Contacts of the strand formed by residues 94 - 100 (chain G) 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 ARG 94 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92G  ALA      4.2     6.7    +      -       -      +
     93G  ASP*     1.3    82.5    -      -       -      +
     95G  TRP*     1.3    62.3    +      -       -      +
     96G  ARG*     4.0    19.4    +      -       +      +
    166G  GLU*     3.4    28.4    +      -       +      +
    167G  ALA      3.4    11.2    -      -       -      +
    168G  PRO*     4.5     7.6    -      -       +      -
    169G  MET*     4.3     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 95 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155F  SER      5.2     4.0    +      -       -      -
    156F  SER*     4.6    17.4    -      -       -      -
     94G  ARG*     1.3    72.7    -      -       -      +
     96G  ARG*     1.3    62.0    +      -       -      +
     97G  VAL*     3.4    37.9    -      -       +      +
    118G  VAL*     4.5     6.5    -      -       +      -
    142G  TYR*     4.3    22.2    -      +       +      -
    143G  THR      4.8     7.1    +      -       -      -
    144G  LEU*     3.6    26.0    -      -       +      -
    145G  PRO*     3.4    33.2    -      -       +      +
    148G  VAL*     5.6     1.8    -      -       +      -
    153G  VAL*     5.7     0.4    -      -       +      -
    165G  VAL*     4.0    26.9    -      -       +      -
    166G  GLU*     2.9    28.3    -      -       -      +
    167G  ALA*     2.8    28.0    +      -       +      +
    169G  MET*     4.0    20.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 96 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94G  ARG*     4.0    20.0    +      -       +      +
     95G  TRP*     1.3    83.9    +      -       -      +
     97G  VAL*     1.3    78.2    +      -       -      +
     98G  SER*     4.4     7.3    +      -       -      +
    164G  THR*     3.9    28.5    +      -       +      +
    165G  VAL      3.3     6.1    -      -       -      +
    166G  GLU*     3.4    27.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 97 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95G  TRP*     3.4    35.4    -      -       +      +
     96G  ARG*     1.3    81.6    -      -       -      +
     98G  SER*     1.3    65.3    +      -       -      +
     99G  LEU*     6.3     0.7    -      -       +      -
    118G  VAL*     6.5     0.2    -      -       +      -
    120G  ILE*     5.0     2.9    -      -       +      -
    142G  TYR*     4.1    42.2    -      -       +      +
    163G  LEU      4.0     0.6    -      -       -      +
    164G  THR*     3.4     5.0    -      -       -      +
    165G  VAL*     2.9    53.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 98 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96G  ARG*     4.4     9.4    +      -       -      -
     97G  VAL*     1.3    79.1    +      -       -      +
     99G  LEU*     1.3    64.6    +      -       -      +
    142G  TYR*     4.6     8.7    +      -       -      -
    162G  THR*     4.2    12.6    -      -       -      -
    163G  LEU      3.3     7.2    -      -       -      -
    164G  THR*     3.6    14.6    +      -       -      +
    131H  HIS*     5.9     3.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 99 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97G  VAL*     6.3     1.1    -      -       +      -
     98G  SER*     1.3    79.0    -      -       -      +
    100G  ASP*     1.3    70.6    +      -       -      +
    101G  VAL*     3.7    23.9    +      -       +      -
    120G  ILE*     4.1    32.8    -      -       +      -
    138G  PHE*     4.1    13.9    -      -       +      -
    140G  ARG*     3.8    35.7    -      -       -      +
    142G  TYR*     5.2     5.6    -      -       +      +
    162G  THR*     3.3     6.7    -      -       -      +
    163G  LEU*     2.6    47.2    +      -       +      +
    131H  HIS*     5.8     5.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 100 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99G  LEU*     1.3    81.3    -      -       +      +
    101G  VAL*     1.3    65.2    +      -       -      +
    102G  ASN*     2.8    34.3    +      -       -      +
    160G  GLU      5.2     0.9    -      -       -      +
    161G  GLY      3.7     9.2    -      -       -      +
    162G  THR*     4.4    10.0    +      -       -      +
----------------------------------------------------------
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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