Contacts of the strand formed by residues 348 - 353 (chain A) in PDB entry 6FY5


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 ASN 348 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196A  LYS*     3.3    36.3    +      -       -      +
    198A  SER*     5.2     0.5    +      -       -      -
    307A  LYS*     3.3     4.4    +      -       -      +
    308A  SER*     3.3    11.0    -      -       -      -
    309A  VAL*     3.2    23.4    +      -       -      +
    346A  LEU*     4.6     0.7    -      -       -      +
    347A  LYS*     1.4    91.5    +      -       -      +
    349A  VAL*     1.3    65.3    +      -       -      +
    350A  TYR*     3.6    33.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 349 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195A  GLN*     5.7     0.9    -      -       +      -
    196A  LYS      2.8     8.5    +      -       -      +
    197A  LEU*     3.2    18.8    -      -       +      +
    198A  SER*     2.8    25.3    +      -       -      -
    298A  LEU*     4.3     4.9    -      -       +      -
    309A  VAL*     3.4    16.6    -      -       +      +
    311A  PHE*     3.8    33.0    -      -       +      -
    334A  ILE*     4.2     7.0    -      -       +      -
    338A  PHE*     4.0    30.3    -      -       +      -
    346A  LEU*     5.3     1.3    -      -       +      -
    347A  LYS      5.7     0.7    -      -       -      -
    348A  ASN*     1.3    79.8    -      -       -      +
    350A  TYR*     1.3    65.1    +      -       -      +
    351A  PHE*     4.1    19.2    +      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 350 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179A  PRO*     3.7    23.6    -      -       +      +
    185A  ILE*     3.6    20.0    -      -       +      -
    196A  LYS*     5.4     3.7    +      -       -      -
    198A  SER*     3.3    19.1    -      -       -      -
    200A  THR*     3.3    22.4    -      -       -      +
    211A  ARG      5.2     1.8    +      -       -      -
    212A  VAL*     3.5    26.5    -      -       +      -
    308A  SER*     4.2     7.6    -      -       -      -
    309A  VAL      2.9    16.6    +      -       -      +
    310A  ALA*     3.4    10.0    -      -       +      -
    311A  PHE*     2.9    29.1    +      -       -      +
    348A  ASN*     3.6    37.1    +      -       +      +
    349A  VAL*     1.3    73.7    -      -       -      +
    351A  PHE*     1.3    63.9    +      -       -      +
    352A  LEU*     3.9     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 351 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197A  LEU*     3.8    27.1    -      -       +      -
    198A  SER      3.0    12.5    +      -       -      -
    199A  LEU*     3.5    29.2    -      -       +      -
    200A  THR*     2.8    27.8    +      -       -      +
    311A  PHE*     3.5    11.7    -      +       +      -
    330A  THR*     4.1     9.0    -      -       +      -
    331A  LEU*     3.6    20.6    -      -       +      -
    334A  ILE*     3.5    33.4    -      -       +      -
    349A  VAL*     4.1    13.7    -      -       +      -
    350A  TYR*     1.3    75.3    -      -       -      +
    352A  LEU*     1.3    60.1    +      -       -      +
    353A  LEU*     3.6     6.1    +      -       +      +
    362A  TYR*     3.8    19.7    -      +       +      -
    366A  MET*     5.0     1.6    -      -       -      -
   1001A  EDO      3.8    19.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 352 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179A  PRO*     6.2     0.4    -      -       +      -
    183A  PHE*     4.1    11.7    -      -       +      -
    200A  THR*     4.2    10.1    -      -       +      -
    202A  SER*     3.3    26.0    -      -       -      +
    204A  ILE*     4.1    11.9    -      -       +      -
    207A  ILE*     3.8    29.4    -      -       +      -
    210A  MET*     3.9    22.4    -      -       -      -
    215A  ILE*     5.1     2.0    -      -       +      -
    310A  ALA*     4.1    17.0    -      -       +      -
    311A  PHE      2.9    16.1    +      -       -      +
    312A  PRO*     4.1    17.9    -      -       +      -
    313A  PRO*     3.3    16.5    -      -       -      +
    350A  TYR*     4.3     6.7    -      -       +      -
    351A  PHE*     1.3    72.1    -      -       -      +
    353A  LEU*     1.3    58.2    +      -       -      +
   1001A  EDO      2.8    19.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 353 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186A  LEU*     5.7     0.4    -      -       +      -
    199A  LEU*     4.0    33.2    -      -       +      -
    200A  THR      2.9    12.3    +      -       -      +
    201A  GLN*     3.3     5.2    -      -       -      -
    202A  SER*     2.9    24.1    +      -       -      -
    313A  PRO*     4.6     9.0    -      -       +      -
    351A  PHE*     4.0     8.7    -      -       +      +
    352A  LEU*     1.3    75.8    -      -       -      +
    354A  PHE*     1.3    63.0    +      -       -      +
    355A  ASP      4.9     0.7    -      -       -      +
    358A  SER*     4.0    22.7    -      -       -      -
    359A  ILE*     3.8    28.3    -      -       +      -
    362A  TYR*     4.1    23.6    -      -       +      -
   1001A  EDO      3.7    28.7    -      -       -      +
----------------------------------------------------------
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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