Contacts of the strand formed by residues 84 - 90 (chain K) in PDB entry 1FSK


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 ALA 84 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37K  GLN*     3.7    21.8    -      -       +      -
     38K  GLN      3.6    14.1    -      -       -      +
     39K  LYS*     4.0     7.2    -      -       +      +
     40K  PRO*     5.1     2.7    -      -       -      -
     82K  ASP      3.1     5.7    +      -       -      +
     83K  LEU*     1.3    78.8    -      -       -      +
     85K  ASP*     1.3    61.6    +      -       -      +
     86K  TYR*     3.6    17.9    -      -       +      +
    103K  LYS*     3.7     5.4    -      -       -      +
    104K  LEU*     2.8    35.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 85 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38K  GLN*     2.8    48.0    +      -       +      +
     84K  ALA*     1.3    73.9    -      -       -      +
     86K  TYR*     1.3    64.0    +      -       -      +
     87K  HIS*     3.3    29.5    +      -       -      +
    100K  GLY      5.0     1.2    -      -       -      +
    101K  GLY*     3.7     3.0    -      -       -      -
    102K  THR      3.2    26.8    +      -       -      -
    103K  LYS*     3.6    13.6    +      -       +      +
     39L  GLN*     5.7     0.3    +      -       -      -
     43L  GLN      5.3     2.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 86 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6K  GLN*     3.5     6.8    +      -       -      +
     21K  LEU*     4.7    10.8    -      -       +      -
     35K  TRP*     5.0     3.4    -      -       +      -
     36K  PHE      3.3     9.4    -      -       -      +
     37K  GLN*     3.1    38.3    +      -       +      -
     47K  LEU*     3.7    18.4    -      -       +      -
     62K  PHE*     3.8    12.3    -      +       -      -
     73K  LEU*     3.7    25.6    -      -       +      -
     75K  ILE*     4.4     5.2    -      -       +      -
     82K  ASP*     2.7    38.1    +      -       -      +
     84K  ALA*     3.6    16.8    -      -       +      -
     85K  ASP*     1.3    76.0    +      -       -      +
     87K  HIS*     1.3    59.6    +      -       -      +
    101K  GLY*     3.3     4.2    -      -       -      -
    102K  THR*     3.1    40.6    +      -       +      +
    104K  LEU*     3.7    23.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 87 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6K  GLN*     3.5     2.2    -      -       -      +
     35K  TRP*     3.1    17.9    -      -       -      -
     36K  PHE*     2.7    56.0    +      -       +      -
     38K  GLN*     3.4    26.9    +      -       +      -
     44K  PRO*     5.0     0.7    -      -       +      -
     85K  ASP*     3.3    41.5    +      -       -      -
     86K  TYR*     1.3    73.1    -      -       -      +
     88K  CYS*     1.3    62.3    +      -       -      +
     98K  PHE*     5.5     0.4    -      -       +      -
     99K  GLY      4.1     6.8    +      -       -      +
    100K  GLY      4.3     4.9    -      -       -      -
    101K  GLY*     3.5    19.4    +      -       -      -
     39L  GLN*     4.5     0.8    +      -       -      -
     43L  GLN      4.8     3.4    -      -       -      -
     44L  GLY*     4.6    10.1    -      -       -      -
     45L  LEU*     4.0    29.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 88 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4K  LEU*     3.8     1.3    -      -       +      -
      6K  GLN*     3.2    14.1    -      -       -      +
     23K  CYS*     2.8    50.9    -      -       -      -
     33K  VAL*     4.5     7.6    -      -       -      -
     34K  PHE      3.6     3.4    -      -       -      -
     35K  TRP*     3.5    32.5    -      -       -      -
     36K  PHE*     5.1     1.6    -      -       -      -
     87K  HIS*     1.3    74.4    -      -       -      +
     89K  GLY*     1.3    60.0    +      -       -      +
     98K  PHE*     2.8    14.6    -      -       -      +
     99K  GLY      2.6    27.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 89 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4K  LEU*     3.5     4.0    -      -       -      -
     33K  VAL*     3.2     5.9    -      -       -      +
     34K  PHE*     3.0    59.9    +      -       -      -
     88K  CYS*     1.3    76.6    -      -       -      +
     90K  GLN*     1.3    58.9    +      -       -      -
     97K  THR      3.3    10.3    -      -       -      -
     98K  PHE*     4.0     4.5    -      -       -      -
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Residues in contact with GLN 90 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2K  ILE*     3.9    16.9    -      -       +      +
      4K  LEU*     3.5    22.2    -      -       +      +
     29K  VAL*     4.4    10.5    -      -       +      -
     32K  TYR      2.9    11.2    -      -       -      +
     33K  VAL*     4.4     4.5    -      -       +      -
     34K  PHE*     3.8     3.8    -      -       -      -
     89K  GLY*     1.3    74.3    -      -       -      -
     91K  SER*     1.3    59.9    +      -       -      +
     92K  TYR*     2.7    32.6    +      -       -      +
     93K  SER*     3.1    15.6    +      -       -      -
     95K  PRO      3.0    27.5    +      -       -      -
     96K  TYR*     3.5    18.2    -      -       -      +
     97K  THR*     3.1    35.1    +      -       -      +
----------------------------------------------------------
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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