Contacts of the strand formed by residues 95 - 99 (chain Z) in PDB entry 5GGR


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 PHE 95 (chain Z).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67Z  TRP*     4.6     4.5    -      +       +      -
     69Z  ARG*     5.9     2.7    -      -       -      -
     79Z  LEU*     3.5    57.8    -      -       +      +
     80Z  ALA*     3.3    13.3    -      -       +      +
     84Z  GLU*     5.3     1.6    -      -       -      +
     93Z  SER*     3.1    26.5    +      -       -      +
     94Z  ARG*     1.3   120.2    -      -       +      +
     96Z  ARG*     1.3    68.0    +      -       -      +
    109Z  SER      3.5     3.8    -      -       -      +
    110Z  VAL*     3.5    31.6    -      -       +      -
    117Z  ASP*     4.7     3.1    -      -       -      -
    121Z  TYR*     4.8     9.6    -      +       -      -
----------------------------------------------------------
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Residues in contact with ARG 96 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67Z  TRP*     4.0     2.4    -      -       -      -
     80Z  ALA*     3.8     5.3    -      -       -      +
     84Z  GLU*     4.1    31.9    +      -       -      +
     93Z  SER*     4.4    15.3    -      -       -      +
     94Z  ARG      4.1     1.8    +      -       -      -
     95Z  PHE*     1.3    81.9    -      -       -      +
     97Z  VAL*     1.3    70.0    +      -       -      +
     98Z  THR*     5.2    16.9    -      -       +      +
    107Z  HIS      3.5     2.8    -      -       -      +
    108Z  MET*     3.6     2.4    -      -       -      -
    109Z  SER*     3.3    36.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 97 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65Z  LEU*     5.2     1.6    -      -       +      +
     67Z  TRP*     4.8     3.4    -      -       +      -
     80Z  ALA*     4.2    18.2    -      -       +      +
     81Z  ALA*     4.3    15.8    +      -       -      +
     82Z  PHE*     3.9    35.9    -      -       +      +
     96Z  ARG*     1.3    81.6    +      -       -      +
     98Z  THR*     1.3    72.0    +      -       -      +
    106Z  PHE*     4.0    22.9    -      -       +      -
    107Z  HIS      3.5     5.8    -      -       -      +
    108Z  MET*     3.6    34.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 98 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82Z  PHE*     5.5     0.7    -      -       -      -
     96Z  ARG*     5.2    18.6    -      -       +      +
     97Z  VAL*     1.3    81.7    -      -       -      +
     99Z  GLN*     1.3    65.9    +      -       -      +
    100Z  LEU*     3.4     6.6    +      -       -      +
    106Z  PHE*     3.6     4.1    -      -       -      -
    107Z  HIS*     2.9    51.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 99 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82Z  PHE*     3.7    33.3    -      -       +      -
     97Z  VAL      4.3     0.4    -      -       -      -
     98Z  THR*     1.3    73.9    -      -       -      +
    100Z  LEU*     1.3    73.4    +      -       -      +
    103Z  GLY*     3.2    33.9    +      -       -      +
    106Z  PHE*     3.5    32.3    -      -       +      -
----------------------------------------------------------
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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