Contacts of the strand formed by residues 425 - 429 (chain A) in PDB entry 1Z6T


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 PHE 425 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123A  PRO*     5.9     6.3    -      -       +      -
    322A  LEU*     4.1    11.2    -      -       +      -
    419A  VAL*     4.3     5.6    -      -       +      -
    422A  SER*     4.1    19.5    -      -       -      -
    424A  LEU*     1.3    82.9    -      -       -      +
    426A  CYS*     1.3    60.5    +      -       -      +
    435A  TYR*     3.2     9.9    -      -       -      +
    436A  TYR*     2.8    72.7    +      +       +      +
    437A  LEU*     4.3     0.9    -      -       -      -
    438A  HIS*     3.9    16.2    -      +       +      -
    441A  GLN*     3.2    28.0    -      -       -      -
    900A  ADP      2.9    34.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 426 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  TYR*     3.6    24.9    -      -       +      +
    121A  GLN*     4.4     1.0    -      -       -      +
    419A  VAL*     4.1     9.2    -      -       +      +
    425A  PHE*     1.3    77.1    -      -       -      +
    427A  ASP*     1.3    69.0    +      -       -      +
    428A  ARG*     3.0    47.1    +      -       -      -
    433A  PHE*     4.1     9.9    -      -       -      -
    434A  ARG      3.3     8.1    -      -       -      -
    435A  TYR*     3.5    31.9    -      -       +      -
    436A  TYR*     4.3     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 427 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  GLY      4.7     6.6    -      -       -      +
    120A  PRO*     3.8    25.2    -      -       -      +
    121A  GLN*     3.9     6.2    +      -       -      +
    394A  LYS*     2.6    34.1    +      -       +      +
    426A  CYS*     1.3    74.4    -      -       -      +
    428A  ARG*     1.3    62.3    +      -       -      +
    429A  ASN      4.1     0.2    +      -       -      -
    432A  SER      3.8     3.6    -      -       -      +
    433A  PHE*     3.8     1.0    -      -       -      -
    434A  ARG*     2.9    50.7    +      -       +      +
    436A  TYR*     2.9    28.9    +      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 428 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  TYR*     3.5    31.5    -      -       +      +
     28A  HIS*     4.2     8.3    -      -       -      -
     77A  HIS*     4.9     0.2    +      -       -      -
     78A  GLU*     3.0    52.3    +      -       -      +
    115A  CYS*     4.1     5.4    -      -       -      -
    121A  GLN*     3.0    55.9    +      -       -      +
    122A  ARG      5.5     2.6    +      -       -      -
    419A  VAL*     5.7     2.2    -      -       -      +
    426A  CYS*     3.0    39.0    +      -       -      +
    427A  ASP*     1.3    73.6    -      -       -      +
    429A  ASN*     1.3    60.6    +      -       -      +
    430A  GLY      3.8     1.1    -      -       -      +
    432A  SER      3.7     3.6    -      -       -      -
    433A  PHE*     3.6    33.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 429 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  GLU      3.8     0.2    -      -       -      -
     79A  GLY*     3.9     9.0    +      -       -      -
    115A  CYS*     3.3    40.6    +      -       -      +
    116A  GLU*     4.7     2.2    -      -       -      +
    118A  GLY*     6.2     2.2    -      -       -      -
    427A  ASP      4.1     1.0    +      -       -      -
    428A  ARG*     1.3    72.5    -      -       -      +
    430A  GLY*     1.3    62.9    +      -       -      +
    431A  LYS*     3.1     4.0    +      -       -      +
    432A  SER*     3.1    27.5    +      -       -      +
    434A  ARG*     5.6     8.0    -      -       -      +
----------------------------------------------------------
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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