Contacts of the strand formed by residues 537 - 539 (chain B) in PDB entry 1QI9


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 537 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    507B  HIS*     4.0     9.0    -      +       +      -
    529B  ILE*     4.8     5.2    -      -       +      -
    530B  LYS      3.3    14.8    -      -       -      +
    531B  LEU*     3.9    16.6    -      -       +      -
    532B  PHE*     4.2     2.7    -      -       -      -
    535B  GLY      3.8     7.2    -      -       -      -
    536B  THR*     1.3    82.2    +      -       -      +
    538B  THR*     1.3    65.9    +      -       -      +
    543B  LYS*     3.8     3.7    -      -       -      +
    544B  CYS*     3.0    66.4    +      -       +      +
    546B  GLY*     3.6    24.5    -      -       -      -
    547B  LEU      3.9     5.2    -      -       -      -
    548B  VAL*     3.5    33.4    -      -       -      -
    549B  TYR*     3.6    32.3    -      +       +      -
    550B  THR      5.1     0.9    -      -       -      -
    555B  CYS*     5.1     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 538 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    528B  VAL      3.6     0.5    +      -       -      +
    529B  ILE*     3.3     7.8    -      -       -      +
    530B  LYS*     3.1    45.2    +      -       -      +
    532B  PHE*     4.1    15.4    -      -       +      -
    536B  THR*     6.4     0.2    -      -       -      -
    537B  PHE*     1.3    79.2    -      -       -      +
    539B  ILE*     1.3    68.3    +      -       -      +
    540B  ASP      4.1     0.2    -      -       -      -
    541B  GLY*     3.9    21.4    +      -       -      +
    542B  PHE      3.1    17.5    -      -       -      +
    543B  LYS*     3.8    14.8    -      -       +      +
    544B  CYS*     4.1     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 539 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    523B  LEU*     4.0    15.3    -      -       +      -
    527B  GLU*     3.8    26.5    -      -       +      -
    528B  VAL      3.5     2.0    -      -       -      +
    529B  ILE*     3.8    32.3    -      -       +      -
    538B  THR*     1.3    78.5    -      -       -      +
    540B  ASP*     1.3    73.4    +      -       -      +
    542B  PHE*     2.8    24.7    +      -       +      +
    544B  CYS*     3.6     7.4    -      -       -      -
    549B  TYR*     4.1     9.4    -      -       +      -
    552B  VAL*     4.6    13.5    -      -       +      +
    555B  CYS*     3.6    33.9    -      -       +      +
----------------------------------------------------------
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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