      +
    265P  ILE*     1.3    78.3    -      -       -      +
    267P  THR*     1.3    72.1    +      -       -      +
    268P  TYR*     3.1    37.4    +      -       +      +
    442P  VAL*     4.9     1.8    -      -       -      -
    656P  ASN*     4.6     7.3    +      -       -      +
    659P  MLY      2.5    54.0    +      -       -      +
    660P  LEU*     5.8     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 267 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229P  LEU*     5.6     0.3    -      -       -      +
    246P  PHE*     4.4    16.7    -      -       +      -
    247P  GLY      3.6     4.4    +      -       -      -
    265P  ILE*     4.5     3.6    -      -       -      +
    266P  GLU*     1.3    82.4    +      -       -      +
    268P  TYR*     1.3    79.5    +      -       -      +
    269P  LEU      4.9     0.2    -      -       -      +
    270P  LEU*     4.9     5.4    -      -       +      -
    438P  PHE*     3.4    38.7    -      -       +      -
    439P  LEU*     4.7    11.9    -      -       +      -
    442P  VAL*     3.7    19.4    -      -       -      +
    656P  ASN*     5.4     2.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 268 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246P  PHE*     3.8     1.6    -      -       -      +
    247P  GLY*     3.0    42.2    +      -       -      +
    248P  MLY      4.1     2.0    -      -       -      -
    249P  PHE*     3.8    29.4    -      -       +      +
    266P  GLU*     3.1    37.3    +      -       +      +
    267P  THR*     1.3    84.0    -      -       -      +
    269P  LEU*     1.3    83.6    +      -       +      +
    270P  LEU      3.7     0.7    -      -       -      -
    462P  LEU*     5.1     0.2    -      -       +      -
    464P  ILE*     4.3    17.0    -      -       +      -
    653P  PHE*     5.5     9.0    -      +       +      -
    656P  ASN*     4.2    29.4    -      -       +      -
    657P  LEU*     5.0     1.3    -      -       -      -
    660P  LEU*     3.5    37.7    -      -       +      +
----------------------------------------------------------
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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