Contacts of the strand formed by residues 165 - 169 (chain A) in PDB entry 1F6A


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 LEU 165 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  ARG*     3.9    33.0    -      -       -      +
     90A  LEU*     3.5    44.2    -      -       +      +
     92A  ALA*     4.0    25.8    -      -       +      -
     95A  GLU*     4.2    18.2    -      -       +      +
    148A  THR*     3.3     1.3    -      -       -      -
    149A  TYR*     2.6    42.9    +      -       +      +
    164A  PRO*     1.3    75.3    -      -       -      +
    166A  ASN*     1.3    79.5    +      -       -      +
    167A  ILE*     3.9     7.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  GLU*     3.9    13.9    -      -       -      +
    147A  GLY      4.0     2.0    -      -       -      -
    148A  THR*     2.8    28.0    +      -       -      +
    165A  LEU*     1.3    85.6    -      -       -      +
    167A  ILE*     1.3    66.9    +      -       -      +
    168A  THR*     4.3     6.3    -      -       +      -
      1F  NAG      1.4    67.7    +      -       -      +
      3F  FUC      5.8     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  ALA*     4.5     9.2    -      -       +      -
     94A  ALA      4.8     5.2    -      -       -      +
     95A  GLU*     3.5    11.9    -      -       -      +
     97A  VAL*     5.7     2.0    -      -       +      -
    103A  LEU*     4.2    23.6    -      -       +      -
    105A  LEU*     3.5    32.3    -      -       +      -
    145A  ASP      4.2    15.5    -      -       -      +
    146A  SER*     3.4     3.9    -      -       -      -
    147A  GLY      3.0    37.2    +      -       -      +
    149A  TYR*     3.7    22.0    -      -       +      -
    165A  LEU*     4.6    10.5    -      -       +      +
    166A  ASN*     1.3    80.8    -      -       -      +
    168A  THR*     1.3    73.5    +      -       -      +
    169A  VAL*     4.7     4.3    -      -       +      -
      3F  FUC      5.7     0.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  GLU      3.2     4.9    +      -       -      -
     96A  VAL*     3.4    31.2    -      -       -      +
     97A  VAL*     3.0    25.6    +      -       -      +
    146A  SER*     3.4     4.3    -      -       -      -
    166A  ASN*     5.4     4.9    -      -       +      -
    167A  ILE*     1.3    80.3    -      -       -      +
    169A  VAL*     1.3    66.6    +      -       -      +
    170A  ILE*     6.2     0.7    -      -       -      -
      3F  FUC      5.6    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 169 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97A  VAL*     3.4    25.4    -      -       +      +
     99A  GLU*     4.0    14.1    -      -       +      -
    103A  LEU*     5.9     2.7    -      -       +      -
    141A  ALA*     4.3     9.9    -      -       +      -
    142A  ALA      3.2    31.9    -      -       -      +
    143A  ALA*     5.1     3.8    -      -       -      -
    145A  ASP*     4.9     3.8    -      -       +      +
    146A  SER*     2.9    20.6    +      -       -      +
    167A  ILE*     4.7     9.2    -      -       +      -
    168A  THR*     1.3    81.3    -      -       -      +
    170A  ILE*     1.3    74.5    +      -       -      +
    171A  LYS*     5.5     0.9    -      -       -      +
----------------------------------------------------------
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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