Contacts of the strand formed by residues 585 - 592 (chain T) in PDB entry 2P8Z


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 ARG 585 (chain T).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    576T  LEU*     3.1    32.5    -      -       +      +
    577T  SER      3.2     6.1    -      -       -      +
    578T  LYS*     3.6    39.8    -      -       +      +
    582T  LYS      5.2     4.5    +      -       -      +
    583T  HIS      5.2     2.0    -      -       -      +
    584T  ASN*     1.3    82.1    -      -       -      +
    586T  ILE*     1.3    66.8    +      -       -      +
    587T  TYR*     4.3     7.0    -      -       +      -
    690T  ASP      4.1     0.2    -      -       -      +
    691T  VAL*     3.5     6.1    -      -       -      +
    692T  THR*     3.0    45.4    +      -       -      +
    708T  THR*     4.5     0.2    -      -       -      -
    840T  ASP      2.9    24.1    +      -       -      -
    841T  LYS      3.0    17.6    +      -       -      -
    842T  LEU*     3.2    33.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 586 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    575T  ALA      3.4     4.9    -      -       -      +
    576T  LEU*     3.6     2.9    -      -       -      +
    577T  SER      2.9    28.1    +      -       -      -
    584T  ASN*     6.4     0.2    -      -       +      -
    585T  ARG*     1.3    77.5    -      -       -      +
    587T  TYR*     1.3    68.4    +      -       -      +
    588T  LEU*     3.9    28.2    +      -       +      -
    659T  ILE*     5.6     0.2    -      -       +      -
    663T  VAL*     4.7     8.1    -      -       +      -
    688T  ILE*     4.7    11.0    -      -       +      -
    690T  ASP      3.8     4.7    -      -       -      +
    691T  VAL*     4.3    17.9    -      -       +      -
    705T  ILE*     4.5    13.0    -      -       +      -
    708T  THR*     3.8    14.8    -      -       +      +
    709T  MET*     3.7    41.1    -      -       +      +
    712T  ALA*     4.1     9.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 587 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    574T  THR*     3.9    22.0    -      -       +      -
    575T  ALA      3.2     5.2    -      -       -      -
    576T  LEU*     3.4    32.9    -      -       +      +
    585T  ARG*     4.3    15.0    -      -       +      -
    586T  ILE*     1.3    74.8    -      -       -      +
    588T  LEU*     1.3    63.4    +      -       -      +
    688T  ILE*     3.8     3.3    -      -       -      +
    689T  LEU*     2.8    28.0    +      -       +      -
    690T  ASP*     2.8    52.7    +      -       +      +
    692T  THR*     4.3    13.9    +      -       +      +
    842T  LEU*     3.4    32.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 588 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    574T  THR*     4.1     1.2    -      -       -      +
    575T  ALA*     2.6    45.8    +      -       +      +
    586T  ILE*     3.9    11.9    -      -       +      -
    587T  TYR*     1.3    73.6    -      -       -      +
    589T  LYS*     1.3    69.7    +      -       -      +
    590T  ALA      4.7     0.2    -      -       -      +
    686T  VAL*     3.7    26.7    -      -       +      -
    687T  ASN      3.1    18.6    -      -       -      +
    688T  ILE*     4.2     4.3    -      -       +      -
    689T  LEU*     4.2     4.9    -      -       -      +
    709T  MET*     4.0    16.4    -      -       +      -
    712T  ALA*     3.6    44.9    -      -       +      +
    713T  THR*     4.0     9.0    -      -       -      +
    716T  GLY*     4.0    14.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 589 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    570T  GLU*     3.6    36.3    +      -       +      +
    571T  SER*     3.3    17.6    +      -       -      +
    573T  GLN*     4.2     4.9    -      -       -      +
    574T  THR*     3.3    38.6    -      -       -      +
    588T  LEU*     1.3    84.5    -      -       -      +
    590T  ALA*     1.3    60.4    +      -       -      +
    686T  VAL*     3.5     2.9    -      -       -      +
    687T  ASN*     2.8    39.7    +      -       +      +
    689T  LEU*     3.7    21.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 590 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    567T  VAL*     4.7     1.8    -      -       +      -
    569T  SER      3.7     0.9    -      -       -      +
    570T  GLU*     3.1     5.2    -      -       -      +
    571T  SER*     2.6    34.4    +      -       -      -
    588T  LEU*     5.3     0.4    -      -       +      -
    589T  LYS*     1.3    75.8    -      -       -      +
    591T  GLU*     1.3    62.9    +      -       -      +
    684T  VAL*     4.6     8.3    -      -       +      -
    685T  ARG      3.1    10.1    -      -       -      +
    686T  VAL*     4.4    11.9    -      -       +      +
    716T  GLY*     3.6    27.5    -      -       -      +
    717T  PHE*     4.0     8.7    -      -       +      +
    720T  ALA*     4.2     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 591 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    567T  VAL*     3.6     6.8    -      -       -      +
    569T  SER      3.9     2.7    -      -       -      -
    570T  GLU*     4.1    18.9    -      -       +      +
    590T  ALA*     1.3    77.1    -      -       -      +
    592T  PRO*     1.3    78.1    -      -       +      +
    685T  ARG*     2.8    72.7    +      -       +      +
    687T  ASN*     2.8    26.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 592 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    567T  VAL*     3.4    14.6    -      -       +      +
    568T  GLU*     3.3    35.2    -      -       -      +
    569T  SER*     3.4    15.9    -      -       -      +
    570T  GLU      4.0     0.9    -      -       -      +
    591T  GLU*     1.3   101.9    -      -       +      +
    593T  ILE*     1.3    64.1    +      -       -      +
    594T  ASP      4.0     0.9    +      -       -      -
    683T  SER*     3.6     7.6    -      -       -      +
    685T  ARG*     4.6     1.6    -      -       -      +
----------------------------------------------------------
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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