Contacts of the strand formed by residues 787 - 793 (chain B) 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 VAL 787 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    665B  THR*     5.0     2.0    -      -       -      -
    666B  VAL*     4.4    20.9    -      -       +      +
    689B  ALA*     5.6     6.3    -      -       +      -
    690B  GLU      3.9     8.7    -      -       -      +
    691B  PRO*     4.4     1.3    -      -       +      -
    692B  LEU*     5.2     1.7    -      -       -      +
    742B  PRO      3.5     3.3    +      -       -      +
    743B  ASN*     3.3    25.1    -      -       -      +
    784B  ILE*     5.8     4.5    -      -       +      -
    785B  ARG*     3.3     8.2    -      -       -      +
    786B  ASN*     1.3    81.7    -      -       -      +
    788B  LYS*     1.3    62.8    +      -       -      +
    789B  PHE      4.3     0.3    +      -       -      -
    820B  PHE*     6.4     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 788 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    689B  ALA*     3.4     5.4    -      -       -      +
    690B  GLU      3.1    34.8    +      -       -      +
    691B  PRO      5.0     4.0    -      -       -      +
    692B  LEU*     5.8     5.1    -      -       +      +
    744B  ILE*     3.3    28.0    -      -       +      +
    745B  LEU*     5.4     0.7    -      -       -      -
    746B  VAL      6.0     0.2    -      -       -      +
    787B  VAL*     1.3    72.5    -      -       -      +
    789B  PHE*     1.3    61.9    +      -       -      +
    790B  LYS*     5.5     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 789 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    687B  MET*     6.3     1.3    -      -       +      -
    688B  ILE      3.7     9.2    -      -       -      +
    689B  ALA*     4.4     6.1    -      -       +      +
    743B  ASN      5.3     0.8    +      -       -      +
    744B  ILE      3.2     7.2    +      -       -      +
    745B  LEU*     3.3    28.8    -      -       +      +
    746B  VAL      3.6     1.6    +      -       -      -
    787B  VAL      4.3     0.2    +      -       -      -
    788B  LYS*     1.3    73.7    -      -       -      +
    790B  LYS*     1.3    59.8    +      -       -      +
    791B  ILE      4.4     0.5    +      -       -      -
    816B  VAL*     5.5    14.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 790 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    687B  MET*     3.3     3.2    -      -       -      +
    688B  ILE*     3.0    35.9    +      -       +      +
    689B  ALA*     6.0     0.4    -      -       -      -
    746B  VAL*     3.3    24.9    -      -       +      +
    749B  THR*     5.1    11.4    -      -       -      -
    788B  LYS      4.2     1.7    +      -       -      +
    789B  PHE*     1.3    74.8    -      -       -      +
    791B  ILE*     1.3    64.6    +      -       -      +
    792B  LEU      3.5     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 791 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    685B  ILE*     6.3     1.3    -      -       +      -
    686B  THR      4.5     2.7    -      -       -      +
    687B  MET*     3.7    11.4    -      -       +      -
    746B  VAL      3.6     8.4    +      -       -      +
    747B  ASP*     4.0    23.2    -      -       +      +
    749B  THR*     4.9     8.7    +      -       -      -
    750B  LEU      5.1     0.9    +      -       -      -
    789B  PHE      4.3     0.4    +      -       -      -
    790B  LYS*     1.3    74.2    -      -       -      +
    792B  LEU*     1.3    63.1    +      -       -      +
    793B  ASP*     4.7     9.2    -      -       -      +
    794B  ALA*     5.5     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 792 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    686B  THR*     2.8    27.0    +      -       -      +
    687B  MET*     3.5     6.5    -      -       -      +
    688B  ILE*     5.1     2.7    -      -       +      +
    749B  THR*     6.1     1.3    -      -       -      -
    750B  LEU*     3.5    31.4    -      -       +      +
    790B  LYS      3.5     4.0    +      -       -      -
    791B  ILE*     1.3    73.1    -      -       -      +
    793B  ASP*     1.3    62.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 793 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    684B  LYS      4.3     2.5    -      -       -      +
    685B  ILE*     3.3     2.3    -      -       -      +
    686B  THR*     2.9    35.0    +      -       -      +
    791B  ILE*     4.7     4.5    -      -       -      +
    792B  LEU*     1.3    79.5    -      -       +      +
    794B  ALA*     1.3    65.1    +      -       -      +
----------------------------------------------------------
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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