Contacts of the strand formed by residues 55 - 62 (chain A) in PDB entry 2KH2


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 LYS 55 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50A  GLU*     3.7    30.9    -      -       +      +
     51A  GLU      3.6     1.0    -      -       -      -
     52A  SER*     2.8    46.3    +      -       -      +
     54A  ASP*     1.3    84.3    -      -       -      +
     56A  ILE*     1.3    62.1    +      -       -      +
    102A  ASN*     2.9    35.5    +      -       +      +
    103A  LYS      3.4     4.0    -      -       -      -
    104A  ILE*     3.6    24.0    -      -       +      +
    113A  GLU*     2.6    29.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 56 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  PHE*     4.7    16.4    -      -       +      -
     50A  GLU      4.5     0.4    -      -       -      -
     51A  GLU*     3.9    19.3    -      -       +      +
     52A  SER      3.2    24.0    -      -       -      +
     53A  ASN      5.4     2.9    -      -       -      +
     54A  ASP      4.9     1.3    -      -       -      +
     55A  LYS*     1.3    76.0    -      -       -      +
     57A  PRO*     1.3    71.6    -      -       +      +
     58A  VAL*     3.4    21.5    +      -       +      +
    102A  ASN*     4.5     1.3    -      -       -      -
    103A  LYS*     2.8    61.8    +      -       -      +
    105A  GLU*     4.9     3.8    -      -       -      +
    231B  LYS*     5.8     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 57 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  PHE*     4.5     2.1    -      -       -      -
     47A  VAL*     3.3    26.1    +      -       +      +
     48A  GLN*     4.6     2.5    -      -       -      +
     49A  GLY*     4.0    20.9    -      -       -      +
     50A  GLU      3.2    30.7    -      -       -      +
     51A  GLU*     3.7    19.3    -      -       +      +
     56A  ILE*     1.3    87.9    -      -       +      +
     58A  VAL*     1.3    65.2    +      -       -      +
    100A  VAL*     4.1    17.9    -      -       +      -
    101A  PHE      3.3     8.5    -      -       -      +
    102A  ASN*     4.3     4.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 58 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  MET*     4.2    30.7    -      -       +      -
     45A  SER      3.3    17.9    -      -       -      +
     46A  PHE*     4.5    10.8    -      -       +      -
     47A  VAL*     3.8     6.7    -      -       -      +
     56A  ILE*     3.9    17.7    -      -       +      -
     57A  PRO*     1.3    79.7    -      -       -      +
     59A  ALA*     1.3    65.2    +      -       -      +
     60A  LEU*     5.1     1.3    -      -       +      -
     99A  PHE      4.7     0.2    -      -       -      -
    100A  VAL      3.8     0.3    -      -       -      -
    101A  PHE*     2.8    40.2    +      -       +      +
    103A  LYS*     3.8    30.1    -      -       +      -
    112A  PHE*     4.6     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 59 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  SER      3.0    15.9    -      -       -      +
     44A  MET*     3.4    11.1    -      -       -      -
     45A  SER*     3.3    17.8    +      -       -      -
     47A  VAL*     3.8    20.8    -      -       +      +
     58A  VAL*     1.3    76.2    -      -       -      +
     60A  LEU*     1.3    66.2    +      -       -      +
     68A  TYR*     4.2    17.3    -      -       +      -
     91A  PRO*     6.2     0.4    -      -       +      -
     95A  MET*     4.3    10.1    -      -       +      -
     99A  PHE      3.6    13.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 60 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  LEU*     4.8     9.6    -      -       +      -
     42A  PHE*     4.3    20.6    -      -       +      -
     43A  SER      3.8     0.4    -      -       -      +
     44A  MET*     3.9    31.2    -      -       +      -
     58A  VAL*     4.2     2.0    +      -       +      +
     59A  ALA*     1.3    82.0    -      -       -      +
     61A  GLY*     1.3    58.4    +      -       -      +
     68A  TYR*     3.6     6.6    -      -       -      -
     69A  LEU*     3.0    51.4    +      -       +      +
     99A  PHE      4.2     5.5    +      -       -      -
    101A  PHE*     3.8    28.8    -      -       +      -
    112A  PHE*     3.9    27.1    -      -       +      -
    122A  ILE*     4.3     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 61 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  PHE*     3.3    10.3    -      -       -      -
     43A  SER*     2.8    36.0    +      -       -      +
     60A  LEU*     1.3    76.0    -      -       -      +
     62A  LEU*     1.3    63.6    +      -       -      -
     67A  LEU      3.4    10.5    -      -       -      -
     68A  TYR*     3.7    23.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 62 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  MET*     3.7    39.9    -      -       +      -
     26A  LEU*     5.3     0.4    -      -       +      -
     40A  VAL*     4.1    17.0    -      -       +      -
     41A  VAL      3.9     2.9    -      -       -      -
     42A  PHE*     3.8    21.1    -      -       +      -
     43A  SER*     4.6     1.4    +      -       -      -
     61A  GLY*     1.3    73.6    -      -       -      -
     63A  LYS*     1.3    67.0    +      -       -      +
     64A  GLU      3.3     0.5    +      -       -      -
     65A  LYS*     3.0    47.4    +      -       +      +
     67A  LEU*     2.9    35.7    +      -       +      +
     68A  TYR*     5.4     0.7    -      -       -      -
     69A  LEU*     5.6     0.4    -      -       +      -
     82A  LEU*     3.9    21.3    -      -       +      -
----------------------------------------------------------
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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