Contacts of the strand formed by residues 986 - 991 (chain B) in PDB entry 4Z02


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 LEU 986 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    950B  PRO*     5.6     1.0    -      -       -      +
    975B  GLY      4.6     1.3    -      -       -      +
    978B  MET*     3.7    44.9    -      -       +      +
    979B  GLN*     3.4    34.0    +      -       +      +
    982B  SER*     4.1    11.9    -      -       -      -
    984B  GLU      4.1     6.7    -      -       -      +
    985B  LYS*     1.3    82.5    +      -       -      +
    987B  PHE*     1.3    60.9    +      -       -      +
   1000B  TRP*     3.7    35.2    -      -       +      +
   1001B  LEU*     3.7     6.5    -      -       -      +
   1002B  PRO*     3.6    34.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 987 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    947B  ILE*     4.3    22.7    -      -       +      -
    950B  PRO*     6.2     3.1    -      -       +      -
    985B  LYS*     3.5    39.0    -      -       +      -
    986B  LEU*     1.3    75.0    -      -       -      +
    988B  LEU*     1.3    61.5    +      -       -      +
    989B  VAL*     3.7     4.0    +      -       -      +
   1000B  TRP*     3.4     6.5    -      -       -      -
   1001B  LEU      2.9    34.3    +      -       -      +
   1003B  LYS*     4.2    20.0    -      -       +      -
   1006B  MET*     3.7    29.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 988 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    947B  ILE*     3.4     5.5    -      -       -      +
    948B  ILE*     2.7    65.2    +      -       +      +
    950B  PRO*     4.9     6.1    -      -       +      +
    967B  PRO*     4.0    28.5    -      -       +      -
    971B  VAL*     3.6    25.6    -      -       +      -
    972B  LEU*     4.6     4.9    -      -       +      -
    987B  PHE*     1.3    71.2    -      -       -      +
    989B  VAL*     1.3    60.6    +      -       -      +
    998B  TRP*     3.9    15.9    -      -       +      -
    999B  GLN      3.5    16.4    -      -       -      +
   1000B  TRP*     3.7    38.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 989 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    933B  VAL*     4.5     1.1    -      -       +      -
    935B  ALA*     4.4     8.5    -      -       +      -
    945B  ALA*     3.8    17.5    -      -       +      -
    946B  LEU      3.2     4.9    -      -       -      +
    947B  ILE*     4.2    10.5    -      -       +      -
    948B  ILE*     4.9     0.2    -      -       -      -
    987B  PHE      4.4     5.4    -      -       -      +
    988B  LEU*     1.3    78.3    -      -       -      +
    990B  LEU*     1.3    59.0    +      -       -      +
    991B  PHE*     4.0    28.0    -      -       +      -
    997B  SER      3.9     0.3    -      -       -      +
    998B  TRP*     3.3    11.9    -      -       -      -
    999B  GLN*     2.9    46.5    +      -       +      +
   1001B  LEU*     4.6     7.9    -      -       +      -
   1006B  MET*     3.7    29.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 990 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    945B  ALA*     3.3     1.4    -      -       -      -
    946B  LEU*     2.8    49.9    +      -       +      +
    948B  ILE*     4.0    15.3    -      -       +      -
    965B  PRO*     3.9    31.2    -      -       +      -
    989B  VAL*     1.3    71.4    -      -       -      +
    991B  PHE*     1.4    66.9    +      -       -      +
    992B  PHE*     4.4     2.1    -      -       -      -
    996B  ARG*     3.5    41.5    -      -       +      +
    997B  SER      3.5     1.8    -      -       -      +
    998B  TRP*     3.7    37.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 991 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    935B  ALA*     3.7    32.3    -      -       +      -
    937B  CYS*     3.6    23.6    -      -       -      -
    943B  TYR*     3.6    24.7    -      +       +      -
    944B  PRO      3.5     2.2    -      -       -      -
    945B  ALA*     3.7    10.8    -      -       +      -
    989B  VAL*     4.0    14.1    -      -       +      -
    990B  LEU*     1.4    78.5    -      -       -      +
    992B  PHE*     1.3    59.0    +      -       -      +
    993B  ASP*     3.2    29.0    +      -       -      +
    996B  ARG*     3.7    12.0    -      -       -      +
    997B  SER*     2.8    25.7    +      -       -      +
    999B  GLN*     3.7    24.5    -      -       +      -
   1101B  4K8      3.7    37.7    -      +       -      -
----------------------------------------------------------
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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