Contacts of the strand formed by residues 162 - 168 (chain H) in PDB entry 6GJH


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 162 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98H  SER*     4.2    23.8    -      -       -      -
     99H  LEU      3.5    12.1    -      -       -      +
    100H  ASP*     4.7     8.1    +      -       -      +
    156H  SER      3.7     1.9    -      -       -      +
    157H  LEU*     3.6     3.2    -      -       -      +
    158H  SER*     3.0    35.3    +      -       -      -
    160H  GLU*     4.7     7.4    +      -       -      +
    161H  GLY*     1.3    76.5    -      -       -      +
    163H  LEU*     1.3    63.3    +      -       -      +
    164H  THR*     3.8     9.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 163 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97H  VAL      3.8     1.7    -      -       -      +
     98H  SER*     3.3     3.3    -      -       -      -
     99H  LEU*     2.8    50.6    +      -       +      +
    101H  VAL*     3.9    14.6    -      -       +      -
    109H  LEU*     4.7    19.1    -      -       +      -
    111H  VAL*     4.2    12.1    -      -       +      -
    120H  ILE*     3.8    32.3    -      -       +      -
    155H  SER*     4.4    10.3    -      -       -      -
    156H  SER*     3.5    30.5    -      -       -      +
    157H  LEU*     3.8    11.3    -      -       +      +
    162H  THR*     1.3    71.3    -      -       -      +
    164H  THR*     1.3    61.0    +      -       -      +
    165H  VAL*     4.1    10.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 164 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96H  ARG*     4.0    22.4    -      -       +      +
     97H  VAL      3.5     7.4    -      -       -      +
     98H  SER*     4.3    10.8    -      -       -      -
    154H  SER      3.6     1.7    -      -       -      +
    155H  SER*     3.3     4.2    -      -       -      -
    156H  SER*     3.1    39.0    +      -       -      +
    162H  THR*     3.8     9.4    +      -       -      +
    163H  LEU*     1.3    73.7    +      -       -      +
    165H  VAL*     1.3    62.6    +      -       -      +
    166H  GLU*     3.5    26.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 165 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95H  TRP*     4.2    10.0    -      -       +      -
     96H  ARG*     3.5     1.0    -      -       -      +
     97H  VAL*     2.9    44.4    +      -       +      +
    111H  VAL*     4.2    24.0    -      -       +      -
    118H  VAL*     4.3    10.5    -      -       +      -
    120H  ILE*     4.3    12.1    -      -       +      -
    153H  VAL*     3.5    27.6    -      -       +      -
    154H  SER      3.2     5.2    -      -       -      +
    155H  SER*     3.7    18.8    -      -       -      -
    163H  LEU*     4.1    11.9    +      -       +      +
    164H  THR*     1.3    77.2    -      -       -      +
    166H  GLU*     1.3    65.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 166 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94H  ARG*     3.4    33.4    +      -       -      -
     95H  TRP*     3.1    17.3    -      -       -      +
     96H  ARG*     3.8    19.6    +      -       +      -
    152H  GLN      3.8     0.7    -      -       -      +
    153H  VAL*     3.5     3.5    -      -       -      +
    154H  SER*     3.0    46.0    +      -       -      +
    164H  THR*     3.5    22.7    -      -       +      +
    165H  VAL*     1.3    76.6    -      -       -      +
    167H  ALA*     1.3    62.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 167 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94H  ARG*     3.6     5.5    -      -       -      +
     95H  TRP*     2.8    44.0    +      -       +      +
    144H  LEU*     5.2     0.7    -      -       +      -
    148H  VAL*     3.6    30.2    -      -       +      +
    152H  GLN      3.9     2.5    -      -       -      +
    153H  VAL*     4.0    16.6    -      -       +      -
    166H  GLU*     1.3    77.7    -      -       -      +
    168H  PRO*     1.3    70.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 168 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93H  ASP      3.8     9.6    -      -       -      +
     94H  ARG*     4.4     3.1    -      -       +      +
    148H  VAL*     4.2    17.5    -      -       +      +
    149H  ASP      5.1     1.6    +      -       -      -
    152H  GLN*     3.5    41.3    -      -       +      +
    167H  ALA*     1.3    88.7    -      -       +      +
    169H  MET*     1.3    68.0    +      -       -      +
    170H  PRO*     4.0     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