Contacts of the strand formed by residues 106 - 113 (chain A) in PDB entry 1ZN8


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 106 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102A  SER*     3.5     9.4    +      -       -      -
    103A  LEU      3.0    27.7    +      -       -      -
    104A  GLU      3.5     0.2    -      -       -      -
    105A  TYR*     1.3    80.0    -      -       -      +
    107A  LYS*     1.3    66.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 107 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100A  SER*     3.8    22.7    -      -       -      +
    101A  TYR      3.4     8.1    -      -       -      +
    102A  SER*     5.2     2.0    -      -       -      -
    103A  LEU*     5.0     1.1    -      -       -      -
    106A  GLY*     1.3    78.5    -      -       -      +
    108A  ALA*     1.3    60.7    +      -       -      +
    109A  GLU*     6.1     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  LYS*     6.1     1.1    -      -       +      +
    100A  SER*     3.3     5.0    +      -       -      -
    101A  TYR*     3.0    59.0    +      -       +      +
    103A  LEU*     4.2    13.3    -      -       +      +
    106A  GLY      4.3     0.4    +      -       -      -
    107A  LYS*     1.3    73.9    -      -       -      +
    109A  GLU*     1.3    65.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  LYS*     3.6     7.4    -      -       -      +
     89A  ARG*     3.0    65.5    +      -       +      +
     98A  TRP*     3.7    16.4    +      -       +      -
     99A  ALA      3.3     7.6    -      -       -      +
    100A  SER*     3.7    25.6    -      -       -      +
    101A  TYR*     4.1     1.7    +      -       -      -
    107A  LYS*     6.1     0.4    -      -       +      -
    108A  ALA*     1.3    82.2    -      -       -      +
    110A  LEU*     1.3    64.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 110 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  LEU*     5.0     3.1    -      -       +      -
     65A  ASP      4.8    10.1    -      -       -      +
     86A  ILE*     3.8    26.5    -      -       +      +
     87A  ARG      3.1    19.5    -      -       -      +
     88A  LYS*     4.0    12.6    -      -       +      +
     98A  TRP*     3.1     5.8    -      -       -      +
     99A  ALA      2.9    34.4    +      -       -      +
    101A  TYR*     3.9    20.6    -      -       +      +
    109A  GLU*     1.3    77.6    -      -       -      +
    111A  GLU*     1.3    61.3    +      -       -      +
    135A  THR*     3.7    37.9    -      -       +      +
    138A  ALA*     4.1     9.6    -      -       +      -
    139A  ALA*     4.2     5.6    -      -       +      +
    142A  LEU*     3.7     9.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  ILE*     3.6     4.2    -      -       -      +
     87A  ARG      2.6    37.9    +      -       -      +
     88A  LYS      4.2     0.5    -      -       -      +
     89A  ARG*     3.4    16.0    +      -       -      +
     90A  GLY*     2.8    30.4    +      -       -      -
     91A  LYS      3.9     5.4    +      -       -      -
     92A  LEU*     3.8    16.3    +      -       +      +
     96A  THR*     2.6    45.0    +      -       +      +
     97A  LEU      3.3    10.8    -      -       -      +
     98A  TRP*     3.9    12.8    -      -       +      -
    110A  LEU*     1.3    75.8    -      -       -      +
    112A  ILE*     1.3    65.6    +      -       -      +
    142A  LEU*     4.0     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 112 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84A  VAL*     5.1     4.7    -      -       +      -
     85A  LEU      3.7    12.3    -      -       -      +
     86A  ILE*     3.7    22.9    -      -       +      -
     92A  LEU*     4.1     4.3    -      -       -      -
     96A  THR*     3.2     8.6    -      -       -      -
     97A  LEU*     3.0    55.2    +      -       +      -
    111A  GLU*     1.3    75.8    -      -       -      +
    113A  GLN*     1.3    69.3    +      -       -      +
    116A  ALA*     3.6    25.6    -      -       +      -
    142A  LEU*     4.1    18.6    -      -       +      +
    143A  LEU*     4.0    22.4    -      -       +      -
    146A  LEU*     4.1    11.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 113 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85A  LEU      5.1     0.4    +      -       -      -
     92A  LEU*     4.0    24.8    -      -       +      +
     93A  PRO*     2.8    41.9    +      -       -      +
     94A  GLY*     5.0     0.6    -      -       -      -
     95A  PRO      3.5     8.5    -      -       -      +
     96A  THR*     4.2     1.3    -      -       +      -
     97A  LEU*     4.4     0.4    -      -       -      -
    112A  ILE*     1.3    81.1    -      -       -      +
    114A  LYS*     1.3    64.5    +      -       -      +
    115A  ASP*     3.6    15.2    -      -       -      +
    116A  ALA*     2.9    25.0    +      -       +      +
    146A  LEU*     3.9     4.7    -      -       -      +
     14B  ARG*     2.9    32.2    +      -       -      +
     16B  PHE*     4.2     4.9    -      -       -      -
     28B  ASP*     3.5    11.4    +      -       -      +
     30B  SER*     4.3     9.7    +      -       -      -
----------------------------------------------------------
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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