Contacts of the strand formed by residues 333 - 338 (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 333 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    292D  TYR*     3.8     9.5    -      -       -      +
    306D  CYS*     3.8    25.0    -      -       +      +
    307D  SER      3.3    17.9    +      -       -      +
    310D  SER      5.6     3.1    -      -       -      +
    311D  THR      4.8    10.3    -      -       -      +
    312D  ALA*     5.6     1.8    -      -       +      -
    331D  ASN      3.9     1.3    +      -       -      +
    332D  ALA*     1.3    75.5    -      -       -      +
    334D  ALA*     1.3    66.1    +      -       -      +
    335D  THR      3.7     2.0    -      -       -      +
    347D  THR*     5.2     9.4    -      -       -      -
    348D  GLY      4.2     5.8    -      -       -      +
    349D  SER*     3.7    14.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 334 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    292D  TYR*     3.9    17.1    -      -       -      +
    293D  GLY*     4.3     7.3    +      -       -      -
    306D  CYS*     4.9     0.7    -      -       -      -
    332D  ALA      4.1     2.0    +      -       -      -
    333D  VAL*     1.3    74.8    -      -       -      +
    335D  THR*     1.3    59.1    +      -       -      +
    348D  GLY      2.9    10.6    +      -       -      +
    349D  SER*     4.1     2.2    -      -       -      +
    350D  HIS*     5.5     2.7    -      -       +      +
    375D  VAL      3.8     8.1    -      -       -      +
    376D  ARG*     3.8    34.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 335 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    293D  GLY*     5.4     3.6    -      -       -      -
    306D  CYS*     4.5     6.7    -      -       -      +
    333D  VAL*     4.9     0.3    -      -       -      +
    334D  ALA*     1.3    79.2    -      -       -      +
    336D  VAL*     1.3    65.0    +      -       -      +
    347D  THR*     3.9     2.3    -      -       -      -
    348D  GLY*     3.5    26.0    +      -       -      +
    376D  ARG      3.8    21.1    -      -       -      -
    377D  ALA*     4.6     7.2    -      -       -      -
    378D  VAL*     4.6    11.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 336 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    293D  GLY*     5.6     2.2    -      -       -      +
    294D  LEU      4.4     9.3    -      -       -      +
    295D  ASP*     3.5    20.0    -      -       +      +
    304D  VAL*     5.3    11.9    -      -       +      +
    305D  THR      5.2     2.2    -      -       -      -
    306D  CYS*     4.0    23.1    -      -       +      +
    312D  ALA*     5.7     3.6    -      -       +      -
    335D  THR*     1.3    78.6    -      -       -      +
    337D  ARG*     1.3    61.5    +      -       -      +
    346D  ILE      3.4    11.2    -      -       -      +
    347D  THR*     5.0     5.4    -      -       -      -
    378D  VAL*     5.9     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 337 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    295D  ASP*     4.2     6.5    -      -       -      -
    304D  VAL*     6.1     0.9    -      -       -      -
    336D  VAL*     1.3    75.0    -      -       -      +
    338D  CYS*     1.3    63.2    +      -       -      +
    344D  GLN      3.7     1.1    -      -       -      +
    345D  ILE*     3.6     1.7    -      -       -      +
    346D  ILE*     3.0    40.5    +      -       +      +
    378D  VAL*     4.9    15.9    -      -       +      +
    379D  VAL*     5.2     2.7    -      -       -      +
    380D  LEU*     5.2    17.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 338 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    295D  ASP*     4.4     6.9    -      -       +      +
    296D  LEU      3.8    24.2    -      -       -      +
    297D  HIS*     4.8     6.9    -      -       +      -
    298D  PRO*     5.2     1.0    -      -       -      +
    304D  VAL*     4.9    17.0    -      -       +      -
    337D  ARG*     1.3    76.9    -      -       -      +
    339D  GLN*     1.3    64.3    +      -       -      +
    344D  GLN*     3.3    18.2    -      -       +      +
    345D  ILE*     4.5     5.4    -      -       +      -
----------------------------------------------------------
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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