Contacts of the strand formed by residues 84 - 91 (chain C) in PDB entry 2I6A


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 ALA 84 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9C  LEU*     3.5    25.1    -      -       +      -
     70C  ILE*     3.6    32.8    -      -       +      +
     74C  GLN*     3.1    17.0    +      -       +      +
     77C  ILE*     5.2     1.3    -      -       +      -
     82C  LYS      4.5     2.2    -      -       -      -
     83C  ALA*     1.4    77.1    -      -       +      +
     85C  THR*     1.3    59.9    +      -       -      +
    108C  VAL*     3.2     7.9    -      -       +      +
    109C  ASP*     3.0    25.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 85 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7C  ASN*     2.8    35.1    +      -       -      +
      9C  LEU      2.8    16.7    +      -       -      -
     10C  PHE*     3.8    14.4    -      -       +      -
     11C  GLY*     2.9    25.3    +      -       -      +
     70C  ILE*     3.9     6.8    -      -       -      +
     84C  ALA*     1.3    73.3    -      -       -      +
     86C  PHE*     1.3    66.0    +      -       -      +
     87C  PHE*     3.4    32.3    -      -       +      -
    109C  ASP      3.5    12.1    -      -       -      +
    158C  LEU*     4.2    12.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 86 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11C  GLY      3.2    15.5    -      -       -      -
     13C  GLY      3.6    37.5    -      -       -      -
     14C  ASN      4.4     1.3    -      -       -      -
     15C  PRO*     4.1     9.2    -      -       +      -
     66C  THR*     3.7     7.6    -      -       +      -
     67C  GLN*     3.4    62.4    -      -       +      -
     70C  ILE*     4.2    18.2    -      -       +      -
     84C  ALA      4.3     0.2    +      -       -      -
     85C  THR*     1.3    77.8    -      -       -      +
     87C  PHE*     1.3    70.9    +      -       -      +
    108C  VAL*     4.3     9.9    -      -       +      -
    109C  ASP      3.2     5.9    +      -       -      -
    110C  ALA*     3.4     5.1    -      -       +      -
    111C  HIS      2.8    32.6    +      -       -      +
    112C  TYR*     3.9    24.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with PHE 87 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10C  PHE*     3.3    28.7    -      +       -      -
     11C  GLY      3.2     6.5    +      -       -      -
     12C  MET*     3.4    14.1    -      -       +      +
     13C  GLY      3.2    24.6    +      -       -      +
     85C  THR*     3.4    24.7    -      -       +      -
     86C  PHE*     1.3    88.1    -      -       -      +
     88C  GLY*     1.3    59.1    +      -       -      +
    111C  HIS*     3.1    31.0    -      +       +      +
    144C  TYR*     4.0    15.5    -      -       -      +
    149C  HIS*     3.6    18.2    -      +       +      -
    150C  LEU*     4.3     6.7    -      -       +      -
    155C  ASN*     3.6    33.7    -      -       +      -
    158C  LEU*     4.1     7.0    -      -       +      -
    159C  VAL*     3.7    12.3    -      -       +      -
    171C  PHE*     5.5     0.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 88 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13C  GLY      3.8     7.2    -      -       -      -
     15C  PRO*     3.7    19.1    -      -       -      -
     87C  PHE*     1.3    77.7    -      -       -      +
     89C  CYS*     1.3    55.2    +      -       -      -
    111C  HIS      3.4     4.8    +      -       -      -
    112C  TYR*     3.1    10.2    -      -       -      -
    113C  TYR*     2.6    31.0    +      -       -      +
    144C  TYR*     3.9    14.7    -      -       -      -
    149C  HIS*     5.0     0.2    -      -       -      -
    171C  PHE*     5.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 89 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13C  GLY      4.8     0.4    +      -       -      -
     15C  PRO*     3.6    12.6    -      -       -      +
     88C  GLY*     1.3    71.9    -      -       -      -
     90C  ILE*     1.3    63.0    +      -       -      +
    113C  TYR*     3.2    35.7    -      -       +      -
    115C  GLN*     3.8     9.4    -      -       -      -
    121C  GLY      5.5     0.2    +      -       -      -
    140C  ALA*     3.3    23.8    -      -       -      +
    141C  ALA*     3.4    23.6    +      -       -      +
    143C  CYS*     3.4    24.2    -      -       -      -
    144C  TYR*     4.0    20.3    -      -       +      +
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Residues in contact with ILE 90 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15C  PRO*     3.8    17.9    -      -       +      +
     89C  CYS*     1.3    73.6    -      -       -      +
     91C  GLY*     1.3    65.5    +      -       -      +
     96C  GLY*     4.0     8.1    -      -       -      +
     99C  LEU*     3.8    30.5    -      -       +      -
    100C  LYS*     3.5    33.9    -      -       +      +
    112C  TYR*     3.6    27.8    -      -       +      -
    113C  TYR      2.8    18.6    +      -       -      +
    114C  GLU*     3.4    16.2    -      -       +      +
    115C  GLN*     2.8    29.1    +      -       -      +
    120C  THR*     3.7    11.2    -      -       +      +
    140C  ALA*     3.9     4.5    -      -       -      -
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Residues in contact with GLY 91 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90C  ILE*     1.3    87.2    -      -       -      +
     92C  ILE*     1.3    63.8    +      -       -      -
     93C  ASP*     3.2     9.5    +      -       -      +
     96C  GLY*     3.8     5.9    -      -       -      -
    114C  GLU*     4.3     2.0    -      -       -      +
    115C  GLN*     3.3    15.3    -      -       -      -
    118C  GLN      3.3    11.7    -      -       -      -
    120C  THR*     2.8    29.3    +      -       -      +
    140C  ALA*     3.9     0.2    -      -       -      +
----------------------------------------------------------
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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