Contacts of the strand formed by residues 83 - 89 (chain A) in PDB entry 2FOL


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 GLY 83 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  LYS      3.7     2.4    +      -       -      +
     11A  LEU*     3.3    10.3    -      -       -      +
     12A  LEU      3.3    18.9    +      -       -      -
     81A  ALA*     3.4     1.6    -      -       -      +
     82A  HIS*     1.3    83.3    -      -       -      +
     84A  ILE*     1.3    66.1    +      -       -      +
    114A  VAL*     3.7     0.7    -      -       -      -
    115A  ASN*     3.0    12.8    -      -       -      -
    165A  MET*     3.7    22.0    -      -       -      -
    169A  ILE*     3.8     3.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 84 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  LEU*     3.2    27.4    -      -       +      +
     14A  ILE*     3.1    45.1    -      -       +      -
     78A  TYR*     4.0    25.1    -      -       +      +
     81A  ALA*     4.0     6.3    -      -       +      -
     83A  GLY*     1.3    78.1    -      -       -      +
     85A  ILE*     1.3    62.6    +      -       -      +
     86A  VAL*     4.0     0.9    +      -       -      +
    106A  ILE*     3.6    19.3    -      -       +      -
    110A  ALA*     4.1    13.0    -      -       +      -
    114A  VAL*     3.8    19.7    -      -       +      -
    115A  ASN      2.7    10.9    +      -       -      +
    116A  LYS*     3.4     6.4    -      -       -      +
    117A  LEU      3.3    11.1    +      -       -      +
    165A  MET*     3.1    14.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 85 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  LEU*     4.9     5.8    -      -       +      -
     12A  LEU      2.7    11.4    +      -       -      +
     13A  LEU*     3.4    29.4    -      -       +      -
     14A  ILE*     2.8    33.3    +      -       -      +
     24A  LEU*     6.3     0.4    -      -       +      -
     83A  GLY      5.5     0.2    -      -       -      +
     84A  ILE*     1.3    77.7    -      -       -      +
     86A  VAL*     1.3    59.4    +      -       -      +
     87A  VAL*     3.7     8.5    +      -       +      +
    117A  LEU*     3.5    18.4    -      -       +      +
    119A  VAL*     3.5    30.1    -      -       +      -
    161A  SER*     4.8     4.3    -      -       -      +
    162A  PHE*     3.7    28.3    -      -       +      -
    165A  MET*     3.8    24.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 86 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  ILE*     3.6    15.3    -      -       +      +
     84A  ILE*     4.3     2.7    -      -       +      +
     85A  ILE*     1.3    72.0    -      -       -      +
     87A  VAL*     1.3    62.4    +      -       -      +
     99A  VAL*     3.8    31.0    -      -       +      +
    102A  TRP*     3.8    25.4    -      -       +      +
    103A  LEU*     4.2    12.3    -      -       +      -
    106A  ILE*     3.6    31.0    -      -       +      -
    116A  LYS*     5.7     2.5    -      -       +      -
    117A  LEU      2.9    14.1    +      -       -      +
    118A  LEU*     3.3    13.5    -      -       +      +
    119A  VAL      3.0    21.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 87 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  LEU*     4.7     7.4    -      -       +      -
     14A  ILE      2.9    16.6    +      -       -      +
     15A  GLY*     3.4    20.0    -      -       -      -
     16A  ASP      4.2     2.1    +      -       -      -
     19A  VAL*     3.9    13.9    -      -       +      +
     21A  LYS*     3.8    19.7    -      -       +      -
     24A  LEU*     3.9    22.0    -      -       +      -
     85A  ILE*     4.2    19.1    -      -       +      +
     86A  VAL*     1.3    81.5    -      -       -      +
     88A  TYR*     1.3    77.5    +      -       -      +
     95A  SER      5.0     0.9    -      -       -      +
     99A  VAL*     4.5     1.9    -      -       -      +
    102A  TRP*     5.1     0.9    -      -       -      -
    119A  VAL*     3.3    11.7    -      -       +      +
    121A  ASN*     3.8    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 88 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  VAL*     4.1    13.5    -      -       -      -
     87A  VAL*     1.3    79.1    -      -       -      +
     89A  ASP*     1.3    74.5    +      -       -      +
     90A  VAL*     4.3     5.3    -      -       -      +
     95A  SER*     3.6    22.4    -      -       -      +
     96A  PHE*     3.5    28.9    -      +       +      -
     99A  VAL*     3.9     4.0    -      -       +      -
    118A  LEU*     3.5    32.5    -      -       +      -
    119A  VAL      2.7    23.5    +      -       -      +
    120A  GLY*     3.5    23.4    -      -       -      -
    121A  ASN*     2.7    30.8    +      -       -      +
    131A  VAL*     3.5    30.4    +      -       +      +
    136A  ALA*     3.0    25.9    -      -       +      +
    147A  PHE*     3.6    10.5    -      +       -      -
    149A  GLU*     5.0     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 89 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  GLY      3.8     2.9    -      -       -      +
     19A  VAL*     4.2    17.7    -      -       +      -
     88A  TYR*     1.3    82.2    -      -       -      +
     90A  VAL*     1.3    60.4    +      -       -      +
     91A  THR*     2.7    34.9    +      -       -      +
     92A  ASP*     2.9    40.5    +      -       +      +
     95A  SER*     3.2    12.7    +      -       -      +
    121A  ASN      3.7     4.5    -      -       -      -
    122A  LYS*     3.1    38.8    +      -       +      +
    131A  VAL*     3.9     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