Contacts of the strand formed by residues 43 - 47 (chain C) 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 ILE 43 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26C  GLU*     4.2    14.1    -      -       -      +
     29C  VAL*     2.6    29.6    -      -       +      -
     42C  ARG*     1.3    73.5    -      -       -      +
     44C  GLN*     1.3    62.8    +      -       -      +
     45C  TYR*     3.9    26.5    -      -       +      +
     64C  TYR*     3.1     7.4    -      -       -      +
     65C  THR*     2.8    43.3    +      -       +      +
     66C  ALA      3.5    19.3    -      -       -      +
     67C  PRO*     3.4    21.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 44 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26C  GLU*     3.0     8.7    -      -       -      +
     27C  LYS*     2.3    91.3    +      -       +      +
     28C  GLU      5.0     2.4    +      -       -      -
     29C  VAL*     3.9     0.8    -      -       -      +
     30C  ASP*     5.1     9.1    -      -       -      +
     42C  ARG      4.5     2.2    +      -       -      +
     43C  ILE*     1.3    77.5    -      -       -      +
     45C  TYR*     1.3    59.2    -      -       -      +
     62C  PHE*     4.1     5.1    -      -       +      -
     63C  ILE      3.0     4.5    -      -       -      +
     64C  TYR*     2.6    52.1    +      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 45 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23C  ALA*     3.7    23.1    -      -       +      -
     26C  GLU*     4.1    16.4    -      -       +      +
     27C  LYS      3.8     1.1    -      -       -      +
     43C  ILE*     3.9    19.5    -      -       +      +
     44C  GLN*     1.3    75.4    -      -       -      +
     46C  GLU*     1.3    55.3    +      -       -      +
     47C  ILE*     3.8     9.2    -      -       +      -
     62C  PHE*     2.7    21.0    -      -       -      +
     63C  ILE*     2.5    61.5    +      -       +      -
     65C  THR*     3.5    27.7    -      -       +      +
     74C  VAL      3.4     1.1    +      -       -      -
     75C  SER*     3.3    12.5    +      -       -      -
     76C  LEU*     3.2    60.9    +      -       +      -
     78C  VAL*     4.9     2.2    -      -       +      -
     98C  ILE*     4.3     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 46 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22C  LYS      3.2     2.8    -      -       -      +
     23C  ALA*     3.2     2.0    -      -       -      +
     24C  VAL*     2.7    48.8    +      -       +      +
     25C  SER*     1.9    60.6    +      -       -      +
     27C  LYS*     3.9     8.8    +      -       +      +
     45C  TYR*     1.3    69.7    -      -       -      +
     47C  ILE*     1.3    61.1    +      -       -      +
     61C  GLU      4.6     0.2    -      -       -      +
     62C  PHE*     3.2    30.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 47 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21C  ALA*     3.6    22.7    -      -       +      -
     22C  LYS      2.8    19.3    -      -       -      +
     24C  VAL*     4.9     3.6    -      -       -      -
     45C  TYR*     3.5    13.7    -      -       +      +
     46C  GLU*     1.3    80.4    -      -       -      +
     48C  LYS*     1.3    60.2    +      -       -      +
     49C  GLN*     3.7    11.2    +      -       +      +
     60C  ILE*     2.7    34.6    -      -       +      +
     61C  GLU*     2.8    34.7    +      -       -      +
     62C  PHE      3.8     2.5    -      -       -      +
     63C  ILE*     2.9    37.0    -      -       +      -
     76C  LEU*     6.3     0.7    -      -       +      -
----------------------------------------------------------
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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