Contacts of the strand formed by residues 330 - 335 (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 330 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287F  ASN*     5.9     2.1    -      -       -      +
    288F  LEU      5.4     0.3    -      -       -      +
    289F  LEU*     5.7     2.9    -      -       -      +
    303F  GLY*     4.1    10.3    -      -       -      -
    304F  SER      2.8    38.4    +      -       -      +
    307F  ARG      5.1     4.4    -      -       -      +
    308F  PHE      5.0     8.7    -      -       -      +
    309F  VAL*     5.9     1.8    -      -       -      -
    328F  GLY      3.7     1.7    +      -       -      +
    329F  SER*     1.3    75.0    -      -       -      +
    331F  ASN*     1.3    61.9    +      -       -      +
    332F  GLU      5.0     2.2    -      -       -      +
    344F  SER*     6.1     4.3    -      -       -      -
    345F  ALA      3.7     9.9    -      -       -      +
    346F  SER*     3.8     6.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 331 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69F  VAL      3.6    24.2    -      -       -      +
     70F  TYR*     3.6    17.3    -      -       +      +
    287F  ASN*     5.7     5.8    -      -       +      -
    288F  LEU      4.1    16.4    -      -       -      +
    289F  LEU*     4.5     0.7    -      -       -      +
    290F  ARG*     3.8    22.3    +      -       -      +
    303F  GLY*     5.3     2.7    -      -       -      -
    329F  SER      3.9     1.7    +      -       -      +
    330F  ILE*     1.3    74.8    -      -       -      +
    332F  GLU*     1.3    61.2    +      -       -      +
    345F  ALA      2.8    10.8    +      -       -      +
    346F  SER*     4.7     2.0    -      -       -      -
    347F  SER*     5.3     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 332 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70F  TYR      3.9    13.0    -      -       -      +
     71F  CYS*     4.2    14.1    -      -       +      -
     72F  CYS*     4.4    11.8    -      -       +      +
    290F  ARG*     4.6    15.7    -      -       +      -
    303F  GLY*     5.5     3.6    -      -       -      -
    330F  ILE*     3.8     2.3    -      -       -      +
    331F  ASN*     1.3    81.5    -      -       -      +
    333F  VAL*     1.3    63.2    +      -       -      +
    343F  ILE      3.7     1.6    -      -       -      +
    344F  SER*     3.8     0.7    -      -       -      -
    345F  ALA*     2.9    38.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 333 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    290F  ARG      4.7     5.4    +      -       -      +
    291F  CYS*     4.9     1.6    -      -       -      -
    292F  SER*     3.3    24.1    +      -       -      -
    301F  ALA*     4.1    25.1    -      -       +      +
    302F  ALA*     4.7     2.0    -      -       -      +
    303F  GLY*     4.6    15.7    -      -       -      +
    309F  VAL*     5.9     7.4    -      -       +      -
    332F  GLU*     1.3    77.3    -      -       -      +
    334F  ALA*     1.3    60.1    +      -       -      +
    342F  ILE*     6.3     2.9    -      -       +      -
    343F  ILE      3.4     5.6    -      -       -      +
    344F  SER*     4.7     6.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 334 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72F  CYS*     4.0    21.1    -      -       +      +
     73F  LYS*     4.6    10.1    -      -       -      -
     74F  PHE*     4.9     6.3    -      -       +      +
    292F  SER*     4.6     4.3    -      -       -      -
    301F  ALA*     6.3     1.3    -      -       -      -
    332F  GLU      4.2     0.4    -      -       -      -
    333F  VAL*     1.3    75.2    -      -       -      +
    335F  PHE*     1.3    62.2    +      -       -      +
    336F  HIS      4.2     0.2    +      -       -      -
    342F  ILE*     3.3     7.6    -      -       -      +
    343F  ILE*     2.8    48.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 335 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74F  PHE*     4.3    11.8    -      -       -      +
    292F  SER*     5.0     4.6    -      -       -      -
    293F  TRP      4.4     7.0    -      -       -      +
    294F  SER*     4.2    26.9    -      -       -      -
    295F  PRO*     4.7     2.9    -      -       -      +
    334F  ALA*     1.3    74.5    -      -       -      +
    336F  HIS*     1.3    69.1    +      -       -      +
    337F  PRO*     3.5     3.5    -      -       -      +
    341F  ILE      3.5     5.4    -      -       -      +
    342F  ILE*     4.8     1.3    -      -       +      +
----------------------------------------------------------
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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