Contacts of the strand formed by residues 18 - 25 (chain C) 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 VAL 18 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10C  GLU*     4.2    11.9    -      -       +      +
     12C  VAL*     3.2    44.0    -      -       +      -
     17C  SER*     1.3    71.1    -      -       -      +
     19C  ILE*     1.3    69.3    +      -       -      +
     20C  LEU*     3.6    27.4    -      -       +      -
     81C  MET      3.9     0.3    -      -       -      +
     82C  GLN*     3.4     2.1    -      -       -      +
     83C  VAL*     2.9    50.0    +      -       +      +
     86C  PRO*     3.7    11.9    -      -       +      -
    114C  VAL*     4.3    14.8    -      -       +      -
    116C  VAL*     5.3     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 19 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10C  GLU*     3.3    23.4    +      -       -      +
     17C  SER*     3.7    18.5    +      -       -      +
     18C  VAL*     1.3    82.2    -      -       -      +
     20C  LEU*     1.3    65.8    +      -       -      +
     21C  SER*     3.8     4.2    +      -       -      +
     80C  TYR*     3.7    33.4    -      -       +      -
     81C  MET      3.8     2.0    -      -       -      +
     82C  GLN*     3.3    30.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 20 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6C  GLN*     5.4     2.7    -      -       -      +
     10C  GLU*     4.2    12.6    -      -       +      -
     18C  VAL*     3.6    23.8    -      -       +      -
     19C  ILE*     1.3    78.3    -      -       -      +
     21C  SER*     1.3    61.3    +      -       -      +
     36C  TRP*     3.6    14.8    -      -       +      -
     80C  TYR*     3.0     7.3    -      -       -      -
     81C  MET*     2.8    57.2    +      -       +      +
     83C  VAL*     4.8     6.7    -      -       +      -
     94C  TYR*     3.5    47.6    -      -       +      -
    112C  THR*     4.3    10.1    -      -       +      +
    114C  VAL*     3.8    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 21 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5C  GLN      4.4     1.1    +      -       -      -
      6C  GLN*     3.2    24.1    +      -       -      +
      7C  PRO*     3.5    25.6    -      -       -      +
     19C  ILE*     3.8     5.7    +      -       -      -
     20C  LEU*     1.3    74.6    -      -       -      +
     22C  CYS*     1.3    62.0    +      -       -      +
     23C  LYS*     4.3     1.1    +      -       -      -
     36C  TRP*     4.4     0.2    -      -       -      -
     78C  THR*     4.7     2.5    -      -       -      -
     79C  ALA      3.6     3.8    -      -       -      -
     80C  TYR*     3.8    25.8    -      -       -      -
    112C  THR*     5.0     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 22 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4C  LEU*     4.0    20.4    -      -       -      -
      5C  GLN      3.4     5.6    -      -       -      -
      6C  GLN*     4.3     1.3    -      -       +      -
     21C  SER*     1.3    76.1    -      -       -      +
     23C  LYS*     1.3    61.9    +      -       -      +
     24C  ALA      3.9     0.8    +      -       -      -
     29C  PHE*     5.3     0.7    -      -       -      -
     34C  ILE*     5.1     8.7    -      -       -      -
     36C  TRP*     3.7     8.3    -      -       +      -
     78C  THR*     3.2     3.8    +      -       -      -
     79C  ALA*     2.8    45.0    +      -       +      +
     96C  CYS*     2.4    50.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 23 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3C  GLN      3.5     1.7    -      -       -      +
      4C  LEU*     4.6     1.8    -      -       -      -
      5C  GLN*     2.8    56.5    +      -       +      +
     21C  SER*     5.4     0.8    +      -       -      -
     22C  CYS*     1.3    72.9    -      -       -      +
     24C  ALA*     1.3    73.3    +      -       -      +
     25C  SER*     4.4     4.3    +      -       -      -
     76C  SER*     3.2    23.8    +      -       -      +
     77C  SER*     3.9    12.6    +      -       -      +
     78C  THR*     3.6    15.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 24 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3C  GLN      3.4     7.2    -      -       -      -
      4C  LEU*     4.2     6.7    -      -       +      +
     22C  CYS*     3.9     3.4    +      -       -      -
     23C  LYS*     1.3    89.6    +      -       -      +
     25C  SER*     1.3    66.4    +      -       -      +
     27C  TYR*     3.3    28.5    -      -       +      +
     29C  PHE*     3.5    30.5    -      -       +      -
     34C  ILE*     5.7     0.4    -      -       +      -
     77C  SER*     3.2    15.7    +      -       -      +
     78C  THR*     4.4     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 25 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1C  GLN*     3.1    22.1    +      -       -      -
      2C  VAL*     3.3     2.6    -      -       -      -
      3C  GLN*     2.9    41.9    +      -       -      +
      5C  GLN*     5.9     1.0    -      -       -      +
     23C  LYS*     4.4     5.5    +      -       -      -
     24C  ALA*     1.3    80.1    -      -       -      +
     26C  GLY*     1.3    59.6    +      -       -      +
     27C  TYR*     3.2    14.1    +      -       -      +
----------------------------------------------------------
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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