Contacts of the strand formed by residues 210 - 216 (chain G) 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 VAL 210 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47G  VAL*     4.5     2.9    -      -       +      -
     48G  ALA      3.5     5.2    -      -       -      +
     50G  LYS*     3.6    11.3    -      -       -      +
    192G  LEU*     3.6    25.8    -      -       +      -
    195G  LEU*     4.6     4.9    -      -       +      -
    205G  LEU*     3.7    35.7    -      -       +      -
    206G  THR      3.5    20.4    +      -       -      +
    207G  THR      4.9     3.1    -      -       -      +
    208G  LYS      3.7     1.4    -      -       -      +
    209G  ASN*     1.3    90.1    -      -       -      +
    211G  SER*     1.3    65.1    +      -       -      +
    212G  ILE*     4.1    14.8    -      -       +      -
    225G  ASP*     4.3     2.3    -      -       -      +
    226G  ASP      4.8     1.0    +      -       -      -
    229G  VAL*     3.7    24.5    -      -       +      +
    233G  LEU*     4.9     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 211 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47G  VAL*     3.5     4.0    -      -       -      +
     48G  ALA*     2.9    37.3    +      -       -      +
     50G  LYS*     2.8    32.3    -      -       -      +
     61G  LYS*     5.4     2.4    -      -       -      +
     62G  LYS      5.2     4.1    +      -       -      -
     63G  ILE*     3.6    22.2    -      -       -      +
    210G  VAL*     1.3    72.7    -      -       -      +
    212G  ILE*     1.3    65.4    +      -       -      +
    223G  ILE*     4.9     3.4    -      -       -      +
    224G  TYR      3.6     5.2    -      -       -      -
    225G  ASP*     3.7    14.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 212 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45G  VAL*     4.2     6.1    -      -       +      -
     46G  LEU      3.5     8.7    -      -       -      +
     47G  VAL*     4.7     6.1    -      -       +      -
     63G  ILE*     3.5     7.1    -      -       -      +
    188G  VAL*     3.7    30.3    -      -       +      -
    192G  LEU*     4.5     5.8    -      -       +      -
    210G  VAL*     4.1    11.4    -      -       +      -
    211G  SER*     1.3    80.5    -      -       -      +
    213G  GLY*     1.3    62.8    +      -       -      +
    214G  ILE*     4.2    19.7    -      -       +      -
    223G  ILE*     3.5     3.8    -      -       -      +
    224G  TYR*     2.8    40.9    +      -       +      +
    229G  VAL*     3.9    19.7    -      -       +      -
    232G  PHE*     3.7    35.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 213 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44G  ALA      3.9     0.3    -      -       -      +
     45G  VAL*     3.2     6.2    -      -       -      +
     46G  LEU*     2.8    36.0    +      -       -      +
     63G  ILE*     3.7     8.0    -      -       -      +
    212G  ILE*     1.3    77.4    -      -       -      +
    214G  ILE*     1.3    63.7    +      -       -      +
    221G  PHE*     4.4    16.1    -      -       -      -
    222G  THR      3.2    10.3    -      -       -      -
    223G  ILE*     4.6     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 214 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43G  HIS*     4.0     9.9    -      -       +      -
     44G  ALA      3.5     8.1    -      -       -      +
     45G  VAL*     4.2     6.3    -      -       +      -
    184G  LEU*     3.6    32.3    -      -       +      -
    188G  VAL*     3.9    21.3    -      -       +      -
    212G  ILE*     4.2     8.7    -      -       +      -
    213G  GLY*     1.3    80.2    -      -       -      +
    215G  VAL*     1.3    63.5    +      -       -      +
    219G  LEU*     4.0    20.1    -      -       +      +
    220G  GLU      3.4     4.2    -      -       -      +
    221G  PHE*     3.2     5.9    -      -       -      -
    222G  THR*     2.9    31.1    +      -       -      +
    224G  TYR*     3.6    27.8    -      -       +      +
    232G  PHE*     4.1    16.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 215 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43G  HIS*     3.5     5.6    -      -       -      +
     44G  ALA*     2.8    45.8    +      -       +      +
     68G  ASN      4.2     0.4    -      -       -      +
     69G  HIS*     3.7    26.2    -      -       +      +
    135G  ALA*     3.9     6.5    -      -       +      +
    136G  GLY*     3.8    33.2    -      -       -      +
    137G  TYR*     4.3     6.9    -      -       +      +
    214G  ILE*     1.3    79.1    -      -       -      +
    216G  GLY*     1.3    63.4    +      -       -      +
    219G  LEU*     3.6    13.2    -      -       -      +
    220G  GLU*     4.6     0.2    -      -       -      -
    221G  PHE*     3.7    26.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 216 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42G  THR      3.3    13.7    -      -       -      -
     43G  HIS*     4.4     7.6    -      -       -      -
    137G  TYR*     4.0    19.4    -      -       -      +
    215G  VAL*     1.3    79.1    -      -       -      +
    217G  LYS*     1.3    64.8    +      -       -      -
    218G  ASP      3.2     3.5    +      -       -      -
    219G  LEU*     2.8    24.6    +      -       -      +
----------------------------------------------------------
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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