Contacts of the strand formed by residues 3 - 7 (chain R) 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 R).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1R  THR*     3.7     7.2    -      -       +      -
      2R  THR*     1.3    76.3    -      -       -      +
      4R  VAL*     1.3    60.2    +      -       -      +
     14R  VAL*     4.3    11.7    -      -       +      -
     15R  GLY      3.3    11.4    -      -       -      +
     16R  GLY*     3.5    21.1    -      -       -      -
     33R  LYS*     3.7    19.7    -      -       +      +
     34R  VAL*     4.7     0.2    -      -       +      -
     45R  GLY*     4.0    23.6    -      -       -      +
     46R  PHE      3.4    26.7    -      -       -      +
     47R  ALA*     3.8    14.8    -      -       +      -
     96R  ILE*     3.9     8.2    -      -       +      +
    121R  LEU      3.8     0.2    -      -       -      +
    122R  ALA*     2.9     5.4    -      -       -      +
    123R  ILE*     2.8    47.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 4 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2R  THR      4.1     0.2    +      -       -      -
      3R  ILE*     1.3    77.5    -      -       -      +
      5R  SER*     1.3    67.4    +      -       -      +
      6R  VAL*     4.6     3.4    -      -       +      -
     14R  VAL*     3.7     0.3    -      -       -      +
     15R  GLY      2.9    31.5    +      -       -      +
     96R  ILE*     5.1     0.2    -      -       -      -
    120R  ILE*     4.3    15.3    -      -       +      -
    121R  LEU      2.9    11.4    -      -       -      +
    122R  ALA*     4.0     9.4    -      -       +      -
    130R  ALA*     3.9    28.7    -      -       +      +
    134R  ALA*     4.5     4.7    -      -       +      -
    149R  VAL*     3.6    15.6    -      -       +      +
    152R  SER*     4.4     6.1    -      -       -      -
    153R  LEU*     3.3    30.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 5 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4R  VAL*     1.3    73.9    -      -       -      +
      6R  VAL*     1.3    64.3    +      -       -      +
      7R  ARG*     5.8     0.5    -      -       -      +
     12R  VAL*     4.6     5.5    -      -       -      +
     13R  VAL      2.5    23.6    +      -       -      -
     14R  VAL*     3.1    22.4    -      -       -      +
     96R  ILE*     4.1    13.9    -      -       -      -
     98R  ALA*     4.9     3.8    -      -       -      +
    103R  SER*     5.2     4.9    -      -       -      -
    119R  GLN      3.8     1.9    -      -       -      +
    120R  ILE*     3.2     5.0    -      -       -      +
    121R  LEU*     2.4    49.3    +      -       -      +
    149R  VAL*     4.0     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 6 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4R  VAL*     4.6     2.5    -      -       +      -
      5R  SER*     1.3    80.7    +      -       -      +
      7R  ARG*     1.3    72.5    +      -       -      +
      8R  ARG*     4.7     2.5    -      -       +      +
     13R  VAL*     3.1    24.9    +      -       -      +
    118R  ASP      5.6     0.2    -      -       -      +
    119R  GLN      4.1     2.5    -      -       -      -
    120R  ILE*     4.0    21.5    -      -       +      +
    134R  ALA*     4.1     5.2    -      -       +      -
    138R  VAL*     3.4    27.4    -      -       +      -
    145R  ALA*     3.6    23.5    -      -       -      +
    148R  ILE*     3.6    21.1    -      -       +      -
    149R  VAL*     3.2    26.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 7 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5R  SER*     5.8     0.4    -      -       -      +
      6R  VAL*     1.3    77.1    -      -       -      +
      8R  ARG*     1.3    71.5    +      -       -      +
     10R  GLY*     5.8     4.4    -      -       -      +
     11R  GLN      3.2    12.6    -      -       -      +
     12R  VAL*     2.7    39.3    -      -       +      +
     98R  ALA*     4.1     0.8    -      -       -      +
     99R  ASP      3.3     5.7    +      -       -      -
    100R  GLU      3.8     8.7    +      -       -      -
    101R  LYS      3.7    17.1    +      -       -      -
    102R  GLU*     2.5    38.7    +      -       -      +
    103R  SER*     3.3    22.8    +      -       -      +
    118R  ASP      4.0    12.3    -      -       -      +
    119R  GLN*     3.5    29.6    +      -       +      +
----------------------------------------------------------
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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