Contacts of the strand formed by residues 30 - 34 (chain A) in PDB entry 1GCD


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 GLN 30 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  TRP*     3.0    22.6    +      -       +      +
     28A  PRO      4.4     3.5    -      -       -      +
     29A  TRP*     1.3    85.2    -      -       +      +
     31A  VAL*     1.3    80.5    +      -       -      +
     43A  GLY*     3.7    17.6    -      -       -      -
     44A  GLY      3.6    10.0    +      -       -      +
     67A  VAL      4.6     0.7    -      -       -      +
     69A  GLY      4.7     8.8    +      -       -      -
     70A  GLU      5.2     2.8    +      -       -      +
    139A  THR*     2.8    46.1    +      -       -      +
    140A  GLY*     3.5     8.0    +      -       -      -
    141A  TRP*     3.6    28.8    -      -       +      -
    155A  LEU*     4.0    14.4    -      -       +      -
    197A  GLY*     4.5     0.8    -      -       -      -
    198A  PRO*     3.5     9.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 31 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  TRP      3.6     2.5    -      -       -      +
     30A  GLN*     1.3    97.0    +      -       -      +
     32A  SER*     1.3    63.4    -      -       -      +
     33A  LEU*     4.1     6.7    -      -       +      -
     43A  GLY*     3.5     1.6    -      -       -      -
     44A  GLY*     3.0    42.6    +      -       -      +
     46A  LEU*     3.4    37.7    -      -       +      -
     52A  VAL*     3.7    16.8    -      -       +      -
     66A  VAL*     4.1    15.3    -      -       +      -
     67A  VAL      3.0    17.0    -      -       -      +
     68A  ALA*     4.0     9.4    -      -       +      -
    141A  TRP*     3.9     5.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 32 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  VAL*     1.3    76.7    -      -       -      +
     33A  LEU*     1.3    63.4    +      -       -      +
     34A  GLN*     2.8    23.1    +      -       -      +
     40A  HIS*     2.7    27.3    +      -       -      -
     42A  CYS      3.7     3.4    -      -       -      -
     65A  VAL      3.6     2.3    -      -       -      +
     66A  VAL*     3.7     1.0    -      -       -      -
     67A  VAL*     2.8    35.0    +      -       -      +
     70A  GLU*     3.2    24.2    +      -       -      -
     73A  GLN*     3.4     3.4    -      -       -      -
    141A  TRP*     3.9     4.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 33 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  VAL*     4.1    14.1    -      -       +      -
     32A  SER*     1.3    76.4    -      -       -      +
     34A  GLN*     1.3    58.6    +      -       -      +
     40A  HIS*     3.3     4.3    -      -       -      -
     41A  PHE*     3.0    43.2    +      -       +      -
     42A  CYS*     2.6    24.3    +      -       +      +
     43A  GLY      3.7    24.2    -      -       -      +
     44A  GLY*     4.2     2.5    -      -       -      +
     54A  THR*     4.6     3.1    -      -       -      +
     60A  VAL*     3.7    36.6    -      -       +      -
     64A  ASP*     4.7     1.3    -      -       +      -
     65A  VAL      3.7    11.2    -      -       -      +
     66A  VAL*     4.1     6.5    -      -       +      -
     85A  ILE*     4.2     3.1    -      -       +      -
    106A  LEU*     3.7    24.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 34 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  SER*     2.8    26.5    +      -       -      +
     33A  LEU*     1.3    73.2    -      -       -      +
     35A  ASP*     1.3    67.1    +      -       -      +
     38A  GLY*     3.5    30.0    -      -       -      +
     39A  PHE      3.2     3.6    -      -       -      +
     40A  HIS*     3.8     7.4    -      -       -      +
     41A  PHE*     3.6     5.6    -      -       -      -
     64A  ASP*     3.4     4.0    -      -       -      -
     65A  VAL*     2.9    38.6    +      -       +      +
     67A  VAL*     3.6    20.5    -      -       +      +
     70A  GLU*     3.1    29.7    +      -       -      +
     73A  GLN*     3.8     6.7    +      -       -      +
     82A  LYS*     5.7     0.7    -      -       -      +
----------------------------------------------------------
 Back to top of page


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