Contacts of the strand formed by residues 76 - 81 (chain A) in PDB entry 3I8E


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 76 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  PHE*     4.2     1.6    -      -       -      -
     66A  LEU*     3.3     8.1    -      -       -      +
     67A  PHE*     2.8    56.5    +      -       +      +
     69A  PRO*     4.6     4.7    -      -       +      -
     72A  GLU*     3.5    33.4    -      -       +      +
     74A  LYS*     4.2     2.7    -      -       +      +
     75A  ASP*     1.3    76.2    -      -       -      +
     77A  LEU*     1.3    61.4    +      -       -      +
     88A  ILE*     4.2    11.2    -      -       +      -
     89A  LEU      3.3     8.5    -      -       -      +
     90A  GLU*     3.6    37.7    -      -       +      +
    103A  ARG*     3.7    31.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 77 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  VAL*     5.1     0.4    -      -       +      -
     23A  PHE*     3.6    22.0    -      -       +      -
     32A  LEU*     3.7    29.8    -      -       +      -
     39A  LEU*     4.1    17.7    -      -       +      -
     64A  MET*     3.7    20.4    -      -       +      -
     65A  GLU      3.3    18.4    -      -       -      +
     66A  LEU*     3.7     6.3    -      -       +      -
     67A  PHE*     3.9     1.6    -      -       -      -
     76A  LEU*     1.3    74.1    -      -       -      +
     78A  PHE*     1.3    59.9    +      -       -      +
     79A  ILE*     3.7    22.2    -      -       +      -
     87A  CYS      3.9     0.2    -      -       -      +
     88A  ILE*     3.2     5.2    -      -       -      +
     89A  LEU*     2.4    62.7    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 78 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  VAL*     3.9    27.8    -      -       +      -
     64A  MET*     3.4     5.7    -      -       -      -
     65A  GLU*     2.8    46.4    +      -       +      +
     67A  PHE*     3.6    21.5    -      -       +      -
     77A  LEU*     1.3    73.8    -      -       -      +
     79A  ILE*     1.3    69.8    +      -       -      +
     80A  LEU*     4.4    14.1    -      -       +      -
     86A  ALA*     4.2    18.8    -      -       +      -
     87A  CYS      3.5    11.2    -      -       -      -
     88A  ILE*     4.2     8.3    -      -       +      +
    122A  GLY*     5.4     1.1    -      -       -      -
    123A  ILE      6.3     0.2    -      -       -      -
    124A  ILE*     4.5     4.9    -      -       +      -
    131A  ILE*     3.8    44.9    -      -       +      -
    133A  LEU*     4.2    13.5    -      -       +      -
    143A  ILE*     4.9     3.6    -      -       +      -
    152A  LEU*     4.9     4.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 79 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  LEU*     4.4     6.7    -      -       +      -
     57A  MET*     3.8    26.5    -      -       +      -
     61A  ILE*     4.0    16.6    -      -       +      -
     63A  VAL      3.5     5.6    -      -       -      +
     64A  MET*     3.5    37.7    -      -       +      -
     77A  LEU*     3.7    14.8    -      -       +      -
     78A  PHE*     1.3    81.6    -      -       -      +
     80A  LEU*     1.3    68.6    +      -       -      +
     81A  THR*     4.6     2.5    -      -       -      +
     85A  ASN      3.2     3.4    -      -       -      +
     86A  ALA*     3.5     1.6    -      -       -      -
     87A  CYS*     2.9    43.6    +      -       -      +
     89A  LEU*     3.8    26.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 80 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  ALA*     3.2    24.2    +      -       -      +
     63A  VAL*     3.1    42.3    +      -       +      -
     78A  PHE*     4.4     8.5    -      -       +      -
     79A  ILE*     1.3    77.3    -      -       -      +
     81A  THR*     1.3    67.9    +      -       -      +
     84A  TYR*     3.6     5.4    -      -       +      -
     85A  ASN      3.1    36.8    -      -       -      +
     86A  ALA*     3.6     2.9    -      -       +      +
    108A  VAL*     3.5    20.4    -      -       +      -
    120A  ILE*     3.8     7.9    -      -       +      -
    133A  LEU*     4.3    13.2    -      -       +      -
    135A  LEU*     3.7    28.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 81 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57A  MET*     4.7     7.3    -      -       -      +
     58A  TYR      4.0     2.3    +      -       -      +
     59A  GLY*     3.4    31.2    -      -       -      -
     60A  LYS      3.2     9.1    -      -       -      +
     61A  ILE*     4.8     0.8    -      -       -      +
     62A  ALA*     4.8     0.2    -      -       -      -
     79A  ILE*     4.2     2.6    -      -       -      +
     80A  LEU*     1.3    78.0    -      -       -      +
     82A  ALA*     1.3    57.1    +      -       -      +
     83A  LYS*     3.1    18.2    -      -       +      +
     84A  TYR*     2.7    28.2    +      -       -      -
     85A  ASN*     2.9    43.4    +      -       -      +
    120A  ILE*     4.8     1.6    -      -       -      +
   1068A  ILE*     3.5    13.7    -      -       -      +
   1073A  TRP*     5.2     1.1    -      -       +      -
----------------------------------------------------------
 Back to top of page


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