Contacts of the strand formed by residues 77 - 82 (chain B) in PDB entry 7KAC


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 TYR 77 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63B  ILE*     3.4    20.6    -      -       +      +
     66B  LEU*     3.7    42.1    +      -       +      +
     67B  LYS*     3.8    30.1    -      -       +      -
     69B  CYS      5.7     1.4    +      -       -      -
     75B  VAL      3.7     0.8    +      -       -      -
     76B  ALA*     1.3    73.8    -      -       -      +
     78B  HIS*     1.3    64.7    +      -       -      +
     79B  GLY*     3.3    35.3    -      -       -      -
     80B  SER*     2.7    27.0    +      -       -      -
     89B  ILE*     3.7    17.3    -      -       +      -
     90B  CYS      3.7     9.0    -      -       -      -
     91B  MET*     4.4     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 78 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  TYR*     4.3     7.6    -      -       -      +
     42B  LEU      5.3     0.8    +      -       -      -
     43B  VAL*     3.8    22.3    -      -       +      +
     76B  ALA*     4.2    20.4    -      -       +      -
     77B  TYR*     1.3    79.4    +      -       -      +
     79B  GLY*     1.3    58.8    +      -       -      +
     90B  CYS*     2.9    23.2    +      -       -      -
     91B  MET      3.5    25.6    -      -       -      -
     92B  GLU*     3.6    19.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 79 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77B  TYR*     3.3    24.0    -      -       -      -
     78B  HIS*     1.3    81.1    -      -       -      +
     80B  SER*     1.3    60.1    +      -       -      -
     81B  TYR*     4.8     4.7    -      -       -      -
     90B  CYS*     2.8    30.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 80 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  ILE*     3.7    19.6    -      -       -      +
      9B  PHE*     3.0    30.8    +      -       -      +
     63B  ILE*     3.9    17.9    -      -       -      +
     77B  TYR*     2.7    27.9    +      -       -      -
     79B  GLY*     1.3    72.4    +      -       -      -
     81B  TYR*     1.3    66.3    +      -       -      +
     87B  LEU*     4.4    11.2    -      -       -      -
     88B  TRP      3.3     8.5    -      -       -      -
     89B  ILE*     4.1     5.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 81 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  ILE*     4.0     3.1    -      -       -      -
      9B  PHE*     3.2    29.8    -      -       +      -
     11B  ARG*     3.7    24.0    -      -       +      +
     12B  ASP      4.7     2.0    -      -       -      -
     13B  PRO*     4.1    33.9    -      -       +      -
     16B  HIS*     3.1    34.1    +      +       +      -
     17B  TYR*     3.4    34.7    +      +       -      -
     45B  LEU*     4.9     2.5    -      -       +      -
     79B  GLY*     4.8     3.1    -      -       -      -
     80B  SER*     1.3    80.3    -      -       -      +
     82B  LEU*     1.3    58.3    +      -       -      +
     83B  TRP      4.0     0.7    -      -       -      -
     86B  LYS      3.4     0.7    -      -       -      +
     87B  LEU*     3.3     9.9    -      -       -      +
     88B  TRP*     2.9    43.7    +      -       +      +
     90B  CYS*     4.5    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 82 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8B  ILE*     3.5    20.2    -      -       +      -
      9B  PHE      3.2     7.7    +      -       -      +
     10B  ASN*     3.7    37.7    -      -       -      +
     11B  ARG      4.2     0.4    +      -       -      -
     81B  TYR*     1.3    72.9    -      -       -      +
     83B  TRP*     1.3    60.8    +      -       -      +
     85B  GLN      5.4     0.9    -      -       -      -
     86B  LYS      3.5     7.4    -      -       -      +
     87B  LEU*     4.9     3.8    -      -       +      +
----------------------------------------------------------
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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