Contacts of the strand formed by residues 81 - 89 (chain A) in PDB entry 1H8F


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 LEU 81 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  ASP*     6.4     0.7    -      -       +      -
     72A  GLN*     3.1    29.8    -      -       -      +
     73A  ALA      3.6     9.9    -      -       -      +
     74A  LYS*     4.0    21.5    -      -       +      -
     79A  GLY      4.7     2.5    -      -       -      +
     80A  GLU*     1.3    76.9    -      -       -      +
     82A  VAL*     1.3    66.2    +      -       -      +
    133A  ASP*     4.4     4.5    -      -       -      +
    134A  TYR*     3.5    36.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 82 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  TYR*     5.6     1.1    -      -       +      -
     72A  GLN*     3.3     8.1    -      -       -      +
     73A  ALA*     3.0    50.6    +      -       +      +
     75A  LEU*     4.1    30.1    -      -       +      -
     80A  GLU      4.6     0.4    -      -       -      +
     81A  LEU*     1.3    80.6    -      -       -      +
     83A  ALA*     1.3    61.3    +      -       -      +
     84A  ILE*     4.7     6.7    -      -       +      -
    113A  ARG*     3.5    35.0    -      -       -      +
    131A  VAL*     3.8    19.3    -      -       +      -
    132A  LEU      3.3    10.3    -      -       -      +
    133A  ASP*     4.8     0.2    -      -       -      +
    134A  TYR*     3.7     8.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 83 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  ILE*     4.5     2.2    -      -       +      -
     70A  VAL*     4.3    12.8    -      -       +      -
     71A  TYR      3.3    11.7    -      -       -      +
     82A  VAL*     1.3    76.0    -      -       -      +
     84A  ILE*     1.3    62.4    +      -       -      +
    130A  LEU      3.2     2.3    -      -       -      +
    131A  VAL*     3.5     1.8    -      -       -      -
    132A  LEU*     2.8    47.4    +      -       +      +
    133A  ASP      4.4     7.6    -      -       -      +
    134A  TYR*     4.1    17.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 84 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  TYR*     3.5    45.8    -      -       +      +
     59A  THR*     5.4     1.6    -      -       +      +
     70A  VAL*     3.2     5.4    -      -       -      -
     71A  TYR*     2.8    54.2    +      -       +      -
     73A  ALA*     4.4    12.3    -      -       +      -
     82A  VAL*     4.7     9.4    -      -       +      -
     83A  ALA*     1.3    76.8    -      -       -      +
     85A  LYS*     1.3    60.8    +      -       -      +
     86A  LYS*     4.4     6.7    -      -       +      -
    116A  PHE*     4.7     2.5    -      -       +      -
    129A  ASN*     3.9    36.3    -      -       +      +
    130A  LEU      3.4     5.4    -      -       -      +
    131A  VAL*     4.3    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 85 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  GLY      5.8     1.3    -      -       -      +
     69A  VAL      3.8     3.1    -      -       -      +
     70A  VAL*     4.0    25.1    -      -       +      -
     83A  ALA      4.0     0.4    +      -       -      -
     84A  ILE*     1.3    72.1    -      -       -      +
     86A  LYS*     1.3    62.3    +      -       -      +
     87A  VAL*     3.8    17.7    +      -       +      +
     97A  GLU*     2.6    38.1    +      -       -      -
    128A  LEU      3.2     5.7    -      -       -      +
    129A  ASN*     4.4     0.2    -      -       -      -
    130A  LEU*     3.0    50.0    +      -       +      +
    132A  LEU*     4.5    16.9    -      -       +      +
    199A  CYS*     6.1     0.8    -      -       -      -
    200A  ASP*     4.3    26.3    +      -       -      +
    202A  GLY*     4.8     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 86 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  GLY*     3.2    26.5    -      -       -      -
     69A  VAL*     3.0    15.2    +      -       +      +
     71A  TYR*     3.3    41.5    +      -       +      +
     84A  ILE*     4.4     2.7    -      -       +      -
     85A  LYS*     1.3    73.2    -      -       -      +
     87A  VAL*     1.3    62.5    +      -       -      +
    118A  SER*     3.9     9.5    +      -       -      -
    119A  SER      5.4     2.2    +      -       -      -
    120A  GLY*     5.5     0.6    -      -       -      -
    127A  TYR*     3.4    41.7    -      -       +      -
    128A  LEU      3.5     4.5    -      -       -      +
    129A  ASN*     3.3    28.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 87 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67A  PHE*     3.7    30.7    -      -       +      +
     68A  GLY      4.8     0.2    -      -       -      +
     85A  LYS*     4.1    25.4    -      -       +      +
     86A  LYS*     1.3    81.4    -      -       -      +
     88A  LEU*     1.3    64.7    +      -       -      +
     89A  GLN      3.3     0.2    +      -       -      -
     95A  ASN*     4.0    17.5    -      -       -      +
     97A  GLU*     5.1     8.1    -      -       -      +
    127A  TYR*     3.5     6.6    -      -       -      -
    128A  LEU*     2.8    55.4    +      -       +      +
    130A  LEU*     5.4     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 88 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67A  PHE*     4.0    12.2    +      -       +      +
     87A  VAL*     1.3    75.0    -      -       -      +
     89A  GLN*     1.3    66.5    +      -       -      +
     90A  GLY*     4.0     2.9    +      -       -      +
     95A  ASN*     5.2     1.0    +      -       -      -
    125A  GLU*     3.5    38.4    -      -       +      +
    126A  VAL      4.8     0.2    -      -       -      +
    127A  TYR*     3.3    32.8    -      -       +      +
    294B  PRO*     4.6    21.6    -      -       +      +
    295B  GLN      5.8     2.9    -      -       -      +
    296B  ILE*     4.6    23.6    -      -       +      -
----------------------------------------------------------
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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
----------------------------------------------------------
     87A  VAL      3.3     0.8    +      -       -      -
     88A  LEU*     1.3    76.5    -      -       -      +
     90A  GLY*     1.3    65.1    +      -       -      +
     91A  LYS*     3.3    26.3    +      -       +      +
     93A  PHE*     3.2    31.1    +      -       -      +
     94A  LYS      4.6     0.2    -      -       -      -
     95A  ASN*     2.8    43.7    +      -       -      +
    117A  TYR*     4.2    21.1    -      -       +      +
    125A  GLU*     5.4     1.8    -      -       -      +
    126A  VAL*     2.8    40.6    +      -       +      +
    128A  LEU*     4.1    17.6    -      -       +      +
----------------------------------------------------------
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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