Contacts of the strand formed by residues 66 - 70 (chain y) in PDB entry 5GJQ


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 66 (chain y).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    269x  GLU*     4.6    16.3    +      -       -      +
    312x  LYS*     4.6    16.5    +      -       -      +
      4y  PHE*     3.1    23.0    -      -       +      +
      6y  LYS*     4.5    11.7    -      -       +      +
     12y  THR*     4.8     6.1    -      -       -      +
     45y  PHE*     3.3    21.1    -      -       -      -
     64y  GLU      3.8     7.1    +      -       -      -
     65y  SER*     1.3    78.6    +      -       -      +
     67y  LEU*     1.3    74.3    +      -       -      +
     68y  HIS*     3.8    28.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 67 (chain y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3y  ILE*     3.9    23.3    -      -       +      -
      4y  PHE      2.6    16.7    +      -       -      +
      5y  VAL*     3.3    13.4    -      -       +      -
      6y  LYS      2.8    25.6    +      -       -      -
     26y  VAL*     4.5     7.2    -      -       +      -
     43y  LEU*     4.4    24.5    -      -       +      -
     44y  ILE      3.4     6.7    -      -       -      +
     45y  PHE*     3.6    35.2    -      -       +      -
     50y  LEU*     4.3    15.0    -      -       +      -
     56y  LEU*     4.9     3.1    -      -       +      -
     61y  ILE*     3.8    24.0    -      -       +      -
     65y  SER*     4.9     0.9    -      -       -      +
     66y  THR*     1.3    78.4    -      -       -      +
     68y  HIS*     1.3    63.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 68 (chain y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    269x  GLU*     5.7     4.1    +      -       -      -
    271x  GLN*     4.3    21.0    +      -       +      +
    275x  SER*     5.5     2.5    -      -       -      +
    277x  PHE*     6.0     1.1    -      -       +      -
    292x  ARG*     2.5    37.4    +      -       -      +
      6y  LYS*     3.9    13.3    -      -       +      +
     42y  ARG      3.6     1.4    -      -       -      +
     43y  LEU*     3.4     5.1    -      -       -      -
     44y  ILE*     2.7    64.3    +      -       +      +
     45y  PHE*     5.0     2.9    -      -       -      -
     46y  ALA      5.4     3.5    +      -       -      -
     66y  THR*     3.8    31.0    +      -       +      -
     67y  LEU*     1.3    74.6    +      -       -      +
     69y  LEU*     1.3    61.8    +      -       -      +
     70y  VAL*     3.8     6.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 69 (chain y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    277x  PHE*     5.9     0.7    -      -       -      -
    328x  VAL*     5.3     1.9    -      -       -      +
      5y  VAL*     3.9     9.0    -      -       +      -
      6y  LYS      3.1    21.5    +      -       -      +
      7y  THR*     4.2    18.5    -      -       +      +
      8y  LEU*     3.0    29.0    -      -       +      +
     30y  ILE*     4.2    16.2    -      -       +      -
     34y  GLU*     5.3     0.2    -      -       +      -
     36y  ILE*     3.9    28.0    -      -       +      -
     41y  GLN*     3.7    34.3    -      -       +      +
     42y  ARG      3.9     2.5    -      -       -      +
     43y  LEU*     3.6    24.7    -      -       +      -
     67y  LEU      4.0     1.0    +      -       -      -
     68y  HIS*     1.3    69.6    -      -       -      +
     70y  VAL*     1.3    71.7    +      -       -      +
     71y  LEU*     4.6     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 70 (chain y). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200x  ASN*     5.6     0.4    -      -       -      +
    326x  GLN*     3.3    28.5    -      -       -      +
    328x  VAL*     5.2     4.0    -      -       +      -
    330x  PHE*     3.2    23.6    -      -       +      -
    475x  TYR*     4.4     1.1    -      -       -      +
      8y  LEU*     3.7     4.5    -      -       -      -
     41y  GLN*     4.1     0.2    -      -       -      -
     42y  ARG*     2.8    74.0    +      -       -      +
     44y  ILE*     4.6    11.9    -      -       +      -
     68y  HIS*     4.4    13.7    -      -       +      +
     69y  LEU*     1.3    80.0    -      -       -      +
     71y  LEU*     1.3    68.6    +      -       -      +
----------------------------------------------------------
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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