Contacts of the strand formed by residues 85 - 90 (chain A) in PDB entry 1S5H


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 ASN 85 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  TYR      3.9     0.5    -      -       -      +
     37A  GLN*     3.6     2.9    -      -       -      -
     38A  GLN*     2.8    43.0    +      -       +      +
     84A  ALA*     1.3    74.2    +      -       -      +
     86A  TYR*     1.3    62.5    +      -       -      +
     87A  TYR*     3.9    29.1    +      -       +      -
    101A  GLY      5.9     1.1    -      -       -      -
    102A  THR      3.5     3.8    -      -       -      +
    103A  LYS*     3.1    34.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 86 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  GLN*     2.6    26.8    +      -       -      -
     21A  PHE*     3.6    36.3    -      +       +      -
     35A  TRP*     4.8     3.1    -      -       +      -
     36A  TYR      3.4     6.7    -      -       -      +
     37A  GLN*     3.1    24.9    +      -       +      -
     47A  LEU*     3.5    26.7    -      -       +      -
     62A  PHE*     3.9    10.4    -      +       -      -
     73A  LEU*     3.5    25.6    -      -       +      -
     75A  ILE*     3.7    10.1    -      -       +      +
     82A  ASP*     2.6    39.1    +      -       -      +
     84A  ALA*     3.6    17.7    -      -       +      -
     85A  ASN*     1.3    76.9    -      -       -      +
     87A  TYR*     1.3    57.5    +      -       -      +
    101A  GLY*     3.3     0.9    -      -       -      -
    102A  THR      2.8    24.5    +      -       -      +
    104A  LEU*     4.0     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 87 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  GLN*     3.5     2.0    -      -       -      -
     34A  HIS      3.8     0.2    -      -       -      +
     35A  TRP*     3.3     8.7    -      -       -      -
     36A  TYR*     2.8    47.2    +      -       +      +
     38A  GLN*     3.6    24.5    +      -       +      -
     44A  PRO*     6.0     0.2    -      -       +      -
     85A  ASN*     3.9    33.7    +      -       +      -
     86A  TYR*     1.3    76.5    -      -       -      +
     88A  CYS*     1.3    65.5    +      -       -      +
     98A  PHE*     4.7     4.3    -      -       +      -
     99A  GLY      3.4    19.3    -      -       -      -
    100A  SER      3.8    18.9    +      -       -      -
    101A  GLY*     3.7     8.3    -      -       -      -
     39B  GLN*     3.5    10.9    +      -       -      -
     43B  HIS      3.7     2.9    +      -       -      -
     44B  GLY*     3.5    28.8    -      -       -      -
     45B  LEU*     3.9    33.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 88 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  LEU*     4.0    11.0    -      -       -      -
      6A  GLN*     3.3    23.2    +      -       -      -
     23A  CYS*     2.6    49.1    -      -       +      -
     33A  ILE*     4.1     7.2    -      -       +      -
     34A  HIS      3.2     8.3    -      -       -      +
     35A  TRP*     4.1    12.3    -      -       +      -
     87A  TYR*     1.3    76.1    -      -       -      +
     89A  GLN*     1.3    64.3    +      -       -      +
     98A  PHE*     3.4     5.2    -      -       -      -
     99A  GLY*     2.9    26.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 89 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  LEU*     3.8     1.1    -      -       -      -
     32A  ASP      3.8     0.3    -      -       -      +
     33A  ILE*     3.4     7.6    -      -       -      -
     34A  HIS*     2.9    39.5    +      -       -      +
     36A  TYR*     2.7    39.2    +      -       +      -
     88A  CYS*     1.3    78.3    -      -       -      +
     90A  GLN*     1.3    85.3    +      -       -      +
     91A  SER*     3.9     1.8    -      -       -      -
     96A  PHE*     4.0    12.0    -      -       +      +
     97A  THR      3.2    16.6    -      -       -      +
     98A  PHE*     3.6    26.9    -      -       +      -
    103B  GLY      3.0    22.9    +      -       -      +
    105B  PHE*     3.9    10.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 90 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  ILE*     3.4    32.9    -      -       +      +
      4A  LEU*     3.5    10.0    -      -       +      +
     29A  ILE*     4.1     9.9    -      -       +      -
     32A  ASP      3.4    10.1    -      -       -      +
     33A  ILE*     4.0     7.6    -      -       +      -
     89A  GLN*     1.3    85.0    +      -       -      +
     91A  SER*     1.3    60.3    +      -       -      +
     92A  ASN*     2.8    28.1    +      -       -      +
     93A  ARG      3.0    17.6    +      -       -      -
     95A  PRO      2.8    29.5    +      -       -      -
     96A  PHE*     3.3    14.7    -      -       -      -
     97A  THR*     2.9    33.7    +      -       -      +
----------------------------------------------------------
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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