Contacts of the strand formed by residues 4 - 11 (chain A) in PDB entry 4KHS


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 PHE 4 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  MET*     4.4     7.4    -      -       -      -
      2A  LYS      3.9    12.6    -      -       -      -
      3A  GLU*     1.3    75.9    -      -       -      +
      5A  TYR*     1.3    72.3    +      -       -      +
      6A  LEU*     4.1     1.8    -      -       +      -
     19A  TYR*     3.5     0.9    -      -       -      +
     20A  ILE*     2.9    67.9    +      -       +      -
     97A  TYR*     3.7    11.4    -      -       -      -
    101A  ILE*     3.8    24.2    -      -       +      -
    102A  LYS      4.0     1.8    -      -       -      +
    103A  TYR*     3.7    20.6    -      -       +      -
    104A  ASP*     3.6    37.5    -      -       +      -
    107A  LYS*     4.2     3.1    -      -       +      -
    108A  ILE*     3.9    20.9    -      -       +      -
    349A  TYR*     3.6     9.2    -      +       +      -
----------------------------------------------------------
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Residues in contact with TYR 5 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  PHE*     1.3    80.6    -      -       -      +
      6A  LEU*     1.3    68.6    +      -       -      +
      7A  THR*     4.4     6.1    -      -       -      +
      8A  VAL*     5.2     1.1    -      -       +      -
     17A  GLU*     3.2    24.0    -      -       +      +
     18A  ARG      3.8     3.4    -      -       -      +
     19A  TYR*     3.8     0.2    -      -       -      -
     93A  LEU*     3.6    34.1    -      -       +      -
     97A  TYR*     3.4    22.1    +      +       +      -
    101A  ILE*     3.4    26.0    -      -       +      -
    348A  GLY      3.2    17.5    +      -       -      -
    349A  TYR*     2.7    52.9    +      +       -      -
    352A  LYS*     3.5     5.9    -      -       +      -
    353A  ILE      2.7    33.5    +      -       -      -
    354A  GLN*     5.0     3.6    -      -       -      -
    355A  ILE*     4.5     5.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 6 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  PHE*     4.1     1.6    -      -       +      -
      5A  TYR*     1.3    88.2    -      -       -      +
      7A  THR*     1.3    66.8    +      -       +      +
     18A  ARG*     2.7    18.6    +      -       +      +
     19A  TYR*     3.9    21.5    -      -       -      +
     20A  ILE*     3.9    22.4    -      -       +      -
     26A  GLU*     3.7    38.8    -      -       +      +
    107A  LYS      5.3     0.7    -      -       -      +
    108A  ILE*     4.0    28.0    -      -       +      -
    211A  VAL*     3.8    33.1    -      -       +      +
    269A  SER*     4.7     1.6    +      -       -      -
    349A  TYR*     4.1     4.8    +      -       -      +
    355A  ILE*     4.4    16.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 7 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  TYR*     4.8     4.9    -      -       -      -
      6A  LEU*     1.3    85.8    +      -       +      +
      8A  VAL*     1.3    64.2    +      -       -      +
      9A  GLU*     5.5     1.1    -      -       -      -
     17A  GLU*     3.4     5.2    -      -       -      +
     18A  ARG*     3.0    54.9    +      -       -      +
    211A  VAL*     3.9    23.1    -      -       +      +
    245A  HIS*     4.8     1.2    +      -       -      -
    267A  GLY*     3.3    32.6    +      -       -      +
    268A  ILE*     4.3     0.4    -      -       -      -
    269A  SER*     4.0    16.8    -      -       -      +
    354A  GLN*     6.4     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 8 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  TYR*     5.2     1.3    -      -       +      -
      7A  THR*     1.3    75.7    -      -       -      +
      9A  GLU*     1.3    67.5    +      -       -      +
     15A  ILE*     3.6    28.0    -      -       +      -
     16A  PHE      3.4     5.8    -      -       -      +
     17A  GLU*     4.5     2.9    -      -       +      -
     89A  LYS*     4.1    22.2    -      -       +      +
     90A  LEU*     6.4     0.2    -      -       +      -
     92A  TYR*     3.9    18.2    -      -       +      -
     93A  LEU*     4.0    30.3    -      -       +      -
    354A  GLN*     2.8    48.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 9 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  THR*     5.5     1.0    -      -       -      -
      8A  VAL*     1.3    84.7    +      -       -      +
     10A  GLN*     1.3    61.4    +      -       -      +
     11A  ILE*     4.1     2.2    -      -       +      -
     15A  ILE*     3.4    11.4    -      -       -      +
     16A  PHE*     2.9    39.6    +      -       +      +
     89A  LYS*     4.3     9.1    -      -       -      -
    245A  HIS*     4.3     4.5    -      -       +      -
    264A  THR*     5.6     2.8    -      -       -      +
    265A  LEU      4.2     1.7    -      -       -      +
    266A  PHE*     3.4    37.2    -      -       +      -
    267A  GLY*     2.8    39.3    +      -       -      +
    268A  ILE      4.2     7.4    +      -       -      +
    354A  GLN*     3.4    13.7    -      -       -      +
    356A  GLN*     4.7     5.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 10 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  GLU*     1.3    74.1    +      -       -      +
     11A  ILE*     1.3    68.8    +      -       -      +
     12A  GLY      3.4    18.2    +      -       -      +
     14A  SER      3.5     3.1    -      -       -      -
     15A  ILE*     3.9     8.7    -      -       +      -
     65A  MET*     3.7    40.2    -      -       +      +
     87A  ASP*     5.5     0.2    -      -       -      +
     88A  PHE*     3.9    24.5    +      -       -      +
     89A  LYS*     4.3    20.4    +      -       +      +
    247A  LYS*     5.7     0.2    -      -       -      -
    266A  PHE*     3.9    12.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 11 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  GLU*     4.1     2.9    -      -       +      -
     10A  GLN*     1.3    79.7    -      -       -      +
     12A  GLY*     1.3    64.6    +      -       -      +
     13A  ASP      3.4     0.2    +      -       -      -
     14A  SER*     2.9    26.6    +      -       -      +
     16A  PHE*     3.9    31.8    -      -       +      -
    245A  HIS*     4.1    19.1    -      -       +      +
    247A  LYS*     3.6    48.9    -      -       +      +
    266A  PHE*     3.9    15.3    -      -       +      -
----------------------------------------------------------
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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