Contacts of the strand formed by residues 94 - 100 (chain D) 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 D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89D  ARG      4.5     0.7    -      -       -      +
     90D  HIS*     3.7     2.3    -      -       -      +
     91D  THR*     2.9    37.1    +      -       -      +
     93D  ASP*     1.3    92.0    -      -       +      +
     95D  TRP*     1.3    62.4    +      -       -      +
     96D  ARG*     3.8    25.0    +      -       -      +
    152D  GLN      5.0     1.6    +      -       -      -
    154D  SER*     4.8     3.2    +      -       -      -
    166D  GLU*     3.4    31.3    +      -       -      +
    167D  ALA*     3.3    38.0    +      -       -      +
    168D  PRO*     3.7    24.7    -      -       -      +
    169D  MET*     3.7     6.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 95 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90D  HIS*     3.1    38.7    +      +       -      -
     94D  ARG*     1.3    72.2    -      -       -      +
     96D  ARG*     1.3    60.5    +      -       -      +
     97D  VAL*     3.7    28.0    -      -       +      -
    118D  VAL*     4.6     5.4    -      -       +      -
    142D  TYR*     4.0    29.2    -      +       +      -
    143D  THR      4.2    10.3    +      -       -      -
    144D  LEU*     3.7    28.9    -      -       +      -
    145D  PRO*     3.8    24.0    -      -       +      +
    148D  VAL*     5.8     1.6    -      -       +      -
    153D  VAL*     5.7     0.4    -      -       +      -
    165D  VAL*     3.8    30.7    -      -       +      -
    166D  GLU*     3.0     5.7    -      -       -      +
    167D  ALA*     2.8    51.6    +      -       +      +
    168D  PRO      5.8     0.2    -      -       -      -
    169D  MET*     4.2    18.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 96 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89D  ARG*     2.6    96.5    +      -       +      +
     90D  HIS*     2.9    26.3    +      -       -      -
     91D  THR*     4.0    15.0    -      -       -      +
     94D  ARG*     3.8    32.0    +      -       -      +
     95D  TRP*     1.3    75.3    -      -       -      +
     97D  VAL*     1.3    66.8    +      -       -      +
    164D  THR*     4.0    20.0    -      -       +      -
    165D  VAL      3.4     4.5    -      -       -      -
    166D  GLU*     3.4    19.5    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 97 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86D  SER*     5.6     0.2    -      -       -      -
     87D  GLU      3.8     7.6    -      -       -      +
     88D  ILE*     4.2    17.9    -      -       +      -
     89D  ARG*     5.2     0.2    -      -       -      -
     90D  HIS*     3.6    17.3    -      -       +      -
     95D  TRP*     3.7    26.9    -      -       +      -
     96D  ARG*     1.3    81.8    -      -       -      +
     98D  SER*     1.3    64.3    +      -       -      +
     99D  LEU*     6.3     1.1    -      -       +      -
    120D  ILE*     5.5     0.7    -      -       +      -
    142D  TYR*     4.2    31.4    -      -       +      +
    163D  LEU      3.8     0.7    -      -       -      +
    164D  THR*     3.4     4.0    -      -       -      +
    165D  VAL*     2.9    53.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 98 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86D  SER*     3.0     6.2    +      -       -      -
     87D  GLU*     2.8    40.6    +      -       -      -
     89D  ARG*     3.3    34.5    +      -       -      -
     97D  VAL*     1.3    74.9    -      -       -      +
     99D  LEU*     1.3    60.1    +      -       -      +
    162D  THR*     3.8    19.0    -      -       -      +
    163D  LEU      3.3     4.9    -      -       -      -
    164D  THR*     3.5     9.1    +      -       -      +
     85J  VAL*     3.6    12.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 99 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85D  VAL*     4.1     4.7    -      -       -      +
     86D  SER*     3.3    31.0    -      -       -      +
     97D  VAL*     6.3     1.1    -      -       +      -
     98D  SER*     1.3    75.1    -      -       -      +
    100D  ASP*     1.3    71.3    +      -       -      +
    101D  VAL*     3.4    23.9    +      -       +      -
    120D  ILE*     4.5    21.5    -      -       +      -
    138D  PHE*     4.2    17.0    -      -       +      -
    140D  ARG*     4.1    26.2    -      -       +      +
    142D  TYR*     4.6     3.6    -      -       +      +
    162D  THR*     3.6     3.0    -      -       -      +
    163D  LEU*     2.8    42.9    +      -       +      +
     85J  VAL      4.5     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 100 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85D  VAL*     3.4    25.4    -      -       +      +
     99D  LEU*     1.3    75.6    -      -       -      +
    101D  VAL*     1.3    68.6    +      -       -      +
    102D  ASN*     3.2    29.8    +      -       -      +
    161D  GLY      4.0     2.7    -      -       -      -
     84J  GLY*     3.4    34.0    +      -       -      -
     85J  VAL      4.2     1.3    +      -       -      +
----------------------------------------------------------
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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