Contacts of the strand formed by residues 107 - 116 (chain A) in PDB entry 2ZH8


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 VAL 107 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  LYS*     3.8    22.9    -      -       +      +
     27A  ALA*     3.3    32.3    -      -       +      -
     58A  LEU*     3.5    34.8    -      -       +      +
     60A  ILE*     3.9    20.0    -      -       +      -
    103A  VAL*     3.4     5.3    -      -       -      +
    104A  VAL      3.1    24.2    +      -       -      +
    105A  LYS      4.1     1.6    -      -       -      +
    106A  GLY*     1.3    83.1    -      -       -      +
    108A  GLU*     1.3    70.1    +      -       -      +
    109A  VAL*     3.4     7.3    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  LEU      4.2    12.3    +      -       -      +
     59A  GLU*     3.4    25.2    -      -       +      +
     60A  ILE*     2.9    25.5    +      -       -      +
    101A  HIS*     2.8    32.1    +      -       +      -
    102A  GLY      3.6     3.6    -      -       -      +
    103A  VAL*     4.2    16.1    -      -       -      +
    106A  GLY      5.0     4.0    -      -       -      +
    107A  VAL*     1.3    75.0    -      -       -      +
    109A  VAL*     1.3    59.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  ALA*     5.9     0.2    -      -       +      -
     31A  LEU*     4.0    20.9    -      -       +      -
     59A  GLU*     4.9     0.2    -      -       -      -
     60A  ILE*     3.4    20.0    -      -       +      +
     62A  VAL*     4.8     2.2    -      -       +      -
     87A  LEU*     3.9    21.0    -      -       +      +
    100A  VAL      4.0     0.2    -      -       -      +
    101A  HIS*     3.2     7.6    +      -       -      -
    102A  GLY      2.7    41.3    +      -       -      +
    104A  VAL*     3.9    20.6    -      -       +      -
    107A  VAL*     3.4    20.4    -      -       +      +
    108A  GLU*     1.3    76.6    -      -       -      +
    110A  ASP*     1.3    77.4    +      -       -      +
    111A  VAL*     4.1     7.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  GLU*     3.0    23.0    -      -       -      +
     60A  ILE      3.0     6.3    +      -       -      -
     61A  ASP*     3.1    14.0    -      -       -      +
     62A  VAL*     3.0    31.0    +      -       -      +
     93A  ARG*     4.9     0.7    +      -       -      -
     99A  TYR*     3.6    17.7    +      -       +      -
    100A  VAL      3.6     2.9    -      -       -      +
    101A  HIS*     2.6    32.6    +      -       -      -
    109A  VAL*     1.3    74.0    -      -       -      +
    111A  VAL*     1.3    61.7    +      -       -      +
    112A  VAL*     3.8    10.2    -      -       +      +
     34B    C      2.7    30.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  LEU*     5.8     1.1    -      -       +      -
     35A  LEU*     6.1     1.1    -      -       +      -
     62A  VAL*     3.5    10.1    -      -       +      +
     64A  LEU*     3.4    37.0    -      -       +      -
     79A  GLY      4.4     2.8    -      -       -      +
     82A  ILE*     4.9     2.0    -      -       +      -
     83A  GLY*     4.0    30.7    -      -       -      +
     86A  VAL*     4.5     7.6    -      -       +      -
     87A  LEU*     4.1    15.9    -      -       +      -
     99A  TYR*     3.7     1.0    -      -       -      +
    100A  VAL*     2.7    38.0    +      -       +      +
    109A  VAL*     4.1    16.6    -      -       +      -
    110A  ASP*     1.3    72.9    -      -       -      +
    112A  VAL*     1.3    59.1    +      -       -      +
    113A  PRO*     3.7     4.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 112 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  VAL      3.0     5.5    +      -       -      -
     63A  PHE*     3.2    39.3    -      -       +      +
     64A  LEU*     2.7    33.3    +      -       -      -
     99A  TYR*     4.1    26.2    -      -       +      -
    110A  ASP*     4.1    14.1    -      -       +      -
    111A  VAL*     1.3    76.2    -      -       -      +
    113A  PRO*     1.3    72.6    -      -       +      +
    114A  CYS      3.9     0.2    +      -       -      -
    127A  VAL*     3.8    25.6    -      -       +      -
     34B    C      3.8    10.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 113 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  LEU*     3.9    10.8    -      -       +      +
     66A  PHE*     4.1     5.2    -      -       +      -
     75A  LEU*     3.4    43.7    -      -       +      +
     76A  ARG*     4.8     2.0    -      -       -      -
     79A  GLY*     3.8    17.5    -      -       -      -
     98A  PRO      4.3     9.9    -      -       -      +
     99A  TYR*     4.0    14.4    -      -       +      -
    100A  VAL*     6.5     0.2    -      -       +      -
    111A  VAL      3.7     7.9    -      -       -      +
    112A  VAL*     1.3    95.8    -      -       +      +
    114A  CYS*     1.3    64.2    +      -       -      +
    127A  VAL*     4.0     9.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 114 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  PHE*     3.9    25.4    -      -       +      -
     64A  LEU      2.9    17.9    +      -       -      +
     65A  LEU*     3.9    22.0    -      -       -      -
     66A  PHE*     2.9    27.7    +      -       -      +
     75A  LEU*     4.2     8.9    -      -       -      +
    113A  PRO*     1.3    75.4    -      -       -      +
    115A  TYR*     1.3    65.1    +      -       -      +
    127A  VAL*     3.7    18.2    -      -       +      +
    128A  ASP*     3.5    13.9    -      -       -      +
    131A  PRO*     4.0    11.0    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 115 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  LEU*     4.8     0.5    -      -       -      +
     66A  PHE      3.4     4.0    -      -       -      +
     67A  PRO      3.3    22.0    -      -       -      -
     68A  GLU*     3.3    19.3    -      -       -      -
     70A  PHE      2.8    29.1    +      -       -      -
     71A  SER      3.6     0.3    -      -       -      -
     72A  LYS*     3.4    24.2    +      -       +      +
     75A  LEU*     3.3    27.1    -      -       +      -
    114A  CYS*     1.3    82.6    -      -       -      +
    116A  LYS*     1.3    59.2    +      -       -      +
    117A  LEU*     3.2    33.6    +      -       +      +
    124A  LYS*     3.5    33.9    +      -       +      +
    125A  SER*     6.1     0.4    -      -       -      -
    128A  ASP*     2.9    32.6    +      -       -      +
    131A  PRO*     5.4     1.6    -      -       -      +
    132A  PHE*     6.0     0.3    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 116 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  GLU*     3.0    37.9    +      -       -      +
     65A  LEU*     3.4    34.1    -      -       +      -
     66A  PHE      2.6    23.0    +      -       -      +
     67A  PRO*     5.0     2.1    -      -       +      +
     68A  GLU*     4.3     9.4    +      -       -      +
    115A  TYR*     1.3    69.9    -      -       -      +
    117A  LEU*     1.3    64.8    +      -       -      +
----------------------------------------------------------
 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