Contacts of the strand formed by residues 247 - 251 (chain C) in PDB entry 6F0X


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 VAL 247 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208C  GLN*     3.9     2.2    -      -       -      +
    210C  ILE*     4.2    15.0    -      -       +      -
    236C  ILE*     4.3    15.9    -      -       +      -
    239C  LEU*     3.8    15.3    -      -       +      +
    240C  ILE*     3.6    37.7    -      -       +      +
    245C  ALA*     5.5     1.1    -      -       +      -
    246C  LEU*     1.3    76.2    -      -       -      +
    248C  PHE*     1.3    71.1    +      -       -      +
    249C  VAL*     3.9     4.7    -      -       +      +
    292C  ASN*     3.7     9.9    +      -       -      +
    293C  VAL*     3.6    34.1    -      -       +      -
    294C  VAL*     2.9    23.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 248 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127C  LEU*     4.8    13.5    -      -       +      -
    153C  VAL*     5.7     0.2    -      -       +      -
    192C  LEU*     5.9     0.4    -      -       +      -
    193C  ALA*     4.1    23.1    -      -       +      -
    196C  LEU*     3.6    38.4    -      -       +      -
    197C  THR*     5.3     2.2    -      -       -      -
    208C  GLN      2.9    19.7    +      -       -      +
    209C  LEU*     3.1    18.8    -      -       +      +
    210C  ILE*     2.8    28.4    +      -       -      +
    246C  LEU*     3.1    63.0    -      -       +      -
    247C  VAL*     1.3    76.0    -      -       -      +
    249C  VAL*     1.3    66.6    +      -       -      +
    294C  VAL*     3.5    21.3    -      -       +      -
    296C  LEU*     5.0     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 249 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210C  ILE*     4.2     8.3    -      -       +      -
    212C  ILE*     4.1     8.1    -      -       +      -
    233C  PHE*     5.8     2.9    -      -       +      -
    236C  ILE*     4.4    28.7    -      -       +      -
    247C  VAL*     3.9     2.7    -      -       +      -
    248C  PHE*     1.3    73.6    -      -       -      +
    250C  LEU*     1.3    62.0    +      -       -      +
    251C  ILE*     3.6    29.2    -      -       +      -
    293C  VAL*     4.2    14.1    -      -       +      -
    294C  VAL      2.9     8.2    +      -       -      +
    295C  ILE*     3.6    38.6    -      -       +      -
    296C  LEU*     2.8    29.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 250 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186C  THR*     4.8     9.4    -      -       +      -
    189C  CYS*     3.7    30.3    -      -       +      -
    190C  LYS*     4.5    20.2    -      -       +      +
    209C  LEU*     3.7    31.0    -      -       +      -
    210C  ILE      2.9    17.6    +      -       -      +
    211C  GLU*     3.9    24.4    -      -       -      +
    212C  ILE*     2.9    23.8    +      -       -      +
    249C  VAL*     1.3    75.2    -      -       -      +
    251C  ILE*     1.3    59.5    +      -       -      +
    252C  ASP*     3.5    12.7    +      -       +      +
    296C  LEU*     3.8    16.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 251 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212C  ILE*     3.6    25.8    -      -       +      -
    214C  SER*     5.1     2.2    -      -       -      -
    232C  MET*     5.9     0.4    -      -       +      -
    233C  PHE*     5.0    14.8    -      -       +      -
    249C  VAL*     3.6    26.2    -      -       +      -
    250C  LEU*     1.3    70.6    -      -       -      +
    252C  ASP*     1.3    64.3    +      -       -      +
    253C  GLN      3.3     1.0    +      -       -      -
    254C  VAL*     3.2    38.7    -      -       +      +
    257C  LEU*     3.5    34.5    -      -       +      -
    280C  VAL*     5.4     2.0    -      -       +      -
    284C  ILE*     5.9     2.7    -      -       +      -
    295C  ILE*     4.3    11.0    -      -       +      -
    296C  LEU      2.9    18.5    +      -       -      +
    297C  THR*     3.7     8.0    -      -       +      -
    298C  THR      4.0     0.2    +      -       -      -
    309C  PHE*     5.6     4.3    -      -       +      -
----------------------------------------------------------
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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