Contacts of the strand formed by residues 109 - 114 (chain F) in PDB entry 6GJH


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 LEU 109 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101F  VAL*     3.8    29.2    -      -       +      -
    104F  PHE*     3.9    19.7    -      -       +      -
    105F  ALA      3.8    13.7    -      -       -      +
    106F  PRO*     3.4    14.8    +      -       +      +
    107F  ASP      3.4     3.0    -      -       -      +
    108F  GLU*     1.3    81.4    -      -       -      +
    110F  THR*     1.3    66.7    +      -       -      +
    111F  VAL*     5.6     1.8    -      -       +      -
    120F  ILE*     4.9     5.6    -      -       +      -
    121F  THR      3.4    12.1    -      -       -      +
    122F  GLY*     4.0    10.1    -      -       -      -
    138F  PHE*     4.1    17.3    -      -       +      -
    157F  LEU*     4.2    19.3    -      -       +      -
    163F  LEU*     4.8    17.5    -      -       +      -
    130H  GLU      4.5     4.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 110 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109F  LEU*     1.3    77.6    +      -       -      +
    111F  VAL*     1.3    67.4    +      -       -      +
    112F  LYS*     4.0    27.6    -      -       +      +
    119F  GLU      3.6     0.9    -      -       -      +
    120F  ILE*     3.3     6.1    -      -       -      +
    121F  THR*     2.9    48.2    +      -       +      +
    129H  ASP      4.8     0.2    -      -       -      +
    130H  GLU*     3.5    38.9    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 111 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109F  LEU*     5.6     2.2    -      -       +      -
    110F  THR*     1.3    82.4    -      -       -      +
    112F  LYS*     1.3    67.6    +      -       -      +
    113F  THR*     5.0     0.2    -      -       -      +
    118F  VAL*     4.0    24.9    -      -       +      -
    119F  GLU      3.4     3.1    -      -       -      +
    120F  ILE*     4.1    15.7    -      -       +      -
    153F  VAL*     4.8     8.1    -      -       +      -
    155F  SER*     3.8    35.2    -      -       -      +
    163F  LEU*     4.1    17.7    -      -       +      -
    165F  VAL*     4.5     9.4    -      -       +      -
    128H  GLN*     4.3     4.7    -      -       -      +
    129H  ASP      5.5     1.2    -      -       -      +
    130H  GLU      5.3     0.2    +      -       -      -
    131H  HIS      6.1     0.5    -      -       -      -
    132H  GLY*     5.8     4.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 112 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110F  THR*     4.0    18.6    -      -       +      -
    111F  VAL*     1.3    78.5    -      -       -      +
    113F  THR*     1.3    62.6    +      -       -      +
    114F  LYS*     5.7     2.5    -      -       +      -
    117F  VAL      3.9     0.2    -      -       -      +
    118F  VAL*     3.5     4.2    -      -       -      +
    119F  GLU*     2.8    51.0    +      -       +      +
    128H  GLN*     3.8    32.6    +      -       +      +
    129H  ASP*     3.6    32.4    -      -       -      +
    130H  GLU*     4.3     2.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 113 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111F  VAL*     5.0     1.0    -      -       -      +
    112F  LYS*     1.3    77.8    +      -       -      +
    114F  LYS*     1.3    66.6    +      -       -      +
    116F  GLY*     5.2     2.7    -      -       -      +
    117F  VAL      3.4     9.9    -      -       -      +
    118F  VAL*     4.0     9.8    -      -       +      +
    144F  LEU*     3.7    29.6    -      -       +      -
    150F  PRO*     3.8    38.0    -      -       +      +
    153F  VAL*     3.8    22.5    -      -       +      +
    128H  GLN*     3.0    29.9    +      -       -      -
    133H  TYR*     4.5     0.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 114 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112F  LYS*     5.7     2.7    -      -       +      -
    113F  THR*     1.3    77.1    -      -       -      +
    115F  ASP*     1.3    85.2    +      -       -      +
    116F  GLY      3.3     1.6    -      -       -      -
    117F  VAL*     3.0    24.8    +      -       -      +
    150F  PRO*     5.8     1.1    -      -       -      -
    128H  GLN*     5.6     2.2    -      -       -      +
     76L  ALA*     5.2    13.7    -      -       -      +
----------------------------------------------------------
 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