Contacts of the strand formed by residues 304 - 309 (chain D) 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 D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30D  ALA*     4.3    27.1    -      -       +      -
     31D  LEU*     4.8     7.0    -      -       +      +
     34D  ARG*     3.4    22.5    -      -       -      +
     50D  PRO*     4.3     8.5    -      -       +      -
     51D  LYS      4.8     2.7    -      -       -      +
     52D  ASN*     3.7    22.7    -      -       -      +
     53D  ILE*     4.6     4.0    -      -       +      +
     70D  LEU*     4.5    13.2    -      -       +      -
    252D  GLY      2.8    13.3    +      -       -      +
    253D  ILE*     3.3    26.6    -      -       +      +
    254D  VAL      2.9    26.0    +      -       -      -
    303D  ILE*     1.3    72.7    -      -       -      +
    305D  PHE*     1.3    78.1    +      -       -      +
    306D  ILE*     4.4     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 305 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52D  ASN*     2.7    30.4    +      -       +      +
     53D  ILE      2.9    24.4    +      -       -      +
     99D  ILE*     6.3     0.2    -      -       +      -
    100D  ILE*     4.5     6.7    -      -       +      -
    254D  VAL*     3.5    36.1    -      -       +      -
    256D  ILE*     4.1    18.2    -      -       +      -
    285D  LEU*     3.9    26.2    -      -       +      -
    286D  VAL*     3.7    46.9    -      -       +      -
    300D  THR*     4.3     3.6    -      -       -      -
    303D  ILE*     3.5    35.7    -      -       +      -
    304D  LEU*     1.3    74.3    -      -       -      +
    306D  ILE*     1.3    64.5    +      -       -      +
    307D  ALA*     4.0     0.7    -      -       +      -
    327D  LEU*     5.0     4.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 306 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27D  VAL*     4.0    19.3    -      -       +      -
     53D  ILE*     3.2    22.2    -      -       +      +
     55D  MET*     3.1    35.0    -      -       +      -
     67D  ALA*     3.9    17.9    -      -       +      -
     70D  LEU*     4.2     7.6    -      -       +      -
     78D  PHE*     5.6     0.2    -      -       +      -
    253D  ILE*     3.7    28.0    -      -       +      -
    254D  VAL      2.8     9.5    +      -       -      +
    255D  PHE*     3.2    20.7    -      -       +      -
    256D  ILE*     2.8    25.4    +      -       -      -
    304D  LEU*     4.4     5.6    -      -       +      -
    305D  PHE*     1.3    77.3    -      -       -      +
    307D  ALA*     1.3    60.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 307 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53D  ILE      2.6    11.2    +      -       -      +
     54D  LEU*     3.1    19.2    -      -       +      -
     55D  MET*     2.7    27.4    +      -       -      +
    256D  ILE*     3.4    10.5    -      -       +      -
    259D  ILE*     3.9    27.6    -      -       +      -
    305D  PHE*     4.0     1.5    -      -       +      -
    306D  ILE*     1.3    74.7    -      -       -      +
    308D  SER*     1.3    62.9    +      -       -      +
    327D  LEU*     4.0    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 308 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54D  LEU*     4.4     4.9    -      -       -      -
     55D  MET*     3.3     8.7    -      -       -      -
     63D  LYS*     3.7    18.4    -      -       -      -
    255D  PHE*     3.5    23.3    -      -       -      -
    256D  ILE      3.0     6.5    +      -       -      -
    257D  ASP*     2.5    31.4    +      -       -      -
    258D  GLU      3.1     2.9    +      -       -      -
    259D  ILE*     3.0    24.8    +      -       -      +
    307D  ALA*     1.3    75.8    -      -       -      +
    309D  GLY*     1.3    59.8    +      -       -      +
    453D  ATP      4.0     3.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 309 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55D  MET      3.2     4.8    +      -       -      -
     56D  ILE*     3.3     8.1    -      -       -      -
     57D  GLY      3.0    21.9    +      -       -      -
     63D  LYS*     4.3     5.4    -      -       -      +
    258D  GLU*     4.3     4.0    -      -       -      -
    260D  ASP*     3.2    18.6    -      -       -      -
    308D  SER*     1.3    79.3    +      -       -      +
    310D  ALA*     1.3    62.0    +      -       -      -
    311D  PHE*     3.4    11.9    -      -       -      -
    453D  ATP      5.7     1.1    -      -       -      -
----------------------------------------------------------
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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