Contacts of the strand formed by residues 341 - 346 (chain F) in PDB entry 6FF7


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 ILE 341 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    334F  ALA      3.8     0.2    -      -       -      +
    335F  PHE*     3.5     4.5    -      -       -      +
    336F  HIS*     2.9    45.8    +      -       +      +
    339F  GLU*     2.7    14.6    +      -       +      +
    340F  PRO*     1.3    73.9    -      -       -      +
    342F  ILE*     1.3    60.9    +      -       -      +
    343F  ILE      4.1     0.6    +      -       -      -
    353F  MET*     5.7     6.7    -      -       +      -
    354F  GLY      3.2     8.1    -      -       -      +
    355F  GLU*     4.6     3.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 342 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    333F  VAL*     6.3     2.5    -      -       +      -
    334F  ALA      3.3     8.1    -      -       -      +
    335F  PHE*     4.8     1.1    -      -       -      +
    340F  PRO      4.3     0.4    +      -       -      -
    341F  ILE*     1.3    74.2    -      -       -      +
    343F  ILE*     1.3    61.1    +      -       -      +
    344F  SER*     3.7     3.5    +      -       -      -
    352F  TYR      3.1     5.0    -      -       -      +
    353F  MET*     3.4     3.0    -      -       -      -
    354F  GLY*     2.8    43.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 343 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72F  CYS*     5.3    12.0    -      -       +      +
     73F  LYS      6.4     1.6    -      -       -      -
    332F  GLU      3.7     1.7    -      -       -      +
    333F  VAL*     3.4     4.6    -      -       -      +
    334F  ALA*     2.8    50.1    +      -       +      +
    341F  ILE      4.1     1.2    +      -       -      -
    342F  ILE*     1.3    72.1    -      -       -      +
    344F  SER*     1.3    61.0    +      -       -      +
    345F  ALA*     4.0     1.0    +      -       -      +
    351F  LEU*     6.2     2.7    -      -       +      -
    352F  TYR      3.4     6.5    -      -       -      +
    353F  MET*     4.9     1.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 344 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    309F  VAL*     5.2    14.4    -      -       -      -
    330F  ILE*     6.1     4.5    -      -       -      -
    332F  GLU      3.8     3.4    -      -       -      -
    333F  VAL*     4.7     5.6    -      -       -      +
    342F  ILE*     3.7     3.8    +      -       -      -
    343F  ILE*     1.3    74.1    -      -       -      +
    345F  ALA*     1.3    59.5    +      -       -      +
    346F  SER*     5.5     0.8    -      -       -      -
    350F  ARG      3.9     1.7    -      -       -      +
    351F  LEU*     3.4    10.7    -      -       -      +
    352F  TYR*     3.1    37.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 345 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69F  VAL*     4.5    18.4    -      -       +      +
     71F  CYS*     4.6     8.1    -      -       -      +
     72F  CYS*     4.1    24.2    -      -       +      -
    330F  ILE*     3.7     3.7    -      -       -      +
    331F  ASN      2.8    21.7    +      -       -      -
    332F  GLU*     2.9    24.6    +      -       +      +
    343F  ILE      4.0     0.2    +      -       -      -
    344F  SER*     1.3    74.1    -      -       -      +
    346F  SER*     1.3    61.9    +      -       -      +
    350F  ARG      4.4     2.9    -      -       -      -
    351F  LEU*     5.1     3.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 346 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69F  VAL*     3.3    28.8    +      -       -      +
    326F  HIS*     4.5    18.8    -      -       -      -
    328F  GLY      4.7     0.7    -      -       -      -
    329F  SER      3.2    16.6    -      -       -      -
    330F  ILE*     3.8     8.3    -      -       -      -
    331F  ASN      3.9     3.4    -      -       -      +
    344F  SER      5.5     0.4    -      -       -      -
    345F  ALA*     1.3    77.2    -      -       -      +
    347F  SER*     1.3    62.4    -      -       -      +
    348F  ASP*     3.1    12.6    +      -       -      -
    349F  LYS*     3.3     8.4    +      -       -      -
    350F  ARG      4.0    12.0    +      -       -      -
----------------------------------------------------------
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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