Contacts of the strand formed by residues 3 - 7 (chain Q) in PDB entry 1G3I


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 3 (chain Q).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1Q  THR*     3.8     7.0    -      -       +      -
      2Q  THR*     1.3    76.1    -      -       -      +
      4Q  VAL*     1.3    60.6    +      -       -      +
     14Q  VAL*     4.2    11.4    -      -       +      -
     15Q  GLY      3.3    12.1    -      -       -      +
     16Q  GLY*     3.4    21.8    -      -       -      -
     33Q  LYS*     3.7    18.6    -      -       +      +
     34Q  VAL*     4.6     0.7    -      -       +      -
     45Q  GLY*     4.0    22.9    -      -       -      +
     46Q  PHE      3.5    26.2    -      -       -      +
     47Q  ALA*     3.9    15.7    -      -       +      -
     96Q  ILE*     3.9     7.5    -      -       +      +
    122Q  ALA*     2.9     5.1    -      -       -      +
    123Q  ILE*     2.7    49.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 4 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2Q  THR      4.0     0.6    +      -       -      -
      3Q  ILE*     1.3    76.8    -      -       -      +
      5Q  SER*     1.3    67.6    +      -       -      +
      6Q  VAL*     4.7     2.5    -      -       +      -
     14Q  VAL*     3.7     0.6    -      -       -      -
     15Q  GLY      2.9    31.2    +      -       -      +
     96Q  ILE*     5.1     0.4    -      -       -      -
    120Q  ILE*     4.4    15.3    -      -       +      -
    121Q  LEU      2.9    11.9    -      -       -      +
    122Q  ALA*     4.0     9.4    -      -       +      -
    130Q  ALA*     3.9    28.9    -      -       +      +
    134Q  ALA*     4.5     5.2    -      -       +      -
    149Q  VAL*     3.6    20.4    -      -       +      +
    152Q  SER*     4.4     6.1    -      -       -      -
    153Q  LEU*     3.3    25.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 5 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4Q  VAL*     1.3    74.8    -      -       -      +
      6Q  VAL*     1.3    65.3    +      -       -      +
      7Q  ARG*     5.8     0.7    -      -       -      +
     12Q  VAL*     4.6     5.5    -      -       -      +
     13Q  VAL      2.5    22.5    +      -       -      -
     14Q  VAL*     3.1    21.9    -      -       -      +
     96Q  ILE*     4.1    13.9    -      -       -      +
     98Q  ALA*     4.9     4.4    -      -       -      +
    103Q  SER*     5.2     5.0    -      -       -      -
    119Q  GLN      3.6     1.9    -      -       -      +
    120Q  ILE*     3.2     5.0    -      -       -      -
    121Q  LEU*     2.4    50.0    +      -       -      -
    149Q  VAL*     4.0     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 6 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4Q  VAL*     4.7     2.5    -      -       +      -
      5Q  SER*     1.3    80.6    +      -       -      +
      7Q  ARG*     1.3    72.4    +      -       -      +
      8Q  ARG*     4.7     2.7    -      -       +      +
     12Q  VAL*     3.9     0.2    -      -       -      -
     13Q  VAL*     3.2    24.3    +      -       -      -
    119Q  GLN      3.8     2.5    -      -       -      +
    120Q  ILE*     4.1     9.0    -      -       +      -
    134Q  ALA*     4.1    16.8    -      -       +      -
    138Q  VAL*     3.5    26.7    -      -       +      -
    145Q  ALA*     3.5    24.7    -      -       -      +
    148Q  ILE*     3.5    22.4    -      -       +      -
    149Q  VAL*     3.2    26.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 7 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5Q  SER*     5.8     0.9    -      -       -      +
      6Q  VAL*     1.3    77.4    -      -       -      +
      8Q  ARG*     1.3    71.6    +      -       -      +
     10Q  GLY*     5.9     4.2    -      -       -      +
     11Q  GLN      3.2    12.6    -      -       -      +
     12Q  VAL*     2.7    34.3    -      -       +      +
     98Q  ALA*     4.1     1.2    -      -       -      +
     99Q  ASP      3.3     5.9    +      -       -      -
    100Q  GLU      3.8    12.7    +      -       -      -
    101Q  LYS      3.7    17.9    +      -       -      -
    102Q  GLU*     2.5    38.9    +      -       -      -
    103Q  SER*     3.2    15.9    +      -       -      +
    118Q  ASP      4.0    12.8    -      -       -      +
    119Q  GLN*     2.2    50.2    +      -       -      +
----------------------------------------------------------
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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