Contacts of the strand formed by residues 207 - 210 (chain A) in PDB entry 3GW5


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 GLY 207 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205A  MET*     3.4     4.8    -      -       -      +
    206A  LYS*     1.3    82.8    -      -       -      +
    208A  VAL*     1.3    67.6    +      -       -      +
    209A  SER*     4.3     1.6    -      -       -      -
    214A  THR*     4.7    10.3    -      -       -      -
    216A  LEU      3.8     2.7    -      -       -      -
    217A  CYS*     3.5    17.0    -      -       -      -
    269A  SER      3.9     0.3    -      -       -      +
    271A  HIS*     2.9    33.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 208 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205A  MET*     3.5    29.2    -      -       +      -
    207A  GLY*     1.3    78.8    -      -       -      +
    209A  SER*     1.3    64.4    +      -       -      +
    210A  VAL*     4.1     1.2    +      -       +      +
    214A  THR*     4.7     1.5    -      -       -      +
    215A  LEU*     3.4     3.5    +      -       -      +
    216A  LEU*     3.1    49.3    +      -       +      +
    217A  CYS*     4.1     5.4    -      -       +      -
    242A  LEU*     4.8     1.3    -      -       +      -
    268A  ILE*     4.1    14.1    -      -       +      -
    269A  SER      3.3     8.7    -      -       -      +
    270A  PHE*     3.8    23.3    -      -       +      -
    313A  TRP*     3.9    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 209 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207A  GLY      5.2     1.0    -      -       -      -
    208A  VAL*     1.3    74.6    +      -       -      +
    210A  VAL*     1.3    62.5    +      -       -      +
    211A  GLY      4.1    10.7    -      -       -      +
    212A  SER      4.6     2.5    -      -       -      -
    213A  SER      3.8     6.5    -      -       -      -
    214A  THR*     3.2    30.4    +      -       -      +
    267A  ASP      3.7     0.2    -      -       -      +
    268A  ILE*     3.1    10.0    -      -       -      +
    269A  SER*     2.7    49.3    +      -       -      -
    271A  HIS*     6.0     1.6    -      -       -      +
    276A  GLU*     4.1    12.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 210 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208A  VAL*     4.1     1.7    +      -       +      +
    209A  SER*     1.3    76.1    -      -       -      +
    211A  GLY*     1.3    65.9    +      -       -      +
    212A  SER      3.2     3.1    +      -       -      -
    213A  SER*     3.3    21.9    +      -       -      +
    215A  LEU*     4.4    21.5    -      -       +      +
    216A  LEU*     4.8     5.8    -      -       +      -
    242A  LEU*     4.4    27.6    -      -       +      -
    245A  ALA*     4.0    24.5    -      -       +      -
    246A  LEU*     4.0     9.0    -      -       +      -
    266A  PRO*     3.7    24.2    -      -       +      -
    267A  ASP      3.5     4.3    -      -       -      +
    268A  ILE*     4.7     6.1    -      -       +      -
----------------------------------------------------------
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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