Contacts of the strand formed by residues 97 - 105 (chain A) in PDB entry 7KHC


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 GLU 97 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  LYS*     4.3    12.7    -      -       -      +
     96A  ASP*     1.3    81.8    -      -       +      +
     98A  VAL*     1.3    59.3    +      -       -      +
     99A  ILE*     3.2    28.2    -      -       -      +
    145A  LYS*     2.9    42.8    -      -       +      +
    146A  VAL      3.2     2.9    -      -       -      +
    147A  GLN*     3.8    16.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 98 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  VAL*     3.6    31.0    -      -       +      -
     95A  LYS*     4.4    23.1    -      -       +      +
     96A  ASP      5.7     0.4    -      -       -      +
     97A  GLU*     1.3    75.6    -      -       -      +
     99A  ILE*     1.3    69.8    +      -       -      +
    100A  LEU*     3.5    26.4    +      -       +      +
    118A  ASP*     5.1    15.9    -      -       +      +
    120A  ASP*     6.4     0.7    -      -       +      -
    121A  VAL*     5.5     4.0    -      -       +      -
    144A  ILE      3.6     1.9    -      -       -      +
    145A  LYS*     3.6     1.7    -      -       -      -
    146A  VAL*     2.9    39.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 99 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97A  GLU*     3.2    37.2    -      -       -      +
     98A  VAL*     1.3    79.4    -      -       -      +
    100A  LEU*     1.3    63.2    +      -       -      +
    101A  THR*     4.1     6.6    +      -       -      +
    143A  ARG*     4.2    26.0    -      -       +      -
    144A  ILE      3.3    10.8    -      -       -      +
    145A  LYS*     4.4     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 100 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  LEU*     5.8     4.5    -      -       +      -
     90A  VAL*     5.0     3.4    -      -       +      -
     98A  VAL*     3.5    41.1    -      -       +      +
     99A  ILE*     1.3    73.1    -      -       -      +
    101A  THR*     1.3    61.2    +      -       -      +
    115A  ILE*     3.7    33.9    -      -       +      -
    116A  THR      4.9     5.4    -      -       -      +
    118A  ASP*     5.8     2.7    -      -       +      -
    121A  VAL*     3.9    32.8    -      -       +      -
    123A  ILE*     4.8     6.3    -      -       +      -
    143A  ARG*     3.2     5.7    -      -       -      +
    144A  ILE*     2.9    46.0    +      -       +      +
    146A  VAL*     4.1    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 101 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  ILE*     4.1     6.8    +      -       -      +
    100A  LEU*     1.3    76.8    +      -       -      +
    102A  LEU*     1.3    58.7    +      -       -      +
    103A  ASN*     3.8    25.1    -      -       -      +
    115A  ILE*     4.6     1.8    -      -       -      +
    116A  THR*     2.6    54.3    +      -       -      +
    141A  SER*     5.2     0.9    -      -       -      +
    142A  MET      3.5    10.3    -      -       -      +
    143A  ARG*     4.4    14.4    -      -       +      +
    144A  ILE*     5.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 102 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85A  LEU*     5.8     2.7    -      -       +      -
    100A  LEU      4.2     0.6    +      -       -      -
    101A  THR*     1.3    72.5    -      -       -      +
    103A  ASN*     1.3    77.4    +      -       -      +
    104A  LYS*     4.3     2.0    -      -       +      +
    110A  VAL*     4.2    21.8    -      -       +      -
    111A  THR      4.9     2.7    -      -       -      +
    114A  ASP*     3.2    46.4    -      -       +      +
    115A  ILE*     3.3    21.5    -      -       +      +
    130A  ILE*     5.0    12.8    -      -       +      -
    140A  ILE*     4.4     1.3    -      -       +      -
    141A  SER*     3.3     2.6    -      -       -      -
    142A  MET*     2.9    59.8    +      -       +      +
    144A  ILE*     4.4     9.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 103 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  THR*     3.8    21.6    +      -       -      +
    102A  LEU*     1.3    90.6    -      -       -      +
    104A  LYS*     1.3    61.4    +      -       -      +
    114A  ASP*     4.9     6.2    +      -       -      +
    116A  THR*     4.9     4.1    +      -       -      +
    139A  SER*     5.5     0.7    -      -       -      -
    140A  ILE      3.3     5.4    -      -       -      +
    141A  SER*     2.4    32.9    +      -       -      -
    142A  MET      3.6     0.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 104 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  LEU*     4.3     2.8    -      -       +      +
    103A  ASN*     1.3    74.7    -      -       -      +
    105A  SER*     1.3    75.9    +      -       -      +
    106A  GLY      4.2     4.4    +      -       -      -
    107A  ILE      5.1     1.0    +      -       -      -
    108A  GLY*     4.2    13.9    +      -       -      -
    109A  PRO      4.6     2.1    +      -       -      -
    110A  VAL*     3.5    39.8    -      -       +      +
    114A  ASP*     2.9    40.8    -      -       +      +
    133A  LEU*     3.9    12.9    -      -       -      +
    138A  ALA      4.3     0.3    -      -       -      +
    139A  SER*     3.4     4.3    +      -       -      -
    140A  ILE*     2.9    43.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 105 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104A  LYS*     1.3    88.6    +      -       -      +
    106A  GLY*     1.3    69.1    +      -       -      +
    133A  LEU*     4.8     0.7    -      -       -      -
    136A  GLU      5.6     0.4    -      -       -      -
    137A  ASN*     4.9     3.8    -      -       -      -
    138A  ALA      3.3     7.4    -      -       -      -
    139A  SER*     3.2    24.5    -      -       -      -
----------------------------------------------------------
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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