Contacts of the strand formed by residues 16 - 21 (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 LYS 16 (chain d).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15d  LYS*     1.3    73.4    -      -       -      +
     17d  LEU*     1.3    58.4    +      -       -      +
     28d  GLN*     6.2     0.4    -      -       -      -
     29d  GLY      4.4     5.2    -      -       -      -
     30d  ILE*     5.0     1.6    -      -       -      +
     72d  ALA*     3.6     6.4    -      -       -      +
     73d  LEU*     3.1    42.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 17 (chain d). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12d  PHE*     5.2    11.2    -      -       +      +
     15d  LYS*     3.4     4.9    +      -       +      +
     16d  LYS*     1.3    73.9    -      -       -      +
     18d  SER*     1.3    61.1    +      -       -      +
     19d  LEU*     4.1     1.2    +      -       -      +
     28d  GLN*     3.4     4.6    -      -       -      +
     29d  GLY      2.9    45.0    +      -       -      +
     31d  LEU*     5.1    11.2    -      -       +      +
     70d  LEU*     6.1     3.6    -      -       +      -
     71d  GLU      3.4     8.5    -      -       -      +
     72d  ALA*     4.2     4.9    -      -       +      +
     73d  LEU      5.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 18 (chain d). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17d  LEU*     1.3    68.2    -      -       -      +
     19d  LEU*     1.3    60.2    +      -       -      +
     20d  LYS      4.3     0.2    +      -       -      -
     27d  VAL      3.8     5.6    -      -       -      -
     28d  GLN*     4.4     8.1    -      -       -      +
     69d  MET      4.1     0.3    -      -       -      +
     70d  LEU*     3.4     5.0    -      -       -      +
     71d  GLU*     2.2    65.7    +      -       -      +
     72d  ALA*     4.4     1.7    -      -       -      +
     73d  LEU*     5.2     6.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 19 (chain d). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17d  LEU      4.1     1.3    +      -       -      +
     18d  SER*     1.3    73.5    -      -       -      +
     20d  LYS*     1.3    60.3    +      -       -      +
     21d  LEU*     4.2     1.7    +      -       +      -
     25d  ARG      4.0     1.4    -      -       -      +
     26d  HIS*     3.8     3.0    -      -       -      +
     27d  VAL*     2.8    47.4    +      -       +      +
     67d  ILE*     6.5     0.7    -      -       +      -
     69d  MET      3.8     7.2    -      -       -      +
     70d  LEU*     4.8     2.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 20 (chain d). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18d  SER      4.3     0.4    +      -       -      -
     19d  LEU*     1.3    73.6    -      -       -      +
     21d  LEU*     1.3    62.0    +      -       -      +
     25d  ARG      4.0     6.5    -      -       -      +
     26d  HIS*     4.9     5.2    -      -       +      +
     67d  ILE*     5.7     0.7    -      -       -      -
     68d  ILE*     3.1    31.8    +      -       +      +
     69d  MET*     3.4    15.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 21 (chain d). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19d  LEU*     4.2     1.9    -      -       +      +
     20d  LYS*     1.3    76.9    -      -       -      +
     22d  ASN*     1.3    64.4    +      -       -      +
     23d  GLY*     3.8    10.8    -      -       -      +
     24d  GLY*     3.2    12.7    +      -       -      -
     25d  ARG*     3.5    15.7    +      -       +      +
     66d  SER*     3.7    19.1    -      -       -      +
     67d  ILE*     5.1     1.8    -      -       -      +
     68d  ILE*     4.7     4.5    -      -       -      +
----------------------------------------------------------
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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