Contacts of the strand formed by residues 83 - 86 (chain B) in PDB entry 2Y96


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 HIS 83 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81B  PHE*     3.8     2.3    -      -       -      -
     82B  THR*     1.3   115.6    -      -       +      +
     84B  VAL*     1.3    65.8    +      -       -      +
    106B  ILE*     4.2     0.8    -      -       -      +
    107B  GLN*     3.3    47.6    +      -       +      +
    131B  PHE*     4.1    15.5    -      +       +      -
    135B  ALA*     3.6    30.9    -      -       +      +
    141B  SER*     3.6    13.0    -      -       -      -
    142B  LYS      3.3     1.5    +      -       -      +
    143B  ILE*     3.4    25.5    -      -       +      +
    144B  LEU*     2.9    25.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 84 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70B  ALA*     4.7     1.3    -      -       +      -
     76B  LEU*     3.8    29.4    -      -       +      -
     81B  PHE*     5.6     2.0    -      -       +      -
     83B  HIS*     1.3    77.7    -      -       -      +
     85B  LEU*     1.3    61.6    +      -       -      +
    101B  TYR*     4.0    11.0    -      -       +      +
    106B  ILE*     3.9    16.3    -      -       +      +
    107B  GLN      3.0     7.1    +      -       -      +
    108B  TYR*     3.3    24.7    -      -       +      -
    109B  HIS      3.1    24.3    +      -       -      +
    131B  PHE*     4.2     4.5    -      -       -      -
    144B  LEU*     3.3    13.0    -      -       +      +
    146B  HIS*     3.5    32.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 85 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83B  HIS      4.3     0.4    -      -       -      -
     84B  VAL*     1.3    73.4    -      -       -      +
     86B  ASN*     1.3    60.4    +      -       -      +
     87B  ALA      3.6     0.6    +      -       -      +
    109B  HIS*     3.5    25.1    -      -       +      +
    111B  VAL*     4.3    22.4    -      -       +      -
    128B  ALA*     4.2    20.4    -      -       +      +
    131B  PHE*     4.1    22.0    -      -       +      -
    132B  ILE*     4.0    32.8    -      -       +      -
    143B  ILE*     4.5     2.0    -      -       +      +
    144B  LEU      2.8    11.7    +      -       -      +
    145B  VAL*     3.4    19.9    -      -       +      +
    146B  HIS*     2.8    28.9    +      -       -      +
    157B  LEU*     4.4     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 86 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67B  GLU*     5.4     3.6    +      -       -      -
     84B  VAL      4.0     0.8    -      -       -      -
     85B  LEU*     1.3    71.8    -      -       -      +
     87B  ALA*     1.3    53.3    +      -       -      +
     88B  ALA*     2.7    35.1    +      -       -      +
     89B  HIS*     3.5    18.2    +      -       -      +
     95B  ASP      6.0     0.2    -      -       -      -
     96B  THR*     4.4    11.9    -      -       -      +
    108B  TYR*     3.0    33.9    +      -       +      +
    109B  HIS      2.9     8.6    +      -       -      +
    110B  GLY*     3.3     0.9    -      -       -      -
    111B  VAL      2.7    32.2    +      -       -      +
    146B  HIS*     3.2    39.0    +      -       -      +
----------------------------------------------------------
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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