Contacts of the strand formed by residues 42 - 48 (chain C) 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 GLY 42 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38C  LYS*     3.6     0.5    -      -       -      -
     39C  ALA*     2.6    40.5    +      -       -      +
     40C  ALA      3.4     2.4    +      -       -      -
     41C  ASN*     1.3    81.7    +      -       -      +
     43C  VAL*     1.3    62.1    +      -       -      +
    143C  PRO*     4.2     7.8    -      -       -      +
    183C  LEU*     4.6    11.0    -      -       -      -
    212C  CYS      3.3    13.5    -      -       -      -
    213C  ASN*     4.3     2.5    -      -       -      -
    214C  GLU*     5.3     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 43 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37C  ILE      3.4    18.2    -      -       -      +
     38C  LYS*     4.0     4.9    -      -       -      -
     42C  GLY*     1.3    78.1    -      -       -      +
     44C  VAL*     1.3    74.6    +      -       -      +
     45C  LEU*     4.9     0.2    -      -       +      -
    136C  CYS*     3.7    26.9    -      -       +      -
    137C  GLY      4.3     3.6    -      -       -      +
    143C  PRO*     3.5    23.3    -      -       +      -
    144C  TYR      3.9    18.8    -      -       -      +
    145C  LEU*     4.4    11.7    -      -       +      -
    183C  LEU*     5.2     1.5    -      -       -      +
    211C  ILE*     3.4     6.4    -      -       -      +
    212C  CYS*     2.9    42.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 44 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35C  VAL      3.8     0.6    -      -       -      +
     36C  GLY*     3.2     5.7    -      -       -      -
     37C  ILE*     2.8    37.9    +      -       +      +
     42C  GLY      5.6     0.4    -      -       -      -
     43C  VAL*     1.3    78.8    -      -       -      +
     45C  LEU*     1.3    69.6    +      -       -      +
     46C  ALA*     4.8     0.4    -      -       +      +
    183C  LEU*     3.9     8.3    -      -       +      +
    186C  ALA*     3.7    17.7    -      -       +      +
    187C  ILE*     3.6    40.4    -      -       +      +
    190C  ALA*     4.1    20.4    -      -       +      -
    209C  VAL*     3.9    24.9    -      -       +      -
    210C  GLY      3.6     3.6    -      -       -      +
    211C  ILE*     5.1     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 45 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35C  VAL      3.5     1.1    -      -       -      -
     36C  GLY*     3.9    14.6    -      -       -      -
     43C  VAL*     4.9     0.4    -      -       +      -
     44C  VAL*     1.3    83.7    -      -       -      +
     46C  ALA*     1.3    64.5    +      -       -      +
     64C  VAL*     4.5     6.2    -      -       +      +
     72C  GLY*     4.0    18.4    -      -       -      +
     73C  LEU      4.1     4.0    -      -       -      +
     74C  VAL*     3.7    36.3    -      -       +      -
    134C  LEU*     4.0     9.0    -      -       +      +
    136C  CYS*     3.6    34.3    -      -       +      -
    145C  LEU*     4.0    20.2    -      -       +      -
    209C  VAL*     3.4     2.9    -      -       -      +
    210C  GLY      2.9    35.8    +      -       -      +
    217C  PHE*     4.7     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 46 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34C  SER*     3.2     5.2    -      -       -      -
     35C  VAL*     2.9    38.4    +      -       +      +
     45C  LEU*     1.3    77.3    -      -       -      +
     47C  THR*     1.3    62.5    +      -       -      +
     64C  VAL*     5.4     0.4    -      -       -      -
     74C  VAL*     5.0     3.2    -      -       -      +
    190C  ALA*     4.7    22.0    -      -       +      +
    191C  ILE*     6.0     1.8    -      -       +      -
    194C  LEU*     5.8     6.7    -      -       +      -
    207C  ILE*     5.9     2.7    -      -       +      -
    208C  GLU      3.3    10.3    -      -       -      +
    209C  VAL*     4.1    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 47 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33C  PRO      3.1     6.7    +      -       -      -
     34C  SER*     2.8    25.1    +      -       -      -
     46C  ALA*     1.3    75.1    -      -       -      +
     48C  GLU*     1.3    62.6    +      -       -      +
     63C  LYS*     2.8    54.5    +      -       +      -
     64C  VAL*     4.2    10.3    -      -       +      -
     74C  VAL*     4.4     6.3    -      -       +      -
    194C  LEU*     6.1     4.7    -      -       -      -
    207C  ILE*     3.2     8.5    -      -       -      +
    208C  GLU*     2.9    44.0    +      -       +      +
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Residues in contact with GLU 48 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32C  ALA*     3.5    12.9    -      -       +      +
     33C  PRO*     3.3    40.1    +      -       +      +
     47C  THR*     1.3    75.2    +      -       -      +
     49C  LYS*     1.3    58.6    +      -       -      +
     50C  LYS*     3.4    43.2    +      -       +      +
     63C  LYS*     3.3    19.0    +      -       -      +
    194C  LEU*     5.2     3.9    -      -       +      +
    197C  SER*     4.9     1.7    -      -       -      +
    198C  PHE*     4.1    32.3    +      -       +      +
    199C  GLU      5.1     0.2    +      -       -      -
    206C  ASN      3.8     6.3    -      -       -      +
    207C  ILE*     4.4     7.4    -      -       +      +
----------------------------------------------------------
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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