Contacts of the strand formed by residues 766 - 771 (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 PHE 766 (chain T).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    733T  ILE      4.1     0.9    -      -       -      -
    734T  GLN*     3.2     4.2    -      -       -      +
    735T  CYS*     2.8    30.5    +      -       -      +
    737T  GLU*     3.2    57.9    -      -       +      -
    740T  VAL*     4.0    17.5    -      -       +      -
    757T  GLU*     4.0    26.5    -      -       +      -
    758T  GLU      3.4    16.4    -      -       -      -
    759T  GLN*     3.1    35.7    -      -       +      -
    764T  PRO      5.7     1.6    -      -       -      -
    765T  LEU*     1.3    82.4    -      -       -      +
    767T  THR*     1.3    71.8    +      -       -      +
    768T  VAL*     4.2     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 767 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    732T  GLU*     4.8     8.3    -      -       -      -
    733T  ILE      3.0     7.4    -      -       -      -
    734T  GLN*     3.4    33.4    -      -       +      +
    756T  SER      3.5     4.3    -      -       -      +
    757T  GLU*     3.8     0.8    -      -       -      -
    758T  GLU*     3.2    51.3    +      -       -      +
    759T  GLN      4.6     5.9    +      -       -      -
    765T  LEU      5.1     3.1    -      -       -      +
    766T  PHE*     1.3    84.5    -      -       -      +
    768T  VAL*     1.3    62.4    +      -       -      +
    769T  LYS*     3.9     3.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 768 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    731T  VAL      3.3     3.5    -      -       -      +
    732T  GLU*     3.6     0.3    -      -       -      -
    733T  ILE*     2.8    39.8    +      -       +      +
    735T  CYS*     5.8     0.4    -      -       -      -
    740T  VAL*     4.1    24.9    -      -       +      -
    743T  ILE*     3.9    43.3    -      -       +      -
    744T  TYR*     4.2    11.7    -      -       +      +
    747T  LEU*     5.1     0.4    -      -       +      -
    754T  VAL*     3.9    25.6    -      -       +      -
    756T  SER      3.3     4.3    -      -       -      +
    757T  GLU*     4.5     8.3    -      -       +      -
    766T  PHE*     5.2     0.7    -      -       +      -
    767T  THR*     1.3    78.1    -      -       -      +
    769T  LYS*     1.3    65.6    +      -       -      +
    770T  ALA*     5.0     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 769 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    730T  LEU*     4.3    19.4    -      -       +      +
    731T  VAL      3.3     3.6    -      -       -      +
    732T  GLU*     3.7    41.4    +      -       +      -
    754T  VAL*     3.7     3.5    -      -       -      +
    755T  VAL*     2.6    35.3    +      -       +      -
    756T  SER*     2.8    34.9    +      -       -      +
    758T  GLU*     4.1    17.2    +      -       -      +
    767T  THR*     5.0     4.0    -      -       -      +
    768T  VAL*     1.3    75.4    -      -       -      +
    770T  ALA*     1.3    56.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 770 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    730T  LEU*     2.5    28.1    +      -       -      +
    731T  VAL*     2.7    34.1    +      -       +      +
    733T  ILE*     6.2     0.9    -      -       +      -
    747T  LEU*     3.6    28.9    -      -       +      -
    753T  GLN      3.0    19.5    -      -       -      +
    754T  VAL*     3.8     4.3    -      -       +      -
    755T  VAL*     3.7     6.2    -      -       -      +
    768T  VAL*     5.0     2.2    -      -       +      -
    769T  LYS*     1.3    77.1    -      -       -      +
    771T  TYR*     1.3    57.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 771 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    730T  LEU*     3.1    30.1    -      -       +      +
    747T  LEU*     4.8     0.5    -      -       -      +
    751T  ARG      4.7     0.3    -      -       -      +
    752T  GLY*     3.4     5.5    -      -       -      -
    753T  GLN*     2.8    58.2    +      -       +      +
    755T  VAL*     3.7    28.9    -      -       +      +
    770T  ALA*     1.3    76.0    -      -       -      +
    772T  LEU*     1.3    60.4    +      -       -      +
    773T  PRO*     4.2     2.6    -      -       +      +
    799T  ASP*     3.5    29.2    +      -       +      -
    800T  HIS*     3.6    28.6    +      +       +      +
----------------------------------------------------------
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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