Contacts of the strand formed by residues 101 - 108 (chain A) in PDB entry 5NKS


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 THR 101 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  GLY      3.5     8.1    -      -       -      +
     71A  ASP*     3.9    12.1    -      -       +      -
     96A  ALA*     2.9    27.5    +      -       +      +
     97A  LEU*     3.1    28.4    +      -       -      +
     99A  GLY      4.6     0.5    +      -       -      -
    100A  GLY*     1.3    79.2    -      -       -      +
    102A  THR*     1.3    59.7    +      -       -      +
    103A  MET      3.3    26.5    -      -       -      +
    104A  ILE*     4.2     0.7    -      -       +      -
    133A  CYS*     4.7     0.5    -      -       -      -
    358A  ILE*     4.4     8.1    +      -       +      -
    361A  ARG*     2.9    30.2    +      -       -      +
    362A  MET*     3.8     7.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 102 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  GLY*     3.2    32.3    +      -       -      -
     69A  GLY      2.9     3.8    +      -       -      +
     70A  VAL*     5.7     0.3    -      -       -      +
     97A  LEU*     3.9    12.6    -      -       +      -
    100A  GLY      4.7     0.7    -      -       -      +
    101A  THR*     1.3    77.7    -      -       -      +
    103A  MET*     1.3    62.9    +      -       -      +
    133A  CYS*     3.4    19.9    -      -       -      +
    134A  ASP*     3.6     7.8    +      -       -      +
    408A  ASP*     3.4    26.9    +      -       +      +
    409A  LEU      4.7     0.9    -      -       -      +
    446A  VAL*     3.9    19.7    -      -       +      -
    447A  ILE      3.6    23.8    -      -       -      +
    448A  SER*     4.4     4.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 103 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  GLY      3.1     2.8    +      -       -      -
     70A  VAL*     3.4    16.7    -      -       +      -
     71A  ASP      2.7    32.0    +      -       -      -
    101A  THR*     3.3     6.7    -      -       -      +
    102A  THR*     1.3    80.5    -      -       -      +
    104A  ILE*     1.3    61.5    +      -       -      +
    105A  LEU*     3.8    17.3    -      -       +      -
    133A  CYS*     4.4     0.4    -      -       -      -
    134A  ASP*     3.3    23.1    -      -       +      +
    135A  TYR      3.9     2.9    -      -       -      +
    136A  SER*     3.9     8.7    -      -       -      -
    394A  PHE*     3.7    41.7    -      -       +      -
    398A  LYS*     3.9    23.1    -      -       +      -
    469A  VAL*     3.7    30.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 104 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  ASP*     3.4     6.1    -      -       +      -
     74A  THR*     3.5    35.4    -      -       +      +
     76A  LEU*     3.5    26.2    -      -       +      -
     89A  PHE*     4.0    13.7    -      -       +      -
     93A  THR*     3.6    19.1    -      -       +      -
     96A  ALA*     4.2    16.2    -      -       +      -
    101A  THR*     4.2    14.1    -      -       +      -
    103A  MET*     1.3    81.6    -      -       -      +
    105A  LEU*     1.3    65.2    +      -       -      +
    106A  ASP      4.8     0.7    -      -       -      +
    133A  CYS*     4.4     6.1    -      -       -      -
    134A  ASP      3.3     3.7    +      -       -      +
    135A  TYR*     3.2    18.9    -      -       +      +
    136A  SER      3.0    23.6    +      -       -      -
    358A  ILE*     4.2     2.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 105 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  VAL*     4.7     3.8    -      -       +      -
     71A  ASP      2.8    13.8    +      -       -      +
     72A  VAL*     3.6    18.8    -      -       +      +
     73A  HIS*     3.6     5.4    -      -       -      -
     74A  THR*     3.0    22.9    +      -       -      -
    103A  MET*     3.8    14.8    -      -       +      -
    104A  ILE*     1.3    75.1    -      -       -      +
    106A  ASP*     1.3    62.1    +      -       -      +
    136A  SER*     3.3    33.4    -      -       -      -
    138A  HIS*     3.3    36.4    -      -       +      +
    392A  PHE*     3.8    29.4    -      -       +      -
    394A  PHE*     4.2    12.6    -      -       +      -
    471A  ARG*     4.8     3.8    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 106 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  THR*     2.7    24.2    +      -       -      +
     75A  ARG*     4.3     0.2    -      -       -      -
     76A  LEU*     2.8    33.6    +      -       -      +
     77A  GLN      4.3     1.4    +      -       -      -
     89A  PHE*     3.6    32.2    -      -       +      -
    104A  ILE*     3.9     1.3    -      -       +      -
    105A  LEU*     1.3    74.4    -      -       -      +
    107A  HIS*     1.3    63.4    +      -       -      +
    108A  VAL      3.6     0.6    +      -       -      -
    123A  TRP*     2.9    30.7    +      -       -      -
    136A  SER      2.9     6.6    +      -       -      +
    137A  LEU*     3.2    14.5    -      -       +      +
    138A  HIS      2.8    31.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 107 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  VAL      4.6     0.2    +      -       -      -
     73A  HIS*     3.3    43.4    +      +       -      +
     74A  THR      3.0    14.2    +      -       -      +
     75A  ARG*     3.4    34.5    +      -       +      +
     78A  MET*     4.8     5.4    +      -       -      +
    105A  LEU      4.4     1.1    -      -       -      -
    106A  ASP*     1.3    73.3    -      -       -      +
    108A  VAL*     1.3    63.0    +      -       -      +
    109A  PHE*     3.5     3.5    +      -       -      +
    123A  TRP*     3.3    21.2    +      -       -      -
    138A  HIS*     3.4    26.3    +      +       -      +
    140A  ASP*     2.6    24.6    +      -       -      +
    165A  LEU*     3.8     9.6    -      -       +      -
    196A  GLN*     3.2    30.9    +      -       -      -
    253A  THR*     4.8     0.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  ASP      3.6     0.2    +      -       -      -
    107A  HIS*     1.3    70.0    -      -       -      +
    109A  PHE*     1.3    62.6    +      -       -      +
    110A  PRO*     3.9     3.0    -      -       +      +
    116A  LEU*     4.7     2.0    -      -       -      +
    119A  ALA*     3.6    38.8    -      -       +      +
    120A  TYR*     3.7     8.3    -      -       +      +
    123A  TRP*     3.6    33.7    -      -       +      -
    137A  LEU*     3.9    20.4    -      -       +      -
    138A  HIS      2.8    20.3    +      -       -      +
    139A  VAL*     4.1    18.6    -      -       +      -
    140A  ASP*     2.8    33.8    +      -       -      +
----------------------------------------------------------
 Back to top of page


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