Contacts of the strand formed by residues 432 - 436 (chain C) 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 SER 432 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    427C  ASP      3.7     2.9    -      -       -      +
    429C  ASN*     3.1    38.7    +      -       -      +
    431C  LYS*     1.3    85.5    -      -       -      +
    433C  PHE*     1.3    62.0    +      -       -      +
    434C  ARG*     5.3     9.1    -      -       -      +
    478C  GLU*     4.9    13.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 433 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21C  LYS*     3.7    29.1    -      -       +      +
     23C  SER*     4.5     7.2    -      -       -      -
     24C  TYR*     3.7    25.8    -      +       -      -
     78C  GLU*     5.4     0.7    -      -       -      -
     80C  TYR*     4.9     1.1    -      -       -      -
    396C  PRO*     3.5     6.6    -      -       -      +
    397C  THR*     3.3    38.0    +      -       -      +
    412C  GLU*     3.6    17.9    -      -       +      +
    426C  CYS*     4.0     9.0    -      -       -      -
    427C  ASP      3.8     2.5    -      -       -      -
    428C  ARG*     3.7    23.3    -      -       +      -
    430C  GLY      3.5    20.6    -      -       -      -
    431C  LYS      3.5     6.4    +      -       -      -
    432C  SER*     1.3    81.5    -      -       -      +
    434C  ARG*     1.3    62.8    +      -       -      +
    435C  TYR*     3.2    27.6    -      -       +      +
    478C  GLU*     5.0     2.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 434 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201C  ASN*     4.4    23.0    +      -       -      +
    205C  ARG*     6.1     3.0    -      -       -      +
    394C  LYS*     4.0    39.5    +      -       +      +
    395C  VAL      3.2     9.4    -      -       -      +
    396C  PRO*     4.5     9.7    -      -       +      +
    425C  PHE      3.9     0.2    -      -       -      +
    426C  CYS*     3.3     3.0    -      -       -      -
    427C  ASP*     2.9    44.3    +      -       +      +
    432C  SER*     5.3     8.3    -      -       -      -
    433C  PHE*     1.3    80.7    -      -       -      +
    435C  TYR*     1.3    63.9    +      -       -      +
    436C  TYR*     4.2     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 435 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24C  TYR*     4.7     2.8    +      -       -      -
    389C  LEU*     4.6     5.8    -      -       +      +
    393C  VAL      3.9     1.4    -      -       -      +
    394C  LYS*     3.5     0.5    -      -       -      -
    395C  VAL*     2.8    42.8    +      -       +      +
    397C  THR*     3.6    23.3    -      -       +      -
    400C  LEU*     4.4    13.9    -      -       +      -
    412C  GLU*     3.4    19.6    +      -       -      +
    415C  LEU*     3.4    37.3    -      -       +      +
    416C  GLN      5.2     0.4    -      -       -      -
    419C  VAL*     4.4     5.2    -      -       +      -
    424C  LEU*     3.8    24.9    -      -       +      -
    425C  PHE      3.2    14.6    -      -       -      +
    426C  CYS*     3.5    27.3    -      -       +      -
    433C  PHE*     3.2    28.1    -      -       +      -
    434C  ARG*     1.3    74.1    -      -       -      +
    436C  TYR*     1.3    64.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 436 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120C  PRO*     4.3    11.1    -      -       -      +
    389C  LEU*     4.8     4.9    -      -       -      -
    392C  ASP*     6.2     0.9    -      -       -      +
    393C  VAL      3.7    18.4    -      -       -      +
    394C  LYS*     3.7    37.5    +      -       +      -
    424C  LEU*     3.4     9.1    -      -       -      +
    425C  PHE*     2.8    74.6    +      +       +      +
    426C  CYS      4.8     0.9    +      -       -      -
    427C  ASP*     2.9    38.8    +      -       -      -
    434C  ARG      4.2     3.6    -      -       -      -
    435C  TYR*     1.3    78.7    -      -       -      +
    437C  LEU*     1.3    71.3    +      -       -      +
    438C  HIS*     5.6     0.9    -      -       -      -
----------------------------------------------------------
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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