Contacts of the strand formed by residues 551 - 558 (chain A) in PDB entry 1AUQ


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 VAL 551 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    509A  CYS*     3.6    26.0    -      -       -      +
    511A  ARG      3.5    19.5    -      -       -      +
    513A  LEU*     3.2    28.0    -      -       +      +
    515A  LEU*     4.7     1.8    -      -       +      -
    544A  LEU*     3.7    30.5    -      -       +      -
    545A  ARG      2.9    18.3    +      -       -      +
    546A  ILE*     3.0    11.5    -      -       +      +
    547A  SER      2.7    27.5    +      -       -      -
    550A  TRP*     1.3    79.4    -      -       -      +
    552A  ARG*     1.3    69.1    +      -       -      +
    553A  VAL*     4.4     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 552 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    513A  LEU      2.8     7.3    +      -       -      +
    514A  ASP*     2.6    39.5    +      -       -      +
    515A  LEU      2.8    26.5    +      -       -      -
    546A  ILE*     5.1     2.2    -      -       -      -
    547A  SER      3.7    13.0    -      -       -      +
    548A  GLN*     3.1    45.3    +      -       -      +
    551A  VAL*     1.3    74.6    -      -       -      +
    553A  VAL*     1.3    64.1    +      -       -      +
    568A  LEU*     3.5    32.9    +      -       +      +
    569A  LYS*     3.7    16.4    -      -       -      +
    610A  ASP*     3.3    36.8    +      -       -      -
    611A  ARG*     3.4    29.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 553 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    515A  LEU*     3.2     8.3    -      -       +      +
    517A  PHE*     3.9    25.8    -      -       +      -
    541A  MET*     3.7    24.7    -      -       +      -
    544A  LEU*     3.9    20.4    -      -       +      -
    546A  ILE*     4.1    23.3    -      -       +      +
    551A  VAL*     4.4     2.7    -      -       +      -
    552A  ARG*     1.3    80.2    -      -       -      +
    554A  ALA*     1.3    62.0    +      -       -      +
    566A  ILE*     3.2    16.3    -      -       +      +
    567A  GLY      3.4    12.3    -      -       -      +
    568A  LEU*     3.7     4.7    +      -       -      -
    577A  LEU*     4.2    17.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 554 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    515A  LEU      3.0     5.1    +      -       -      -
    516A  VAL*     4.0    27.1    -      -       +      -
    517A  PHE*     2.9    27.6    +      -       -      -
    553A  VAL*     1.3    76.2    -      -       -      +
    555A  VAL*     1.3    66.0    +      -       -      +
    556A  VAL*     4.3     0.9    -      -       +      -
    566A  ILE*     3.1    17.0    -      -       -      +
    567A  GLY*     4.3     0.9    -      -       -      -
    568A  LEU*     4.0    18.4    -      -       +      +
    605A  ILE*     4.4    11.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 555 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    517A  PHE*     3.5    20.4    -      -       +      -
    519A  LEU*     4.3    19.1    -      -       +      -
    537A  VAL*     4.3    11.0    -      -       +      -
    541A  MET*     4.6     9.0    -      -       +      -
    553A  VAL*     5.4     0.4    -      -       +      -
    554A  ALA*     1.3    80.6    -      -       -      +
    556A  VAL*     1.3    68.9    +      -       -      +
    557A  GLU      5.2     0.2    -      -       -      +
    564A  ALA*     3.5     0.3    -      -       -      -
    565A  TYR*     2.9    31.3    +      -       +      -
    566A  ILE*     3.0    31.6    +      -       +      +
    581A  ALA*     4.5    12.1    -      -       +      -
    584A  VAL*     4.2    25.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 556 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    516A  VAL*     4.5     1.8    -      -       +      -
    517A  PHE      2.9     8.1    +      -       -      +
    518A  LEU*     3.3    20.6    -      -       +      -
    519A  LEU*     2.7    32.2    +      -       -      +
    555A  VAL*     1.3    85.7    -      -       -      +
    557A  GLU*     1.3    59.2    +      -       -      +
    558A  TYR*     3.8     1.0    +      -       -      -
    562A  SER*     3.5    32.8    -      -       -      +
    563A  HIS      3.5    12.6    -      -       -      +
    564A  ALA*     4.1    13.5    -      -       +      +
    566A  ILE      5.0     2.0    -      -       -      +
    597A  VAL*     4.4     7.9    -      -       +      -
    600A  TYR*     4.1     5.6    -      -       +      -
    605A  ILE*     4.1    26.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 557 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    519A  LEU*     3.4    12.1    -      -       +      +
    521A  GLY*     4.1     4.6    -      -       -      -
    530A  PHE*     4.2    22.4    -      -       +      -
    555A  VAL*     4.3     0.6    -      -       +      +
    556A  VAL*     1.3    73.5    -      -       -      +
    558A  TYR*     1.3    66.4    +      -       -      +
    559A  HIS*     2.8    31.2    +      -       -      +
    562A  SER*     3.8     0.7    -      -       -      -
    563A  HIS*     2.9    45.6    +      -       -      +
    565A  TYR*     3.7    33.4    +      -       +      -
    584A  VAL*     4.1     8.1    -      -       +      -
    585A  LYS*     3.8    10.4    -      -       -      +
    587A  ALA*     3.9    20.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 558 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    518A  LEU*     3.4    15.0    -      -       +      -
    519A  LEU      2.8    48.2    +      -       -      -
    520A  ASP*     3.8     8.4    +      -       -      +
    521A  GLY*     2.7    32.9    +      -       -      -
    556A  VAL      4.4     0.2    -      -       -      -
    557A  GLU*     1.3    74.6    -      -       -      +
    559A  HIS*     1.3    63.6    +      -       -      +
    561A  GLY      3.5     8.5    -      -       -      +
    562A  SER*     4.3     0.7    -      -       -      +
    592A  ALA*     3.8    14.5    -      -       +      +
    593A  SER      3.4    25.8    -      -       -      +
    594A  THR*     3.7    30.6    -      -       +      +
    597A  VAL*     3.3    33.7    -      -       +      -
    620A  LEU*     3.7    18.4    -      -       +      +
    621A  LEU      3.2    15.2    +      -       -      -
    622A  MET*     3.8     8.1    -      -       -      +
    624A  SER*     5.8     0.2    -      -       -      -
----------------------------------------------------------
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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