Contacts of the strand formed by residues 263 - 268 (chain J) in PDB entry 6O81


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 263 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127J  SER*     5.6     0.4    -      -       -      +
    128J  LEU*     3.4    34.5    -      -       +      +
    130J  MET*     5.1     0.4    -      -       -      -
    166J  ARG*     3.3    28.2    -      -       -      +
    167J  LEU*     3.4    39.0    +      -       +      +
    229J  ILE*     5.0     1.8    -      -       -      +
    232J  LEU*     3.4    43.7    -      -       +      +
    233J  VAL*     3.7    12.6    -      -       +      +
    236J  GLN*     4.3     8.4    -      -       +      +
    261J  LEU*     3.8    14.4    -      -       +      -
    262J  ASP*     1.3    76.8    -      -       -      +
    264J  TYR*     1.3    66.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 264 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120J  LEU*     4.0    28.3    -      -       +      +
    124J  TYR*     3.2    47.3    -      +       +      +
    126J  ALA*     3.7    17.3    -      -       +      -
    128J  LEU      2.9    10.4    +      -       -      +
    129J  ALA*     3.2     7.4    -      -       +      -
    130J  MET*     2.9    26.0    +      -       -      +
    163J  THR*     6.0     0.2    -      -       -      -
    165J  LYS*     3.3    31.6    -      -       +      -
    166J  ARG*     3.6    30.2    +      -       +      +
    167J  LEU*     4.1     3.7    -      -       -      +
    262J  ASP*     3.6    25.0    -      -       +      +
    263J  ILE*     1.3    80.5    -      -       -      +
    265J  SER*     1.3    62.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 265 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117J  VAL*     5.9     0.2    -      -       -      -
    120J  LEU*     4.2     6.4    -      -       -      +
    130J  MET*     3.0    19.3    -      -       -      -
    132J  MET*     4.9     9.8    -      -       -      +
    158J  ILE*     5.4     2.1    -      -       -      +
    160J  VAL*     4.4    11.1    -      -       -      +
    164J  GLY      3.7     4.9    -      -       -      +
    165J  LYS*     2.7    32.2    +      -       -      +
    167J  LEU*     3.7    21.9    -      -       -      +
    264J  TYR*     1.3    76.4    -      -       -      +
    266J  PHE*     1.3    60.8    +      -       -      +
    267J  ILE*     4.0    16.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 266 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112J  VAL*     5.4     3.8    -      -       +      -
    116J  GLU*     3.1    46.4    -      -       +      +
    117J  VAL*     5.2     2.7    -      -       +      -
    120J  LEU*     4.0    16.5    -      -       +      +
    130J  MET      2.9     9.8    +      -       -      +
    131J  LEU*     3.4    13.7    -      -       +      +
    132J  MET*     2.9    28.2    +      -       -      +
    164J  GLY      5.1     4.3    -      -       -      -
    165J  LYS*     6.1     2.5    -      -       +      -
    265J  SER*     1.3    74.9    +      -       -      +
    267J  ILE*     1.3    84.3    +      -       -      +
    268J  LYS*     3.7    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 267 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132J  MET*     3.5    13.5    -      -       +      +
    134J  LYS*     3.8    20.9    -      -       -      -
    158J  ILE*     5.8     1.8    -      -       +      -
    160J  VAL*     5.6     6.5    -      -       +      -
    164J  GLY      4.8    11.0    +      -       -      +
    196J  HIS*     5.1    17.9    -      -       +      +
    199J  LEU*     3.7    45.5    -      -       +      -
    265J  SER*     4.0    15.9    -      -       -      +
    266J  PHE*     1.3    93.9    -      -       -      +
    268J  LYS*     1.3    65.2    +      -       -      +
    269J  GLU*     4.0     1.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 268 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112J  VAL*     4.0    25.4    -      -       +      -
    131J  LEU*     3.9    16.8    -      -       +      -
    132J  MET      2.9    15.5    +      -       -      +
    133J  ARG*     4.0    17.9    -      -       +      +
    134J  LYS*     4.0    18.5    +      -       -      +
    266J  PHE*     3.7    14.2    +      -       +      -
    267J  ILE*     1.3    78.8    -      -       -      +
    269J  GLU*     1.3    61.0    +      -       -      +
    270J  ALA      3.8     1.6    -      -       -      +
    271J  ASN      5.1     1.7    -      -       -      +
----------------------------------------------------------
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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