Contacts of the strand formed by residues 207 - 213 (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 ILE 207 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46C  ALA*     5.9     2.9    -      -       +      -
     47C  THR      3.2    15.7    -      -       -      +
     48C  GLU*     4.5     7.4    -      -       +      -
     49C  LYS*     3.8     6.2    -      -       -      +
    191C  ILE*     4.5    21.5    -      -       +      -
    194C  LEU*     5.5     8.5    -      -       +      -
    198C  PHE*     5.5     4.9    -      -       +      -
    202C  MET*     3.9    38.4    -      -       +      -
    203C  THR      3.9    11.9    -      -       -      +
    204C  GLU*     3.8    16.3    -      -       -      +
    205C  ASP*     4.4     2.1    -      -       -      -
    206C  ASN*     1.3    88.6    +      -       +      +
    208C  GLU*     1.3    62.5    +      -       -      +
    209C  VAL*     4.1    20.6    -      -       +      -
    225C  VAL*     5.2    10.0    -      -       +      +
    229C  LEU*     5.4     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 208 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46C  ALA*     3.3     2.9    -      -       -      -
     47C  THR*     2.9    39.0    +      -       +      -
     49C  LYS*     3.7    19.6    +      -       +      +
     62C  HIS*     3.0    32.3    -      -       -      -
     63C  LYS*     2.7    31.3    +      -       -      +
     64C  VAL*     2.9    22.7    +      -       +      +
    207C  ILE*     1.3    74.8    -      -       -      +
    209C  VAL*     1.3    66.8    +      -       -      +
    219C  ARG*     3.4    23.2    -      -       +      -
    220C  LEU      5.8     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 209 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44C  VAL*     3.9    20.4    -      -       +      -
     45C  LEU      3.4    12.6    -      -       -      +
     46C  ALA*     4.1    11.7    -      -       +      -
     64C  VAL*     4.5     4.0    -      -       -      -
    187C  ILE*     4.7     7.6    -      -       +      -
    191C  ILE*     5.3     9.0    -      -       +      -
    207C  ILE*     4.1    22.4    -      -       +      -
    208C  GLU*     1.3    81.7    -      -       -      +
    210C  GLY*     1.3    62.7    +      -       -      +
    211C  ILE*     5.0     0.7    -      -       +      -
    219C  ARG*     3.5     8.7    -      -       -      +
    220C  LEU*     2.9    54.4    +      -       +      +
    225C  VAL*     5.0    10.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 210 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44C  VAL*     3.6     3.5    -      -       -      -
     45C  LEU*     2.9    34.5    +      -       -      +
     64C  VAL*     3.9    19.5    -      -       -      +
    209C  VAL*     1.3    74.4    -      -       -      +
    211C  ILE*     1.3    65.6    +      -       -      +
    217C  PHE*     4.3     7.0    -      -       -      -
    218C  ARG      3.4    10.5    -      -       -      -
    219C  ARG*     4.2     1.8    -      -       -      -
    220C  LEU      4.4     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 211 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43C  VAL      3.4     8.1    -      -       -      +
     44C  VAL*     5.1     1.6    -      -       +      -
    136C  CYS*     5.3     0.2    -      -       -      -
    183C  LEU*     5.9     5.6    -      -       +      -
    187C  ILE*     3.9    27.6    -      -       +      -
    209C  VAL*     5.0     0.7    -      -       +      -
    210C  GLY*     1.3    79.3    -      -       -      +
    212C  CYS*     1.3    62.7    +      -       -      +
    213C  ASN*     4.5    20.0    -      -       +      +
    216C  GLY      4.1     1.1    -      -       -      +
    217C  PHE*     3.1     7.3    -      -       -      -
    218C  ARG*     2.9    72.3    +      -       +      +
    220C  LEU*     3.8    27.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 212 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42C  GLY*     3.3     3.5    -      -       -      -
     43C  VAL*     2.9    39.2    +      -       +      +
     70C  HIS      3.7    13.9    -      -       -      -
    136C  CYS*     3.6    22.9    -      -       -      -
    137C  GLY*     3.5    15.7    -      -       -      -
    138C  TRP*     3.5    35.8    -      -       -      +
    143C  PRO*     5.2     0.2    -      -       -      +
    211C  ILE*     1.3    77.0    -      -       -      +
    213C  ASN*     1.3    59.3    +      -       -      +
    214C  GLU*     5.0     1.0    -      -       -      +
    216C  GLY      4.0     4.3    -      -       -      -
    217C  PHE*     3.9     6.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 213 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41C  ASN      3.8    19.1    -      -       -      +
     42C  GLY*     4.3     2.2    -      -       -      -
    138C  TRP*     3.5    13.7    -      -       -      +
    183C  LEU*     5.9     4.3    -      -       +      -
    211C  ILE*     4.1    20.7    -      -       +      +
    212C  CYS*     1.3    76.2    -      -       -      +
    214C  GLU*     1.3    66.7    +      -       -      +
    215C  ALA*     3.0    31.8    +      -       -      +
    216C  GLY*     3.3    21.3    +      -       -      +
----------------------------------------------------------
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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