Contacts of the strand formed by residues 68 - 74 (chain A) in PDB entry 2KUL


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 CYS 68 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  TRP*     3.6    12.3    -      -       -      -
     53A  LEU*     4.1     2.6    -      -       -      +
     54A  ALA*     3.1    36.7    +      -       -      +
     64A  SER      4.7     1.1    -      -       -      +
     65A  ASP*     2.9    29.6    -      -       -      -
     66A  ALA      2.7    11.4    +      -       -      +
     67A  PRO*     1.3    75.2    -      -       -      +
     69A  VAL*     1.3    67.9    +      -       -      +
    114A  TRP*     3.8    13.7    -      -       +      +
    130A  ILE*     3.6    24.7    -      -       +      -
    131A  MET      3.3    13.9    -      -       -      +
    133A  ARG*     4.1     3.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 69 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  ILE*     3.9    25.4    -      -       +      -
     51A  ILE*     4.1    13.5    -      -       +      -
     52A  TYR      3.4    11.0    -      -       -      +
     53A  LEU*     4.2     8.5    -      -       +      +
     54A  ALA      4.5     0.9    -      -       -      +
     68A  CYS*     1.3    79.7    -      -       -      +
     70A  VAL*     1.3    60.6    +      -       -      +
    130A  ILE*     3.3     7.5    -      -       -      +
    131A  MET*     2.7    44.2    +      -       +      +
    132A  ASP      3.2    21.5    -      -       -      +
    133A  ARG*     3.8    17.5    -      -       +      +
    134A  PHE*     4.3    14.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 70 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  ILE*     5.2     8.7    -      -       +      -
     37A  TRP*     6.5     0.2    -      -       +      -
     39A  VAL*     5.3     6.1    -      -       +      -
     51A  ILE*     3.2     6.6    -      -       -      +
     52A  TYR*     2.9    59.1    +      -       +      +
     53A  LEU      5.3     2.9    -      -       -      -
     54A  ALA*     5.5     2.9    -      -       +      +
     69A  VAL*     1.3    76.4    -      -       -      +
     71A  LYS*     1.3    65.4    +      -       -      +
     72A  VAL*     3.9     4.4    +      -       +      +
    128A  PHE*     3.4    33.4    -      -       +      -
    129A  MET      3.1    15.0    -      -       -      +
    130A  ILE*     3.5    21.3    -      -       +      -
    131A  MET*     6.0     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 71 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  GLY      4.9     1.6    -      -       -      +
     48A  PHE*     3.6    32.7    -      -       +      -
     51A  ILE*     3.4    27.3    -      -       +      +
     70A  VAL*     1.3    73.8    -      -       -      +
     72A  VAL*     1.3    64.5    +      -       -      +
     73A  GLU*     2.8    34.0    +      -       -      -
     79A  PRO*     5.3     1.4    -      -       -      +
     80A  LEU*     3.7    14.1    -      -       -      +
     83A  GLU*     2.6    29.4    +      -       -      +
    127A  ARG      3.8     0.5    -      -       -      +
    128A  PHE*     3.3     6.9    -      -       -      -
    129A  MET*     2.9    58.2    +      -       +      +
    131A  MET*     4.9    15.0    -      -       +      +
    196A  VAL*     6.1     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 72 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  PHE*     3.5    24.3    -      -       -      -
     49A  GLY      4.8     0.9    -      -       -      +
     50A  CYS*     3.9    17.3    +      -       +      +
     51A  ILE*     4.6     0.2    -      -       -      +
     52A  TYR*     3.5    38.1    -      -       +      -
     70A  VAL*     4.4     6.5    -      -       +      +
     71A  LYS*     1.3    79.6    -      -       -      +
     73A  GLU*     1.3    62.6    +      -       -      +
     74A  PRO*     4.5     1.5    -      -       +      +
    126A  TYR*     3.9    35.9    -      -       +      -
    127A  ARG      3.9     2.9    -      -       -      +
    128A  PHE*     4.8     5.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 73 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  PHE*     3.3    27.9    -      -       -      -
     71A  LYS*     2.8    29.3    +      -       -      -
     72A  VAL*     1.3    76.3    -      -       -      +
     74A  PRO*     1.3    88.5    -      -       +      +
     78A  GLY      4.8     2.6    +      -       -      +
     79A  PRO*     3.8    24.9    -      -       +      +
     80A  LEU*     3.3    41.2    -      -       +      +
    126A  TYR*     3.6     6.2    -      -       -      -
    127A  ARG*     2.7    39.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 74 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  PHE*     5.1     3.6    -      -       +      -
     72A  VAL      4.5     2.2    -      -       -      +
     73A  GLU*     1.3   108.4    -      -       -      +
     75A  SER*     1.3    57.6    +      -       -      +
     76A  ASP*     3.0    20.2    +      -       +      +
     77A  ASN*     3.1    18.9    +      -       -      +
     80A  LEU*     4.7     2.4    -      -       -      +
    124A  LYS*     5.0    12.1    -      -       -      -
    125A  SER      4.1     4.5    -      -       -      +
    126A  TYR*     4.3    14.3    -      -       +      -
----------------------------------------------------------
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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