Contacts of the strand formed by residues 94 - 99 (chain B) in PDB entry 1GXD


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 GLN 94 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92B  LYS*     3.5    17.8    -      -       +      +
     93B  ASN*     1.3    77.5    -      -       -      +
     95B  ILE*     1.3    64.7    +      -       -      +
     96B  THR*     4.2     6.7    +      -       -      +
    129B  ARG*     3.4    43.3    +      -       +      +
    131B  SER*     5.3     7.5    +      -       -      +
    139B  ASP*     4.6     0.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 95 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90B  TRP*     3.5    43.7    -      -       +      +
     92B  LYS*     3.7    22.0    -      -       +      +
     93B  ASN      4.1     8.1    -      -       -      +
     94B  GLN*     1.3    74.1    -      -       -      +
     96B  THR*     1.3    64.9    +      -       -      +
    128B  LEU*     4.2    11.4    -      -       +      -
    129B  ARG      3.0    16.3    +      -       -      +
    130B  PHE*     3.4    27.8    -      -       +      -
    131B  SER*     3.2    20.0    +      -       -      -
    139B  ASP*     3.8    20.6    -      -       +      -
    140B  ILE*     3.9    22.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 96 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94B  GLN      4.4     6.1    -      -       -      +
     95B  ILE*     1.3    83.8    -      -       -      +
     97B  TYR*     1.3    59.6    -      -       -      +
    131B  SER*     3.3    12.3    -      -       -      +
    133B  ILE*     3.6    29.0    -      -       +      +
    137B  GLU      4.7     0.7    +      -       -      -
    138B  ALA*     3.5     8.0    -      -       -      -
    139B  ASP*     2.6    61.3    +      -       -      +
    140B  ILE      2.8     7.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 97 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96B  THR*     1.3    75.0    -      -       -      +
     98B  ARG*     1.3    65.6    +      -       -      +
     99B  ILE*     4.3    12.6    -      -       +      +
    112B  ASP      5.4     0.7    +      -       -      -
    115B  PHE*     4.7     6.2    -      -       +      +
    116B  ALA*     4.4    17.2    +      -       -      +
    119B  PHE*     3.1    48.9    -      +       +      -
    130B  PHE*     4.3     4.3    -      -       +      -
    131B  SER*     3.1    17.5    +      -       -      -
    132B  ARG*     3.3    48.0    -      -       +      +
    133B  ILE      3.2    23.0    +      -       -      -
    138B  ALA*     3.6     3.6    -      -       -      +
    140B  ILE*     2.8    20.6    -      -       +      +
    142B  ILE*     3.6    18.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 98 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97B  TYR*     1.3    80.0    -      -       -      +
     99B  ILE*     1.3    68.8    +      -       -      +
    100B  ILE*     3.6    22.2    +      -       +      +
    132B  ARG*     4.8     3.4    -      -       +      -
    133B  ILE*     3.3    22.7    -      -       -      +
    134B  HIS*     3.7    15.7    +      -       +      +
    135B  ASP*     3.4     4.9    +      -       -      +
    136B  GLY      2.9    45.1    +      -       -      +
    138B  ALA*     3.9    11.2    -      -       +      -
    140B  ILE      2.9     6.8    +      -       -      +
    141B  MET*     3.6     9.4    -      -       -      +
    142B  ILE*     2.6    36.0    +      -       -      +
    282B  THR*     3.8    39.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 99 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97B  TYR*     4.3    14.8    -      -       +      +
     98B  ARG*     1.3    81.6    +      -       -      +
    100B  ILE*     1.3    62.2    +      -       -      +
    101B  GLY      3.3    22.7    -      -       -      +
    102B  TYR*     3.6    24.3    +      -       +      +
    112B  ASP*     3.1    29.8    -      -       +      +
    115B  PHE*     3.6    37.0    -      -       +      -
    132B  ARG*     3.5    27.1    +      -       -      +
    142B  ILE*     3.5     5.4    -      -       +      +
    282B  THR      4.9     1.0    -      -       -      +
    283B  ASP*     4.3    13.0    -      -       -      +
----------------------------------------------------------
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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