Contacts of the strand formed by residues 304 - 309 (chain S) 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 LEU 304 (chain S).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30S  ALA*     4.7    25.4    -      -       +      +
     34S  ARG*     4.2    17.5    -      -       -      +
     50S  PRO*     4.4    15.3    -      -       +      -
     51S  LYS      4.1    17.9    -      -       -      +
     52S  ASN*     3.8     9.4    -      -       -      +
     53S  ILE*     5.3     1.1    -      -       +      +
     70S  LEU*     5.3     2.0    -      -       +      -
    252S  GLY      2.7    17.4    +      -       -      +
    253S  ILE*     3.2    16.2    -      -       +      -
    254S  VAL      2.7    32.2    +      -       -      -
    303S  ILE*     1.3    76.9    -      -       -      +
    305S  PHE*     1.3    58.2    +      -       -      +
    306S  ILE*     3.6    34.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 305 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52S  ASN*     2.5    42.9    +      -       +      +
     53S  ILE      3.0    25.8    +      -       -      +
     99S  ILE*     5.8     0.4    -      -       +      -
    100S  ILE*     5.6     1.8    -      -       +      -
    254S  VAL*     3.3    46.2    -      -       +      +
    256S  ILE*     5.0    13.0    -      -       +      -
    285S  LEU*     3.1    47.3    -      -       +      -
    286S  VAL*     3.3    30.7    -      -       +      -
    300S  THR      5.2     1.8    -      -       -      -
    303S  ILE*     4.4    25.1    -      -       +      -
    304S  LEU*     1.3    74.5    -      -       -      +
    306S  ILE*     1.3    68.2    +      -       -      +
    307S  ALA*     4.2     1.1    -      -       +      +
    327S  LEU*     5.0     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 306 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27S  VAL*     5.0     6.7    -      -       +      -
     53S  ILE*     3.3    22.9    -      -       +      +
     55S  MET*     3.2    38.1    -      -       +      -
     67S  ALA*     4.2    14.4    -      -       +      -
     70S  LEU*     4.1    21.3    -      -       +      -
    253S  ILE*     4.4     7.9    -      -       +      -
    254S  VAL      2.7    11.3    +      -       -      +
    255S  PHE*     3.0    20.0    -      -       +      -
    256S  ILE*     2.9    23.3    +      -       -      -
    304S  LEU*     3.6    23.8    -      -       +      -
    305S  PHE*     1.3    81.4    -      -       -      +
    307S  ALA*     1.3    60.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 307 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53S  ILE      2.9     7.5    +      -       -      -
     54S  LEU*     3.2    27.1    -      -       +      +
     55S  MET*     2.7    32.9    +      -       -      +
    256S  ILE*     3.4    24.5    -      -       +      +
    259S  ILE*     4.1    21.7    -      -       +      +
    305S  PHE*     4.2     0.6    -      -       +      -
    306S  ILE*     1.3    74.3    -      -       -      +
    308S  SER*     1.3    55.4    +      -       -      +
    327S  LEU*     5.2     3.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 308 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55S  MET*     3.6     7.0    -      -       -      -
     63S  LYS*     3.0    28.3    +      -       -      -
    255S  PHE*     3.8    18.8    -      -       -      -
    256S  ILE      2.9     7.0    +      -       -      +
    257S  ASP*     2.5    39.1    +      -       -      -
    258S  GLU      3.1     2.7    +      -       -      -
    259S  ILE*     3.0    28.4    +      -       -      +
    306S  ILE      4.1     1.2    +      -       -      -
    307S  ALA*     1.3    74.5    -      -       -      +
    309S  GLY*     1.3    56.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 309 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55S  MET      2.9    11.7    +      -       -      +
     56S  ILE*     3.5     4.2    -      -       -      +
     57S  GLY      3.1    25.9    +      -       -      -
     63S  LYS*     3.9     3.6    -      -       -      +
    258S  GLU*     4.6     3.1    -      -       -      -
    259S  ILE*     4.4     0.7    -      -       -      -
    260S  ASP*     3.0    15.7    -      -       -      -
    308S  SER*     1.3    77.6    -      -       -      +
    310S  ALA*     1.3    64.4    +      -       -      -
    311S  PHE*     3.3    13.2    -      -       -      +
----------------------------------------------------------
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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