Contacts of the strand formed by residues 103 - 107 (chain L) 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 L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5L  SER*     4.2    11.4    +      -       -      -
      7L  ARG*     3.8    11.5    +      -       -      +
     12L  VAL*     4.3     2.1    -      -       -      +
     96L  ILE*     5.4     0.2    -      -       -      +
     97L  VAL      3.4     6.3    -      -       -      -
     98L  ALA*     3.4    13.4    -      -       -      +
    102L  GLU*     1.3    82.0    +      -       -      +
    104L  LEU*     1.3    74.8    +      -       -      +
    115L  PRO*     3.3    21.0    -      -       -      +
    119L  GLN*     3.7    25.3    +      -       -      +
    121L  LEU*     3.9    14.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 104 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    443F  ILE*     4.7     4.9    -      -       +      -
     71L  LEU*     3.6    17.2    -      -       +      +
     72L  LEU*     3.5    36.8    -      -       +      -
     75L  ALA*     3.7    21.8    -      -       +      -
     96L  ILE*     3.3     4.9    -      -       -      -
     97L  VAL*     2.6    47.4    +      -       +      +
    102L  GLU*     4.0     8.1    -      -       +      +
    103L  SER*     1.3    96.8    -      -       -      +
    105L  ILE*     1.3    61.2    +      -       -      +
    106L  ILE*     5.1     0.9    -      -       +      -
    112L  VAL*     4.7     4.7    -      -       +      -
    113L  VAL      3.7    21.1    -      -       -      +
    114L  GLN*     4.3    13.5    -      -       +      -
    121L  LEU*     3.5    10.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 105 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27G  MET*     4.2    24.9    -      -       +      -
     94L  MET*     5.0     5.8    -      -       +      -
     95L  LEU      3.3    13.9    -      -       -      +
     96L  ILE*     4.3     4.9    -      -       +      -
    104L  LEU*     1.3    78.4    -      -       -      +
    106L  ILE*     1.3    64.6    +      -       -      +
    107L  THR*     5.1     3.4    -      -       +      +
    111L  ASP      3.8     1.0    -      -       -      +
    112L  VAL*     3.5     3.3    -      -       -      -
    113L  VAL*     3.0    55.2    +      -       +      +
    121L  LEU*     4.2    20.6    -      -       +      -
    122L  ALA      4.4     5.2    -      -       -      +
    123L  ILE*     3.3    30.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 106 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56L  LEU*     3.8     7.3    -      -       +      +
     60L  PHE*     3.5    41.3    -      -       +      -
     75L  ALA*     3.9    21.5    -      -       +      +
     78L  LEU*     4.6    20.0    -      -       +      -
     79L  ALA*     5.4     1.8    -      -       +      -
     82L  TRP*     5.3     2.7    -      -       +      -
     94L  MET*     3.2     3.3    -      -       -      -
     95L  LEU*     2.7    46.9    +      -       +      +
     97L  VAL*     4.2    17.0    -      -       +      -
    104L  LEU*     5.1     0.7    -      -       +      -
    105L  ILE*     1.3    78.2    -      -       -      +
    107L  THR*     1.3    75.2    +      -       -      +
    111L  ASP      3.6    12.1    -      -       -      +
    112L  VAL*     4.4     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 107 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27G  MET*     5.4     8.1    -      -       +      -
     56L  LEU*     4.4     2.9    -      -       -      -
     82L  TRP*     4.2     4.9    -      -       -      -
     93L  ALA      3.7     4.0    -      -       -      -
     94L  MET*     4.1    24.7    -      -       -      +
    105L  ILE*     5.1     4.5    -      -       +      +
    106L  ILE*     1.3    86.6    -      -       -      +
    108L  GLY*     1.3    58.9    +      -       -      +
    109L  ILE*     2.8    24.0    -      -       +      +
    110L  GLY*     3.0    17.3    +      -       -      -
    111L  ASP*     2.2    40.6    +      -       -      +
    113L  VAL*     5.7     4.7    -      -       +      -
----------------------------------------------------------
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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