Contacts of the strand formed by residues 94 - 100 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  ALA      4.2     7.9    +      -       -      +
     93A  ASP*     1.3    81.7    -      -       -      +
     95A  TRP*     1.3    64.1    +      -       -      +
     96A  ARG*     3.9    28.6    +      -       +      +
    166A  GLU*     4.0    21.6    +      -       +      +
    167A  ALA      3.6     9.6    -      -       -      +
    168A  PRO*     4.6     6.7    -      -       +      -
    169A  MET*     4.3     5.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 95 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  ARG*     1.3    71.3    -      -       -      +
     96A  ARG*     1.3    64.4    +      -       -      +
     97A  VAL*     3.5    39.2    -      -       +      +
    118A  VAL*     4.5     7.0    -      -       +      -
    142A  TYR*     4.3    19.3    -      -       +      -
    143A  THR      4.5     8.7    +      -       -      -
    144A  LEU*     3.5    31.0    -      -       +      -
    145A  PRO*     3.5    31.1    -      -       +      +
    148A  VAL*     5.4     1.8    -      -       +      -
    153A  VAL*     5.2     0.2    -      -       +      -
    165A  VAL*     4.2    24.5    -      -       +      -
    166A  GLU*     2.9    36.7    -      -       -      +
    167A  ALA*     2.8    23.0    +      -       +      +
    169A  MET*     4.2    18.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 96 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  ARG*     3.9    21.3    +      -       -      +
     95A  TRP*     1.3    84.2    +      -       -      +
     97A  VAL*     1.3    75.7    +      -       -      +
     98A  SER*     4.5     7.7    +      -       -      -
    164A  THR*     3.4    35.5    +      -       +      +
    165A  VAL      3.4     5.2    -      -       -      +
    166A  GLU*     3.6    21.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 97 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  TRP*     3.5    37.9    -      -       +      +
     96A  ARG*     1.3    81.9    -      -       -      +
     98A  SER*     1.3    63.3    +      -       -      +
     99A  LEU*     6.3     0.2    -      -       +      -
    118A  VAL*     6.4     0.2    -      -       +      -
    120A  ILE*     5.4     0.2    -      -       +      -
    142A  TYR*     4.0    42.4    -      -       +      -
    163A  LEU      3.9     0.5    -      -       -      +
    164A  THR*     3.5     4.7    -      -       -      +
    165A  VAL*     3.0    48.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 98 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  ARG*     4.5     9.9    +      -       -      -
     97A  VAL*     1.3    77.1    +      -       -      +
     99A  LEU*     1.3    63.3    +      -       -      +
    142A  TYR*     4.3     7.1    +      -       -      -
    162A  THR*     4.3    13.4    -      -       -      +
    163A  LEU      3.4     6.7    -      -       -      -
    164A  THR*     3.9    14.0    +      -       -      +
    131B  HIS*     6.1     1.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 99 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97A  VAL*     6.3     0.4    -      -       +      -
     98A  SER*     1.3    77.6    -      -       -      +
    100A  ASP*     1.3    71.2    +      -       -      +
    101A  VAL*     3.6    22.1    +      -       +      -
    120A  ILE*     4.2    35.0    -      -       +      -
    138A  PHE*     4.2    14.4    -      -       +      -
    140A  ARG*     3.9    27.1    -      -       -      +
    142A  TYR*     4.1    13.9    -      -       +      +
    162A  THR*     3.4     5.3    -      -       -      +
    163A  LEU*     2.7    45.0    +      -       +      +
    131B  HIS*     6.3     0.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 100 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  LEU*     1.3    80.9    -      -       -      +
    101A  VAL*     1.3    66.7    +      -       -      +
    102A  ASN*     2.5    38.1    +      -       -      +
    160A  GLU      5.6     1.4    -      -       -      +
    161A  GLY      3.8     5.6    -      -       -      -
    162A  THR*     4.5    11.1    +      -       -      +
----------------------------------------------------------
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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