Contacts of the strand formed by residues 34 - 39 (chain F) 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 ILE 34 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4F  LEU*     4.7    11.0    -      -       +      -
     22F  CYS*     5.1     5.2    -      -       -      -
     24F  ALA*     5.7     0.4    -      -       +      -
     27F  TYR*     3.5    22.9    -      -       -      +
     29F  PHE*     4.6    11.0    -      -       +      -
     32F  TYR      4.5     3.4    -      -       -      +
     33F  TRP*     1.3    82.9    -      -       -      +
     35F  ASN*     1.3    63.2    +      -       -      +
     36F  TRP*     3.3    34.6    -      -       +      +
     50F  ASN*     3.3     4.2    -      -       -      -
     51F  ILE*     3.1    39.3    +      -       +      +
     53F  PRO*     5.0     2.7    -      -       +      -
     72F  VAL*     6.3     0.4    -      -       +      -
     79F  ALA*     4.4    17.7    -      -       +      -
     96F  CYS*     4.2    11.9    -      -       +      -
     97F  THR      3.3    12.1    -      -       -      +
     98F  ARG*     4.6     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 35 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45D  GLU*     4.9     0.8    +      -       -      -
     96E  TYR*     3.3    15.0    +      -       -      -
     33F  TRP*     3.9    19.4    -      -       -      +
     34F  ILE*     1.3    76.4    -      -       -      +
     36F  TRP*     1.3    62.9    +      -       -      +
     37F  VAL      3.9     0.2    +      -       -      -
     47F  TRP*     2.7    24.4    +      -       -      +
     49F  GLY      3.8     2.7    -      -       -      -
     50F  ASN*     3.3    15.8    +      -       -      +
     97F  THR*     2.8    55.7    +      -       -      +
     98F  ARG*     5.8     1.2    -      -       -      +
    104F  TRP*     4.2    17.9    -      -       -      +
    105F  PHE*     3.6    18.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 36 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6F  GLN*     4.2    10.3    -      -       -      -
     20F  LEU*     3.6    35.4    -      -       +      -
     21F  SER      4.4     0.7    -      -       -      -
     22F  CYS*     3.7    23.8    -      -       +      -
     34F  ILE*     3.3    27.5    -      -       +      +
     35F  ASN*     1.3    72.9    -      -       -      +
     37F  VAL*     1.3    52.6    +      -       -      +
     47F  TRP*     4.0     3.5    -      -       -      -
     48F  VAL*     2.6    50.0    +      -       +      +
     49F  GLY      3.0    14.2    +      -       -      +
     51F  ILE*     4.5     4.6    -      -       +      +
     70F  LEU*     4.1    19.9    -      -       +      +
     79F  ALA*     3.7    25.7    -      -       +      +
     80F  TYR      5.0     0.6    -      -       -      -
     81F  MET*     3.5    43.5    -      -       +      +
     94F  TYR*     4.7     7.0    -      -       +      -
     95F  TYR      3.4    11.9    -      -       -      -
     96F  CYS*     3.9    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 37 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98E  PHE*     4.4     9.9    -      -       +      -
     35F  ASN      4.6     0.4    -      -       -      +
     36F  TRP*     1.3    75.7    -      -       -      +
     38F  LYS*     1.3    66.6    -      -       -      +
     45F  LEU*     3.8    20.6    -      -       +      -
     46F  GLU      3.2    30.7    -      -       -      +
     47F  TRP*     4.5     3.4    -      -       +      -
     48F  VAL*     4.0     1.1    -      -       -      -
     94F  TYR*     3.7     2.9    -      -       -      +
     95F  TYR*     2.9    40.3    +      -       +      +
     97F  THR*     4.0     9.4    -      -       +      -
    105F  PHE*     4.8     7.0    -      -       +      -
    108F  TRP*     3.5    32.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 38 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37F  VAL*     1.3    74.2    -      -       -      +
     39F  GLN*     1.3    67.7    +      -       -      +
     40F  ARG*     4.1    16.8    -      -       -      +
     45F  LEU      3.8     0.2    -      -       -      -
     46F  GLU*     3.0    51.6    +      -       +      +
     48F  VAL*     3.6    12.0    -      -       +      +
     64F  PHE*     4.0    22.6    -      -       +      -
     89F  GLU*     3.2    36.0    +      -       -      -
     90F  ASP*     3.8    11.7    +      -       -      -
     92F  ALA*     4.4     6.7    -      -       +      -
     93F  VAL      3.5     4.5    -      -       -      -
     94F  TYR*     3.3    47.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 39 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38E  GLN*     3.0    42.3    +      -       -      -
     85E  ASP*     5.8     0.4    +      -       -      -
     87E  HIS*     4.6     1.6    +      -       -      -
     38F  LYS*     1.3    77.9    -      -       -      +
     40F  ARG*     1.3    68.0    +      -       -      +
     41F  PRO      4.1     0.2    -      -       -      -
     42F  GLY*     5.7     0.9    -      -       -      +
     43F  GLN      3.0    28.3    +      -       -      +
     44F  GLY      4.1     4.9    -      -       -      +
     45F  LEU*     3.4    23.9    -      -       +      +
     92F  ALA*     3.8     3.8    -      -       -      -
     93F  VAL*     2.9    51.0    +      -       +      +
     95F  TYR*     3.4    20.4    +      -       +      -
----------------------------------------------------------
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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