Contacts of the strand formed by residues 318 - 322 (chain A) in PDB entry 2FY2


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 CYS 318 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  ILE*     4.0     6.4    -      -       -      +
    102A  PHE*     3.0    41.5    +      -       +      +
    103A  ALA      5.1     2.0    +      -       -      +
    105A  GLN*     3.8    11.9    -      -       +      -
    107A  PHE*     4.0    11.0    -      -       -      -
    116A  PHE*     3.8    26.2    -      -       +      -
    285A  ARG*     5.2     1.6    -      -       -      +
    289A  LEU*     4.3     7.7    -      -       -      +
    311A  VAL*     3.0    11.0    -      -       -      +
    312A  VAL*     3.9    13.9    -      -       -      -
    316A  GLY      3.3    16.3    +      -       -      +
    317A  THR*     1.3    81.7    -      -       -      +
    319A  GLY*     1.3    58.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 319 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100A  VAL      3.2    13.5    -      -       -      -
    102A  PHE*     3.5    23.8    -      -       -      -
    289A  LEU*     3.6    11.3    -      -       -      +
    310A  PHE*     3.4     4.3    -      -       -      +
    311A  VAL      2.7    35.5    +      -       -      +
    318A  CYS*     1.3    76.1    -      -       -      +
    320A  VAL*     1.3    57.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 320 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99A  ALA*     3.5     2.3    -      -       -      +
    100A  VAL*     2.9    52.9    +      -       +      +
    102A  PHE*     4.2     7.4    -      -       +      -
    289A  LEU*     3.6     1.9    -      -       -      +
    308A  LEU*     3.8    19.3    -      -       +      -
    309A  GLN      3.3    14.4    -      -       -      +
    310A  PHE*     3.6    29.2    -      -       +      -
    319A  GLY*     1.3    75.7    -      -       -      +
    321A  VAL*     1.3    75.0    +      -       -      +
    322A  CYS*     3.9     0.9    +      -       -      +
    332A  LEU*     4.6     5.6    -      -       +      -
    336A  THR*     4.0    18.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 321 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97A  SER*     4.4    13.5    -      -       -      +
     98A  PRO      3.8     8.3    -      -       -      +
     99A  ALA*     4.4     1.6    -      -       +      +
    289A  LEU*     3.0    41.1    -      -       +      +
    290A  LEU      5.1     1.8    -      -       -      +
    302A  ARG*     4.3    12.3    -      -       -      +
    304A  TYR*     4.1    18.6    -      -       +      -
    306A  LYS      5.1     0.2    -      -       -      +
    307A  SER      3.5     3.8    -      -       -      +
    308A  LEU*     3.7     1.2    -      -       -      -
    309A  GLN*     2.8    57.5    +      -       +      +
    311A  VAL*     4.2     9.0    -      -       +      -
    320A  VAL*     1.3    74.7    -      -       -      +
    322A  CYS*     1.3    62.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 322 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97A  SER*     3.1    22.3    -      -       -      -
     98A  PRO*     2.9    32.9    +      -       +      +
    307A  SER      3.3     4.3    -      -       -      +
    308A  LEU*     4.4     2.0    -      -       +      -
    320A  VAL      3.9     2.4    +      -       -      +
    321A  VAL*     1.3    74.5    -      -       -      +
    323A  GLU*     1.3    74.1    +      -       -      +
    324A  HIS*     4.3     5.4    -      -       -      -
    327A  PHE*     3.3    38.1    -      -       -      -
    328A  ASP      6.4     0.2    -      -       -      -
    332A  LEU*     3.8    35.0    -      -       +      -
----------------------------------------------------------
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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