Contacts of the strand formed by residues 19 - 25 (chain q) 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 CYS 19 (chain q).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16q  GLY*     3.0    27.8    +      -       -      -
     17q  LYS      3.4    19.0    -      -       -      -
     18q  ASN*     1.3    79.2    -      -       -      +
     20q  VAL*     1.3    64.1    +      -       -      +
    112q  LEU*     4.2     4.7    -      -       -      +
    119q  PRO*     3.5     9.6    -      -       -      +
    158q  MET      4.1     2.5    -      -       -      -
    159q  ASP      4.6     0.2    -      -       -      -
    160q  PRO*     4.0    28.3    -      -       +      -
    163q  LEU*     3.7    12.8    -      -       -      -
    189q  ILE*     3.9    10.3    -      -       +      -
    190q  ILE      3.3    14.4    -      -       -      +
    191q  GLU*     4.2    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 20 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14q  MET      3.3    15.7    -      -       -      +
     15q  LYS*     4.2     3.8    -      -       +      -
     19q  CYS*     1.3    78.5    -      -       -      +
     21q  ALA*     1.3    61.6    +      -       -      +
    110q  ALA*     4.1     7.9    -      -       +      -
    111q  GLY*     3.7    21.3    -      -       -      +
    112q  LEU*     4.2     9.4    -      -       +      -
    119q  PRO*     4.2     6.3    -      -       +      -
    120q  PHE      4.0     6.7    -      -       -      +
    121q  ILE*     3.5    26.5    -      -       +      -
    163q  LEU*     3.8     4.3    -      -       -      -
    188q  HIS      4.1     0.2    -      -       -      +
    189q  ILE*     3.3     2.3    -      -       -      +
    190q  ILE*     2.8    56.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 21 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13q  ALA*     3.3     4.2    -      -       -      +
     14q  MET      2.9    32.8    +      -       -      +
     20q  VAL*     1.3    74.8    -      -       -      +
     22q  ILE*     1.3    63.0    +      -       -      +
    110q  ALA*     4.2     3.6    -      -       -      +
    163q  LEU*     3.7    24.7    -      -       +      +
    167q  ILE*     3.6    24.7    -      -       +      -
    187q  VAL*     4.9     1.1    -      -       +      -
    188q  HIS      3.3     9.6    -      -       -      +
    189q  ILE*     4.2     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 22 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11q  VAL*     4.3     1.3    -      -       +      -
     12q  MET      3.2    12.3    -      -       -      +
     13q  ALA*     4.0     5.8    -      -       +      -
     21q  ALA*     1.3    77.9    -      -       -      +
     23q  ALA*     1.3    65.3    +      -       -      +
     42q  ILE*     3.8    21.5    -      -       +      +
     50q  TYR*     4.2    14.6    -      -       +      +
     51q  ILE      4.3     3.1    -      -       -      -
     52q  GLY*     3.8    34.1    -      -       -      +
    108q  VAL*     4.0    16.2    -      -       +      +
    110q  ALA*     3.6    22.0    -      -       +      +
    167q  ILE*     4.1     2.0    -      -       -      -
    187q  VAL*     3.6     0.3    -      -       -      -
    188q  HIS*     2.9    48.6    +      -       +      +
    190q  ILE*     6.4     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 23 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11q  VAL*     3.3     1.9    -      -       -      +
     12q  MET*     2.9    32.2    +      -       -      +
     22q  ILE*     1.3    76.0    -      -       -      +
     24q  ALA*     1.3    65.4    +      -       -      +
     42q  ILE*     3.6     5.6    -      -       -      +
    167q  ILE*     3.9    13.4    -      -       +      +
    171q  MET*     3.6    29.8    -      -       +      +
    185q  VAL*     4.5     1.1    -      -       +      -
    186q  ILE      3.2    13.7    -      -       -      +
    187q  VAL*     4.1    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 24 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10q  ALA      3.1    14.6    -      -       -      +
     11q  VAL*     3.9    11.9    -      -       +      -
     23q  ALA*     1.3    77.7    -      -       -      +
     25q  ASP*     1.3    71.8    +      -       -      +
     41q  LYS*     4.4     7.6    -      -       +      -
     42q  ILE*     3.5    22.1    -      -       +      +
    171q  MET*     3.9     7.9    -      -       -      -
    186q  ILE*     3.0    36.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 25 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9q  GLY*     3.8     2.3    -      -       -      -
     10q  ALA      2.9    25.3    +      -       -      +
     24q  ALA*     1.3    80.5    -      -       -      +
     26q  ARG*     1.3    60.4    +      -       -      +
     27q  ARG*     3.7     6.4    +      -       -      +
     39q  PHE      4.6     0.7    -      -       -      +
     41q  LYS*     2.8    43.6    +      -       -      +
    171q  MET*     3.7     5.1    -      -       +      +
    175q  VAL*     4.4    13.0    -      -       +      -
    180q  VAL      4.4     0.3    -      -       -      +
    181q  SER*     3.4     9.3    -      -       -      -
    182q  GLY*     2.9    37.5    +      -       -      +
    184q  GLY      3.1    14.4    -      -       -      +
    185q  VAL*     4.4     0.9    -      -       +      +
    186q  ILE*     4.9     1.6    -      -       -      +
----------------------------------------------------------
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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