Contacts of the strand formed by residues 57 - 60 (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 TYR 57 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  ARG*     3.0    26.5    -      -       -      +
     72A  ASP*     3.7    40.8    +      -       +      +
     73A  GLU*     4.9     3.8    -      -       -      +
     84A  SER*     5.6     0.2    -      -       -      -
     97A  LYS*     5.4     2.0    -      -       -      -
     33C  TRP*     3.7     9.9    -      +       -      -
     51C  ILE*     3.2     3.5    -      -       -      -
     52C  PHE*     2.9    31.9    +      -       +      -
     55C  ASP*     3.0    24.6    +      -       -      +
     56C  SER*     1.3    76.9    -      -       -      +
     58C  THR*     1.3    86.3    +      -       -      +
     59C  ASN*     3.3    28.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 58 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50C  ASN*     3.3    13.5    -      -       -      +
     51C  ILE*     3.6    20.4    -      -       +      -
     56C  SER      3.0    20.4    -      -       -      +
     57C  TYR*     1.3    90.8    -      -       -      +
     59C  ASN*     1.3    65.3    +      -       -      +
     60C  TYR*     2.9    32.6    -      -       +      +
     70C  LEU*     4.9     4.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 59 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  ASP      4.8     1.4    +      -       -      -
     94B  TYR*     3.2    44.8    +      -       +      +
     33C  TRP*     3.7     2.8    -      -       -      -
     47C  TRP*     3.9    11.0    -      -       +      -
     49C  GLY*     3.0     4.3    -      -       -      -
     50C  ASN*     2.8    46.4    +      -       -      +
     57C  TYR*     3.3    28.1    +      -       -      -
     58C  THR*     1.3    77.8    +      -       -      +
     60C  TYR*     1.3    65.9    +      -       -      +
     70C  LEU*     4.7     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 60 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95B  PRO*     5.4     1.0    -      -       -      +
     47C  TRP*     4.2     4.9    -      -       -      -
     48C  VAL*     4.0     7.6    -      -       +      +
     49C  GLY*     5.3     0.2    -      -       -      -
     58C  THR*     2.9    32.6    -      -       -      +
     59C  ASN*     1.3    77.8    -      -       -      +
     61C  ASN*     1.3    69.6    +      -       -      +
     62C  GLN*     3.5     4.0    +      -       -      +
     64C  PHE*     4.5     4.5    -      -       +      -
     65C  LYS*     3.9    28.3    -      -       +      -
     68C  ALA*     3.2    32.3    -      -       +      -
     69C  THR*     3.4     9.0    -      -       -      +
     70C  LEU*     2.8    43.7    +      -       +      +
----------------------------------------------------------
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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