Contacts of the strand formed by residues 2075 - 2082 (chain r) 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 SER2075 (chain r).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1934r  GLY      3.8     5.8    -      -       -      -
   1936r  LEU*     4.1     6.4    -      -       -      +
   2069r  GLY*     3.4     2.9    -      -       -      -
   2070r  ASP*     3.2    39.3    +      -       -      +
   2073r  SER*     4.2    15.5    -      -       -      -
   2074r  ASN*     1.3    77.2    -      -       -      +
   2076r  LEU*     1.3    62.5    +      -       -      +
   2077r  ILE*     3.3     2.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU2076 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1931r  SER*     4.4    16.6    -      -       -      +
   1934r  GLY*     3.3    33.6    +      -       -      +
   1935r  TRP      4.0    12.6    -      -       -      +
   1936r  LEU*     4.0     7.2    -      -       -      +
   1939r  ALA*     5.7     2.2    -      -       +      -
   2068r  ILE      4.3     4.5    -      -       -      +
   2069r  GLY*     4.5     1.3    -      -       -      -
   2075r  SER*     1.3    72.6    -      -       -      +
   2077r  ILE*     1.3    63.0    +      -       -      +
   2078r  SER*     3.5     4.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE2077 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2068r  ILE*     3.1    14.3    +      -       +      +
   2069r  GLY*     3.8    12.6    -      -       -      -
   2070r  ASP*     4.4     6.5    -      -       +      +
   2075r  SER*     3.3     5.5    +      -       -      +
   2076r  LEU*     1.3    75.6    -      -       -      +
   2078r  SER*     1.3    64.9    +      -       -      +
   2094r  PHE*     3.9    18.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER2078 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2067r  VAL*     3.7     2.6    -      -       -      +
   2068r  ILE*     2.9    41.3    +      -       -      +
   2076r  LEU*     3.5     5.1    -      -       -      +
   2077r  ILE*     1.3    80.0    +      -       -      +
   2079r  ILE*     1.3    63.9    +      -       -      +
   2092r  LEU*     4.8    11.7    -      -       -      -
   2093r  ASP      4.0    22.7    -      -       -      -
   2094r  PHE*     4.4     5.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE2079 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1931r  SER*     4.8    19.3    -      -       -      -
   2065r  TRP*     6.5     0.7    -      -       +      -
   2066r  VAL      3.6     9.6    -      -       -      +
   2067r  VAL*     4.2     7.6    -      -       +      +
   2076r  LEU*     6.2     2.0    -      -       +      -
   2078r  SER*     1.3    78.4    -      -       -      +
   2080r  LYS*     1.3    64.8    +      -       -      +
   2092r  LEU*     4.9     7.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS2080 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2065r  TRP*     3.5     6.4    -      -       -      +
   2066r  VAL*     2.9    40.4    +      -       +      +
   2079r  ILE*     1.3    80.1    -      -       -      +
   2081r  ARG*     1.3    63.3    +      -       -      +
   2090r  VAL*     5.9     6.3    -      -       +      -
   2091r  LYS      5.6     2.7    -      -       -      +
   2092r  LEU*     4.9    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG2081 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2064r  TRP      3.4     9.4    -      -       -      +
   2065r  TRP*     5.2     1.8    -      -       +      -
   2080r  LYS*     1.3    78.7    -      -       -      +
   2082r  LEU*     1.3    63.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU2082 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2063r  GLY*     3.8     1.6    -      -       -      -
   2064r  TRP*     2.9    43.5    +      -       +      +
   2081r  ARG*     1.3    77.8    -      -       -      +
   2083r  THR*     1.3    66.2    +      -       -      +
   2084r  LEU*     4.2     1.7    +      -       +      -
----------------------------------------------------------
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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