Contacts of the strand formed by residues 84 - 90 (chain C) in PDB entry 4GKH


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 84 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69C  MSE      3.5    35.2    -      -       +      +
     72C  LEU*     3.8    23.1    -      -       +      -
     73C  ASN*     3.7    28.7    -      -       +      +
     82C  PRO      3.9     0.6    +      -       -      +
     83C  THR*     1.3    80.9    -      -       -      +
     85C  LYS*     1.3    62.7    +      -       -      +
     86C  HIS*     3.8    16.8    -      -       -      +
     87C  PHE*     4.6     6.1    -      -       +      -
     96C  LEU*     4.2    16.8    -      -       +      -
     97C  LEU      3.9     3.4    -      -       -      -
     98C  THR*     4.4     1.3    -      -       -      -
     89D  ARG*     4.9    13.5    -      -       +      +
     90D  THR      5.9     2.0    -      -       -      -
     91D  PRO*     3.7    20.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 85 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22C  ASP*     4.6     6.6    -      -       +      +
     26C  TYR*     5.2     1.8    +      -       -      -
     50C  PRO*     4.7    14.3    -      -       -      +
     52C  LEU*     4.2    27.1    -      -       +      +
     83C  THR*     3.3     3.3    +      -       +      +
     84C  ILE*     1.3    75.3    -      -       -      +
     86C  HIS*     1.3    66.1    +      -       +      +
     97C  LEU*     2.8    27.5    +      -       +      +
     99C  THR*     3.9    29.6    -      -       +      +
     89D  ARG      4.6     0.2    -      -       -      -
     90D  THR*     4.0     3.8    -      -       -      +
     91D  PRO*     3.4    24.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 86 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17C  SER*     3.3    22.7    +      -       -      -
     18C  ASN*     3.6    10.9    -      -       -      -
     19C  LEU*     3.7    22.7    -      -       +      -
     22C  ASP*     3.0    29.4    -      -       -      +
     84C  ILE*     3.6     4.0    -      -       -      +
     85C  LYS*     1.3    80.0    -      -       -      +
     87C  PHE*     1.3    74.1    +      -       -      +
     88C  ILE*     3.9    19.5    -      -       +      +
     95C  TRP      3.9     0.6    -      -       -      +
     96C  LEU*     3.8     1.7    -      -       -      +
     97C  LEU*     2.8    36.0    +      -       +      +
     88D  ILE*     3.6    29.8    -      -       +      -
     89D  ARG      3.3     9.3    +      -       -      -
     90D  THR*     4.2    11.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 87 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65C  VAL*     4.2     6.5    -      -       +      -
     66C  THR*     3.6    34.8    -      -       -      -
     69C  MSE      3.6    52.5    -      -       +      -
     84C  ILE*     4.6     2.0    -      -       +      -
     86C  HIS*     1.3    78.6    +      -       -      +
     88C  ILE*     1.3    73.5    +      -       -      +
     89C  ARG*     3.8    22.2    -      -       +      -
     94C  ALA*     4.1    11.2    -      -       +      -
     95C  TRP      3.1    23.1    -      -       -      -
     96C  LEU*     4.0    10.1    -      -       +      -
     69D  MSE      4.0     3.4    -      -       +      -
     87D  PHE*     3.7    18.6    -      +       -      -
     88D  ILE*     3.3     5.5    -      -       -      -
     89D  ARG*     2.9    38.5    +      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 88 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18C  ASN*     3.7    22.4    -      -       -      +
     19C  LEU*     3.9    31.4    -      -       +      +
     86C  HIS*     3.9    14.6    -      -       +      +
     87C  PHE*     1.3    84.6    -      -       -      +
     89C  ARG*     1.3    67.5    +      -       -      +
     90C  THR*     4.4     6.3    -      -       +      +
     93C  ASP      4.0     0.4    -      -       -      +
     94C  ALA*     3.2     5.9    -      -       -      +
     95C  TRP*     2.8    49.7    +      -       +      +
     15D  LEU*     5.5     3.8    -      -       +      -
     16D  ASN*     4.7    11.0    -      -       +      +
     86D  HIS*     3.9    25.8    -      -       +      +
     87D  PHE      3.4     3.6    -      -       -      +
     88D  ILE*     4.3     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 89 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59C  GLY      4.9     1.6    +      -       -      -
     62C  ALA*     3.7    14.4    -      -       -      +
     63C  ASN*     3.0    29.1    +      -       -      -
     66C  THR*     3.6    22.8    +      -       -      +
     87C  PHE*     3.8    16.1    -      -       +      -
     88C  ILE*     1.3    74.7    -      -       -      +
     90C  THR*     1.3    92.3    +      -       -      +
     91C  PRO*     3.0    20.8    +      -       -      -
     93C  ASP      3.3    17.4    +      -       -      +
     94C  ALA*     4.0     5.6    -      -       -      -
     69D  MSE      4.7    11.4    -      -       -      -
     73D  ASN*     3.1    21.4    +      -       -      +
     84D  ILE*     4.8    11.2    -      -       +      +
     86D  HIS*     3.3     6.4    -      -       -      -
     87D  PHE*     2.8    48.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 90 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88C  ILE*     4.3     4.2    -      -       +      -
     89C  ARG*     1.3   113.5    +      -       -      +
     91C  PRO*     1.4    64.6    -      -       +      +
     92C  ASP      4.2     0.7    +      -       -      -
     93C  ASP*     2.8    19.0    +      -       -      +
     16D  ASN*     2.6    38.8    +      -       -      +
     17D  SER*     5.5     3.1    -      -       -      -
     84D  ILE*     5.0     2.7    -      -       -      -
     85D  LYS      4.1     2.5    -      -       -      +
     86D  HIS*     3.7    31.4    -      -       +      +
----------------------------------------------------------
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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