Contacts of the strand formed by residues 271 - 274 (chain G) in PDB entry 1G9N


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 VAL 271 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231G  LYS      4.1     9.0    -      -       -      +
    232G  LYS*     3.4    43.5    -      -       +      +
    233G  PHE      4.7     5.6    -      -       -      +
    234G  ASN*     6.0     0.2    -      -       -      -
    266G  ALA*     4.5     5.8    -      -       +      -
    269G  GLU      3.2    17.0    +      -       -      +
    270G  ILE*     1.3    73.3    -      -       -      +
    272G  ILE*     1.3    70.4    +      -       -      +
    273G  ARG*     3.7    33.8    +      -       +      +
    285G  ILE      4.0     0.3    -      -       -      +
    286G  VAL      3.6     0.3    -      -       -      -
    287G  GLN*     2.7    45.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 272 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232G  LYS*     4.9     5.0    +      -       -      +
    270G  ILE*     4.3     2.7    +      -       +      -
    271G  VAL*     1.3    85.7    -      -       -      +
    273G  ARG*     1.3    62.8    +      -       -      +
    277G  PHE*     3.2    34.3    -      -       +      -
    284G  ILE*     4.2     8.5    -      -       +      -
    285G  ILE      3.4     7.2    -      -       -      +
    286G  VAL*     4.1    25.1    -      -       +      -
    345G  ILE*     5.5     2.0    -      -       +      +
    348G  LYS*     3.6    41.7    -      -       +      +
    349G  LEU*     4.0    24.9    -      -       +      -
    352G  GLN*     4.3     9.0    -      -       +      -
    353G  PHE*     5.0     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 273 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95G  MET*     3.0    19.8    -      -       +      +
     96G  TRP*     3.5    19.4    -      -       +      -
    232G  LYS*     5.5     0.4    -      -       -      +
    233G  PHE      2.6    35.2    +      -       -      +
    234G  ASN*     3.8     9.9    -      -       -      +
    271G  VAL*     3.7    23.4    -      -       +      +
    272G  ILE*     1.3    77.8    -      -       -      +
    274G  SER*     1.3    65.3    +      -       -      +
    277G  PHE*     3.6     2.0    -      -       -      -
    284G  ILE*     3.6     2.8    -      -       -      +
    285G  ILE*     2.9    47.6    +      -       +      +
    287G  GLN*     2.7    35.3    +      -       -      +
    481G  SER*     6.1     2.7    -      -       -      +
    484G  TYR*     3.0    42.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 274 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96G  TRP*     3.1    17.9    +      -       -      -
    234G  ASN      5.5     0.4    +      -       -      -
    236G  THR*     5.0     6.6    -      -       -      +
    273G  ARG*     1.3    76.7    -      -       -      +
    275G  GLU*     1.3    63.9    +      -       -      +
    276G  ASN*     2.9     9.8    +      -       -      -
    277G  PHE*     3.2    55.5    +      -       -      -
    282G  LYS*     4.2     7.1    +      -       -      +
    283G  THR      3.7    13.4    +      -       -      -
    284G  ILE*     4.2     5.0    -      -       -      +
----------------------------------------------------------
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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