Contacts of the strand formed by residues 286 - 291 (chain A) in PDB entry 4Z2C


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 286 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274A  ILE*     4.3    23.1    -      -       +      +
    278A  VAL*     4.8    14.6    -      -       +      -
    283A  ILE*     5.2    12.3    -      -       +      +
    284A  GLU*     4.5     4.0    -      -       -      +
    285A  GLY*     1.3    78.7    -      -       -      +
    287A  THR*     1.3    63.4    +      -       -      +
    288A  ALA*     3.6    23.8    -      -       -      +
    289A  VAL*     3.9    13.5    -      -       +      -
    302A  ILE*     5.2     9.0    -      -       +      -
    303A  GLU      3.8     5.2    -      -       -      +
    304A  VAL*     4.6     0.9    -      -       +      +
    305A  LYS*     4.2     8.3    +      -       -      +
    313A  ILE*     4.0    28.5    -      -       +      -
    317A  LEU*     5.0     9.2    -      -       +      -
    407C  LEU*     4.3    17.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 287 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    253A  ARG*     3.3    35.9    +      -       -      +
    285A  GLY      3.6     2.0    +      -       -      -
    286A  ILE*     1.3    73.8    -      -       -      +
    288A  ALA*     1.3    67.4    +      -       +      +
    303A  GLU*     2.6    18.9    +      -       -      +
    305A  LYS*     3.3    31.6    -      -       -      +
    405C  SER*     3.9     9.6    -      -       -      -
    407C  LEU*     3.8    13.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 288 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    286A  ILE*     3.6     5.0    -      -       -      +
    287A  THR*     1.3    85.4    -      -       +      +
    289A  VAL*     1.3    71.6    +      -       -      +
    290A  ARG*     4.1    10.8    -      -       +      -
    301A  VAL*     4.4     0.4    -      -       +      -
    302A  ILE*     3.4     2.8    -      -       -      -
    303A  GLU*     2.9    45.6    +      -       +      +
    404C  LYS      5.1     0.9    -      -       -      +
    405C  SER*     3.6    24.2    -      -       -      +
    407C  LEU*     4.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 289 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    271A  HIS*     3.3    45.1    +      -       +      +
    274A  ILE*     4.0    23.8    -      -       +      -
    275A  VAL*     4.9     1.8    -      -       +      -
    286A  ILE*     3.9    16.6    -      -       +      -
    288A  ALA*     1.3    82.1    -      -       -      +
    290A  ARG*     1.3    59.9    +      -       -      +
    300A  PHE*     3.6    26.0    -      -       +      -
    301A  VAL      3.3     5.8    -      -       -      +
    302A  ILE*     5.1     4.9    -      -       +      -
    405C  SER      3.6     6.7    +      -       -      -
    406C  GLY*     4.0    12.4    +      -       -      -
    407C  LEU*     4.5    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 290 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288A  ALA*     4.1     8.5    -      -       +      -
    289A  VAL*     1.3    78.4    -      -       -      +
    291A  ASP*     1.3    61.5    +      -       -      +
    292A  GLU*     3.8    27.8    -      -       +      -
    300A  PHE*     3.9     5.8    -      -       -      -
    301A  VAL*     2.9    41.3    +      -       +      +
    303A  GLU*     5.3     9.9    -      -       -      -
    403C  MET*     5.2     9.4    -      -       -      -
    404C  LYS      4.3    19.3    -      -       -      +
    405C  SER*     5.6     0.4    -      -       -      -
    406C  GLY      5.7     0.7    -      -       -      +
    420C  SER*     5.4    13.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 291 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    267A  LYS*     3.5    20.6    +      -       -      +
    268A  THR*     5.0     7.8    +      -       -      -
    271A  HIS*     4.9    10.9    +      -       +      -
    289A  VAL      4.1     0.8    +      -       -      -
    290A  ARG*     1.3    71.8    -      -       -      +
    292A  GLU*     1.3    59.7    +      -       -      +
    293A  SER*     3.2    24.5    +      -       -      -
    299A  ARG      3.8     3.0    -      -       -      +
    300A  PHE*     3.9    21.9    -      -       +      -
    420C  SER*     5.9     2.4    -      -       -      -
    447C  ARG*     3.2    57.8    +      -       -      +
----------------------------------------------------------
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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