Contacts of the strand formed by residues 302 - 307 (chain D) 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 302 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    296D  LEU*     4.2     3.3    -      -       -      +
    297D  HIS*     3.5    29.0    +      -       +      +
    300D  ILE*     3.2     8.9    +      -       +      +
    301D  ASP*     1.3    78.5    -      -       -      +
    303D  LEU*     1.3    63.7    +      -       -      +
    314D  ILE*     5.9     4.9    -      -       +      -
    315D  TRP      3.7     9.9    -      -       -      +
    316D  ASP*     5.1     2.9    -      -       +      -
    317D  VAL*     5.3     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 303 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    295D  ASP      3.6    11.0    -      -       -      +
    296D  LEU*     4.7     3.1    -      -       +      +
    297D  HIS      5.1     0.4    -      -       -      +
    302D  VAL*     1.3    77.8    -      -       -      +
    304D  VAL*     1.3    61.9    +      -       -      +
    314D  ILE*     3.3     7.4    -      -       -      +
    315D  TRP*     2.9    45.6    +      -       +      +
    317D  VAL*     6.0     1.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 304 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294D  LEU*     3.3     3.5    -      -       -      +
    295D  ASP*     2.9    39.7    +      -       +      +
    296D  LEU      5.7     0.2    -      -       -      -
    303D  LEU*     1.3    75.7    -      -       -      +
    305D  THR*     1.3    61.9    +      -       -      +
    312D  ALA*     6.2     2.7    -      -       +      -
    313D  ARG      3.5     7.0    -      -       -      +
    314D  ILE*     5.3     1.8    -      -       +      -
    336D  VAL*     5.3    10.8    -      -       +      -
    337D  ARG      6.1     0.7    -      -       -      +
    338D  CYS*     4.9    17.5    -      -       +      -
    345D  ILE*     5.8     7.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 305 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    293D  GLY      3.5     9.6    -      -       -      -
    294D  LEU*     4.2     6.1    -      -       -      +
    303D  LEU      5.8     0.2    -      -       -      -
    304D  VAL*     1.3    75.9    -      -       -      +
    306D  CYS*     1.3    62.0    +      -       -      +
    307D  SER*     4.1     2.3    +      -       -      -
    312D  ALA*     3.1     6.8    -      -       -      +
    313D  ARG*     2.9    40.3    +      -       -      +
    315D  TRP*     6.1     4.0    -      -       -      -
    336D  VAL*     5.2     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 306 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    291D  VAL*     4.1     2.0    -      -       -      +
    292D  TYR*     3.0     7.1    +      -       -      -
    293D  GLY      2.9    38.0    +      -       -      +
    305D  THR*     1.3    75.2    -      -       -      +
    307D  SER*     1.3    59.6    +      -       -      +
    311D  THR      4.1     3.4    -      -       -      -
    312D  ALA*     4.3     5.8    -      -       +      +
    333D  VAL*     3.8    31.0    -      -       +      +
    335D  THR      4.5     6.7    -      -       -      +
    336D  VAL*     4.0    22.2    -      -       +      +
    347D  THR*     6.0     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 307 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287D  HIS*     5.0    13.9    -      -       -      -
    289D  SER*     5.3     2.0    -      -       -      -
    290D  ALA      3.3    15.5    -      -       -      -
    291D  VAL*     4.2     3.6    -      -       -      +
    292D  TYR*     4.1     8.1    -      -       -      +
    305D  THR*     5.3     2.7    -      -       -      -
    306D  CYS*     1.3    73.1    -      -       -      +
    308D  ARG*     1.3    61.1    +      -       -      +
    309D  ASP*     3.8     4.3    -      -       -      -
    311D  THR*     3.2    24.3    +      -       -      +
    332D  ALA*     4.2     0.3    -      -       -      +
    333D  VAL*     3.3    28.3    +      -       -      +
----------------------------------------------------------
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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