Contacts of the strand formed by residues 547 - 551 (chain B) in PDB entry 1Q6X


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 547 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    431B  LEU*     4.2    24.2    -      -       +      +
    432B  GLN*     3.9    15.5    -      -       -      +
    435B  TYR*     4.5    22.7    -      -       +      -
    443B  VAL*     4.5     7.4    -      -       +      -
    444B  PRO      3.7     2.2    +      -       -      -
    445B  THR*     3.3    29.0    -      -       +      +
    446B  TYR*     2.8    26.5    +      -       -      +
    545B  PHE*     4.0     3.2    -      -       -      +
    546B  VAL*     1.3    76.7    -      -       -      +
    548B  SER*     1.3    61.4    +      -       -      +
    549B  THR*     3.3    28.0    -      -       +      -
    570B  TYR*     3.9    10.1    -      -       +      -
    572B  ALA*     4.6     8.7    -      -       +      -
    599B  PHE*     4.4    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 548 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    446B  TYR*     3.9    18.9    -      -       -      +
    545B  PHE*     4.4     2.0    -      -       -      -
    546B  VAL      4.0     0.2    -      -       -      -
    547B  LEU*     1.3    72.5    -      -       -      +
    549B  THR*     1.3    63.4    +      -       -      +
    562B  TYR*     4.2    10.4    -      -       -      -
    563B  GLY      5.5     0.4    -      -       -      -
    564B  PRO*     5.4     0.2    -      -       -      -
    565B  VAL*     4.0    36.7    -      -       -      +
    570B  TYR      3.0    15.4    +      -       -      -
    571B  GLY*     3.4     5.0    -      -       -      -
    572B  ALA      2.8    26.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 549 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    428B  GLN*     3.0    29.3    +      -       -      +
    431B  LEU*     4.0    13.5    -      -       +      -
    445B  THR*     4.6     5.2    -      -       +      -
    446B  TYR*     2.8    27.4    +      -       -      +
    447B  GLU*     3.8     2.5    -      -       -      +
    448B  SER*     3.3    19.2    +      -       -      -
    547B  LEU*     3.3    29.2    -      -       +      -
    548B  SER*     1.3    82.2    +      -       -      +
    550B  SER*     1.3    66.1    +      -       -      +
    562B  TYR*     3.4     4.0    -      -       -      -
    572B  ALA*     3.2    19.7    -      -       +      +
    574B  TYR*     4.6     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 550 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    447B  GLU*     5.2     3.6    -      -       -      -
    448B  SER*     4.0    23.1    -      -       -      +
    549B  THR*     1.3    81.5    -      -       -      +
    551B  GLN*     1.3    61.7    +      -       -      +
    552B  VAL*     4.0     6.4    -      -       -      +
    562B  TYR*     2.7    31.7    +      -       -      -
    572B  ALA      3.3     0.6    +      -       -      -
    573B  CYS*     3.4     8.3    -      -       -      -
    574B  TYR*     3.2    31.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 551 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    340B  ILE*     4.3    10.0    -      -       -      +
    423B  PRO*     5.4     2.6    -      -       -      +
    424B  ASP*     3.2    35.7    +      -       -      +
    447B  GLU*     5.1     2.5    +      -       -      +
    448B  SER      5.8     1.2    +      -       -      -
    550B  SER*     1.3    75.2    -      -       -      +
    552B  VAL*     1.3    66.3    +      -       -      +
    553B  PRO*     3.6    24.0    -      -       +      +
    574B  TYR*     3.5    20.9    +      -       +      -
    576B  PRO*     2.9    39.5    -      -       +      +
----------------------------------------------------------
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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