Contacts of the strand formed by residues 81 - 90 (chain E) in PDB entry 2FI5


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 GLN 81 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65E  VAL      3.5     0.3    -      -       -      +
     67E  LEU*     2.8    51.1    +      -       +      +
     79E  ASN      4.6     4.1    +      -       -      +
     80E  GLU*     1.3    79.3    -      -       -      +
     82E  PHE*     1.3    63.1    +      -       -      +
     83E  ILE*     3.9     8.3    -      -       +      +
    112E  ALA*     3.6    10.4    -      -       -      +
    113E  SER*     2.8    58.1    +      -       -      -
    118E  VAL*     3.6    19.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 82 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64E  GLN*     3.7    29.9    -      -       -      +
     65E  VAL      3.5     4.0    -      -       -      -
     66E  ARG*     3.5    44.2    -      -       +      -
     70E  GLU*     3.5    22.0    -      -       -      -
     76E  VAL*     5.4    13.0    -      -       +      -
     80E  GLU*     3.6    25.5    -      -       +      -
     81E  GLN*     1.3    77.9    -      -       -      +
     83E  ILE*     1.3    63.3    +      -       -      +
     84E  SER      4.3     0.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 83 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64E  GLN*     4.2     2.6    -      -       -      +
     65E  VAL*     2.7    45.1    +      -       -      +
     67E  LEU*     4.1    15.3    -      -       +      -
     81E  GLN*     4.2    10.1    -      -       +      +
     82E  PHE*     1.3    83.1    -      -       -      +
     84E  SER*     1.3    69.9    +      -       -      +
    108E  LEU*     3.9     9.8    -      -       +      +
    109E  LYS*     3.8     4.0    -      -       +      +
    110E  SER*     3.4    51.4    -      -       -      +
    111E  ALA      4.3     1.1    -      -       -      +
    112E  ALA*     3.7    30.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 84 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63E  ILE      3.7     9.6    +      -       -      -
     64E  GLN*     4.1    12.9    +      -       -      +
     82E  PHE      4.3     0.4    +      -       -      -
     83E  ILE*     1.3    77.5    -      -       -      +
     85E  ALA*     1.3    66.1    +      -       -      +
    108E  LEU*     3.8     1.7    -      -       -      -
    109E  LYS*     2.8    45.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 85 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63E  ILE*     3.0    36.1    +      -       +      +
     64E  GLN*     4.6     0.2    -      -       -      +
     65E  VAL*     4.8     2.2    -      -       +      +
     83E  ILE      3.8     1.2    +      -       -      -
     84E  SER*     1.3    76.8    -      -       -      +
     86E  SER*     1.3    60.9    +      -       -      +
     87E  LYS      4.3     6.5    -      -       -      +
     88E  SER*     5.5     2.9    -      -       -      -
    106E  ILE*     3.5    27.8    -      -       +      -
    107E  LYS      3.3     6.7    -      -       -      -
    108E  LEU*     4.8     0.2    -      -       -      +
    109E  LYS*     4.8     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 86 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84E  SER      3.5     1.6    +      -       -      -
     85E  ALA*     1.3    74.3    -      -       -      +
     87E  LYS*     1.3    72.3    +      -       -      +
    107E  LYS*     2.8    29.9    +      -       -      +
    108E  LEU      3.5    11.8    +      -       -      -
    109E  LYS*     3.6    26.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 87 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51E  TRP*     4.9     1.3    -      -       +      -
     85E  ALA*     3.4     2.7    -      -       -      +
     86E  SER*     1.3    97.5    +      -       -      +
     88E  SER*     1.3    61.5    +      -       -      +
     89E  ILE*     4.1    11.0    -      -       +      -
    105E  LEU      4.4     0.2    -      -       -      -
    106E  ILE*     3.3     8.7    -      -       -      +
    107E  LYS*     2.9    48.3    +      -       +      +
    245E  ASN*     2.7    54.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 88 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59E  TYR*     2.9    39.2    -      -       -      -
     60E  LYS      5.6     0.9    -      -       -      -
     63E  ILE*     5.3     6.7    -      -       -      -
     85E  ALA*     5.5     3.4    -      -       -      -
     87E  LYS*     1.3    74.6    -      -       -      +
     89E  ILE*     1.3    62.4    +      -       -      +
     90E  VAL*     3.7     4.0    +      -       -      +
    104E  MET*     4.2    12.1    -      -       -      -
    105E  LEU      3.4     6.1    -      -       -      -
    106E  ILE*     4.5     7.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 89 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51E  TRP*     3.9    19.5    -      -       +      -
     87E  LYS*     4.8     7.2    -      -       +      -
     88E  SER*     1.3    76.3    -      -       -      +
     90E  VAL*     1.3    69.6    -      -       -      +
     91E  HIS      3.8     0.5    +      -       -      -
     92E  PRO*     5.7     1.6    -      -       +      -
    104E  MET*     3.3     3.1    -      -       -      -
    105E  LEU*     2.7    40.8    +      -       +      +
    237E  TRP*     4.2     9.6    -      -       +      -
    241E  THR*     3.8    23.1    -      -       +      -
    245E  ASN*     3.3    39.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 90 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56E  ALA*     3.6    26.2    -      -       +      +
     59E  TYR*     3.9    36.1    -      -       +      -
     88E  SER      3.7     2.5    +      -       -      +
     89E  ILE*     1.3    79.7    -      -       -      +
     91E  HIS*     1.3    78.6    +      -       -      +
     92E  PRO*     3.2     6.9    -      -       -      +
     94E  TYR*     3.7    15.0    -      -       +      -
    103E  ILE      4.0     4.0    -      -       -      -
    104E  MET*     4.0    12.8    -      -       +      -
----------------------------------------------------------
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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