Contacts of the strand formed by residues 25 - 32 (chain D) in PDB entry 1ZMQ


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 ILE 25 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  PHE*     3.9    15.2    -      -       +      -
     15A  TYR*     3.6    30.3    -      -       +      -
     17A  TYR*     4.9     2.2    -      -       +      -
     31A  CYS*     3.7    35.7    -      -       +      +
     32A  LEU*     3.8    13.2    -      -       -      +
     29C  PHE*     5.4     1.1    -      -       +      -
     20D  CYS      3.7     1.0    -      -       -      +
     21D  THR*     3.3     5.4    -      -       -      +
     22D  VAL*     2.8    57.4    +      -       +      +
     23D  MET      3.2     0.4    -      -       -      -
     24D  GLY*     1.3    72.6    -      -       -      +
     26D  ASN*     1.3    65.8    +      -       -      +
     27D  HIS*     3.8    25.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 26 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8D  ARG*     5.1     3.3    -      -       -      +
     19D  THR*     3.9     8.8    -      -       +      +
     20D  CYS      3.6     3.1    -      -       -      -
     21D  THR*     2.7    33.5    +      -       -      +
     23D  MET      5.6     0.4    +      -       -      -
     24D  GLY      4.0     8.7    +      -       -      -
     25D  ILE*     1.3    77.1    -      -       -      +
     27D  HIS*     1.3    65.2    +      -       -      +
     28D  ARG*     3.2    26.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 27 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  ALA      2.9    24.8    +      -       -      -
      2A  PHE*     3.3    34.1    -      +       +      -
     32A  LEU*     2.6    31.5    +      -       -      -
      6D  CYS*     3.0    23.9    +      -       +      -
      7D  ARG      3.2    13.8    -      -       -      +
      8D  ARG*     3.5    26.2    +      -       +      +
     19D  THR*     3.4    11.4    -      -       -      +
     20D  CYS      2.8    33.4    +      -       -      +
     25D  ILE*     3.8     7.6    -      -       +      -
     26D  ASN*     1.3    76.7    -      -       -      +
     28D  ARG*     1.3    64.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 28 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5D  HIS      3.2     2.6    -      -       -      +
      6D  CYS*     3.2     5.7    -      -       -      -
      7D  ARG      2.6    36.8    +      -       -      +
      8D  ARG      4.0    14.4    +      -       -      +
      9D  SER*     4.7     2.5    -      -       -      -
     10D  CYS*     3.7     8.7    -      -       -      +
     16D  SER*     3.3    19.5    +      -       -      +
     18D  GLY      3.5     8.0    +      -       -      -
     19D  THR*     3.1    24.7    +      -       -      +
     20D  CYS*     4.3     1.3    -      -       -      -
     26D  ASN*     3.2    39.8    +      -       -      +
     27D  HIS*     1.3    81.2    +      -       -      +
     29D  PHE*     1.3    60.4    +      -       -      +
     30D  CYS*     3.2    17.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 29 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22C  VAL*     3.7    24.0    -      -       +      -
     23C  MET*     3.5    32.5    -      -       +      -
      4D  CYS*     3.5    22.2    -      -       +      -
      5D  HIS*     3.9     2.9    -      -       -      -
      6D  CYS*     4.1     6.1    -      -       -      -
     15D  TYR      3.6     0.3    -      -       -      +
     16D  SER*     4.2     0.9    -      -       -      -
     17D  TYR*     2.9    33.8    +      -       +      +
     18D  GLY      2.9    28.3    +      -       -      +
     20D  CYS*     3.8    23.1    -      -       -      -
     27D  HIS      4.1     0.2    +      -       -      -
     28D  ARG*     1.3    70.7    -      -       -      +
     30D  CYS*     1.3    60.4    +      -       -      +
     31D  CYS*     3.4    26.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 30 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3D  THR      3.9     0.5    -      -       -      +
      4D  CYS*     2.9     3.6    -      -       -      -
      5D  HIS*     2.7    45.2    +      -       -      +
      7D  ARG*     3.8    14.6    -      -       +      +
     10D  CYS*     2.1    52.7    -      -       +      -
     14D  GLU*     3.4    22.2    -      -       +      +
     15D  TYR      3.4     5.6    -      -       -      -
     28D  ARG*     3.5    18.8    -      -       -      -
     29D  PHE*     1.3    71.2    -      -       -      +
     31D  CYS*     1.3    60.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 31 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2D  PHE*     4.1    13.2    -      -       +      -
      3D  THR      3.3     3.4    -      -       -      -
      4D  CYS*     2.0    45.8    -      -       -      -
     13D  THR      4.4     0.3    -      -       -      +
     14D  GLU*     3.4     6.4    -      -       -      -
     15D  TYR*     2.8    30.1    +      -       -      +
     17D  TYR*     3.5    33.5    +      -       +      -
     29D  PHE*     3.4    20.4    -      -       -      -
     30D  CYS*     1.3    72.3    -      -       -      +
     32D  LEU*     1.3    60.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 32 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1D  ALA      4.2     5.2    -      -       -      +
      2D  PHE*     3.5    16.9    -      -       -      -
      3D  THR*     2.9    39.3    +      -       -      +
     11D  TYR*     5.5     2.5    -      -       +      -
     13D  THR*     3.3    44.0    -      -       +      +
     14D  GLU*     3.9    18.1    -      -       +      +
     31D  CYS*     1.3    75.5    -      -       -      +
----------------------------------------------------------
 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