Contacts of the strand formed by residues 103 - 107 (chain K) 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 SER 103 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5K  SER*     4.2    11.8    +      -       -      -
      7K  ARG*     3.8    20.1    +      -       -      +
     12K  VAL*     4.5     1.6    -      -       -      +
     96K  ILE*     5.3     0.5    -      -       -      +
     98K  ALA*     3.4    17.6    -      -       -      +
    102K  GLU*     1.3    82.4    +      -       -      +
    104K  LEU*     1.3    70.6    +      -       -      +
    115K  PRO*     3.2    28.7    -      -       -      +
    119K  GLN*     5.2     7.4    +      -       -      -
    121K  LEU*     3.7    15.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 104 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    443E  ILE*     5.1     1.1    -      -       +      -
     71K  LEU*     3.7    10.5    -      -       +      -
     72K  LEU*     3.6    36.8    -      -       +      +
     75K  ALA*     3.6    29.6    -      -       +      -
     96K  ILE*     3.4     5.2    -      -       -      -
     97K  VAL*     2.5    46.8    +      -       +      +
    102K  GLU*     4.2     7.6    -      -       -      +
    103K  SER*     1.3    86.2    +      -       -      +
    105K  ILE*     1.3    63.9    +      -       -      +
    106K  ILE*     5.1     0.9    -      -       +      -
    112K  VAL*     4.6     9.4    -      -       +      -
    113K  VAL      3.7    17.9    -      -       -      +
    114K  GLN*     4.2    15.3    -      -       +      -
    115K  PRO*     4.9     0.2    -      -       +      -
    121K  LEU*     3.4    10.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 105 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94K  MET*     4.8     4.5    -      -       -      -
     95K  LEU      3.3    13.9    -      -       -      +
     96K  ILE*     4.3     3.6    -      -       +      -
    104K  LEU*     1.3    79.0    -      -       -      +
    106K  ILE*     1.3    67.3    +      -       -      +
    107K  THR*     5.2     2.9    -      -       +      +
    111K  ASP      3.7     1.0    -      -       -      +
    112K  VAL*     3.5     4.0    -      -       -      -
    113K  VAL*     3.0    58.3    +      -       +      +
    121K  LEU*     4.3    19.1    -      -       +      -
    122K  ALA      4.4     7.0    -      -       -      +
    123K  ILE*     3.3    30.5    -      -       +      -
     27L  MET*     4.4    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 106 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56K  LEU*     4.1     6.8    -      -       +      +
     60K  PHE*     3.4    42.2    -      -       +      -
     75K  ALA*     4.1    18.4    -      -       +      +
     78K  LEU*     4.6    19.7    -      -       +      -
     79K  ALA      5.7     1.6    -      -       -      +
     82K  TRP*     5.1     2.0    -      -       +      -
     94K  MET*     3.2     5.9    -      -       -      +
     95K  LEU*     2.8    44.7    +      -       +      +
     97K  VAL*     4.1    19.3    -      -       +      -
    104K  LEU*     5.1     0.9    -      -       +      -
    105K  ILE*     1.3    79.7    -      -       -      +
    107K  THR*     1.3    74.9    +      -       -      +
    110K  GLY*     5.6     0.4    -      -       -      -
    111K  ASP      3.7    10.5    -      -       -      +
    112K  VAL*     4.6     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 107 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56K  LEU*     4.3     4.7    -      -       -      -
     82K  TRP*     4.0     3.5    -      -       -      -
     93K  ALA      3.7     4.9    -      -       -      -
     94K  MET*     3.8    26.0    -      -       -      -
    105K  ILE*     5.2     4.3    -      -       +      +
    106K  ILE*     1.3    86.5    -      -       -      +
    108K  GLY*     1.3    59.7    +      -       -      +
    109K  ILE*     3.0    21.3    -      -       +      +
    110K  GLY*     2.9    21.8    +      -       -      -
    111K  ASP*     2.1    41.6    +      -       -      +
    113K  VAL*     5.9     3.8    -      -       +      -
     27L  MET*     5.2     8.1    -      -       +      -
----------------------------------------------------------
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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