Contacts of the strand formed by residues 569 - 578 (chain A) in PDB entry 4U6R


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 569 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    565A  ILE*     3.5     4.6    -      -       -      +
    566A  VAL*     3.0    35.0    +      -       +      +
    568A  LYS*     1.3    83.0    -      -       -      +
    570A  SER*     1.3    70.1    +      -       -      +
    571A  PHE*     4.4     8.9    -      -       +      -
    590A  MET      3.6     7.4    -      -       -      +
    591A  PHE*     4.6     3.4    -      -       +      -
    598A  VAL*     3.9    31.4    -      -       +      -
    630A  CYS*     4.1    15.7    -      -       +      -
    632A  GLU*     3.5    25.8    -      -       +      -
    639A  TYR*     3.9    25.4    -      -       +      +
    641A  ALA*     3.8    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 570 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    563A  VAL*     4.4     8.1    -      -       -      -
    564A  VAL      3.2    12.8    -      -       -      -
    565A  ILE*     4.1    15.3    -      -       -      -
    568A  LYS      5.0     1.3    +      -       -      -
    569A  ILE*     1.3    79.8    -      -       -      +
    571A  PHE*     1.3    66.2    +      -       -      +
    589A  GLY*     3.2     0.9    -      -       -      -
    590A  MET*     2.9    51.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 571 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    563A  VAL*     4.2     7.5    -      -       -      +
    564A  VAL*     2.9    62.6    +      -       +      -
    566A  VAL*     5.4     2.2    -      -       +      -
    569A  ILE*     4.4    11.7    -      -       +      -
    570A  SER*     1.3    81.2    -      -       -      +
    572A  CYS*     1.3    67.8    +      -       -      +
    573A  PRO*     3.6     7.3    -      -       +      +
    587A  TYR*     3.6    45.8    -      +       +      -
    588A  ARG      3.2    22.7    -      -       -      +
    589A  GLY*     3.9     3.8    -      -       -      -
    590A  MET*     6.3     0.2    -      -       -      -
    598A  VAL*     4.6     7.6    -      -       +      -
    600A  ARG*     5.6     0.4    -      -       -      -
    639A  TYR*     3.7    35.9    -      +       -      -
----------------------------------------------------------
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Residues in contact with CYS 572 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    562A  SER*     3.2    26.5    -      -       -      +
    563A  VAL*     4.6     5.3    -      -       +      +
    571A  PHE*     1.3    77.7    -      -       -      +
    573A  PRO*     1.3    61.1    -      -       -      +
    574A  LYS*     3.0    31.8    +      -       -      -
    575A  ASP*     3.0    40.9    +      -       -      +
    587A  TYR*     4.2     2.3    -      -       -      -
    588A  ARG      4.4     0.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 573 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    561A  THR*     3.9    22.7    -      -       +      +
    562A  SER      3.5    15.3    -      -       -      +
    564A  VAL*     3.9    21.1    -      -       +      -
    571A  PHE*     3.6    12.3    -      -       +      +
    572A  CYS*     1.3    83.3    -      -       +      +
    574A  LYS*     1.3    62.3    +      -       +      +
    575A  ASP      3.3     0.2    -      -       -      -
    576A  VAL*     3.5     9.9    -      -       -      +
    587A  TYR*     3.3    34.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 574 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    572A  CYS*     3.0    19.2    +      -       -      -
    573A  PRO*     1.3    81.9    -      -       +      +
    575A  ASP*     1.3    60.2    +      -       -      +
    576A  VAL*     3.0    14.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 575 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    572A  CYS*     3.0    34.9    +      -       -      +
    574A  LYS*     1.3    78.8    -      -       -      +
    576A  VAL*     1.3    60.9    +      -       -      +
    577A  LEU*     5.2     0.9    -      -       -      -
    587A  TYR*     3.2     5.6    -      -       -      -
    588A  ARG*     2.8    73.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 576 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    573A  PRO      3.5    21.1    -      -       -      +
    574A  LYS*     3.0     9.8    +      -       -      +
    575A  ASP*     1.3    71.8    -      -       -      +
    577A  LEU*     1.3    65.3    +      -       -      +
    578A  GLY*     3.6    17.7    -      -       -      +
    579A  HIS*     4.6     8.3    -      -       +      -
    585A  ILE*     3.9    27.8    -      -       +      -
    586A  VAL      3.5    10.5    -      -       -      +
    587A  TYR*     4.4     2.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 577 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    575A  ASP      3.6     1.1    +      -       -      +
    576A  VAL*     1.3    76.9    -      -       -      +
    578A  GLY*     1.3    56.7    +      -       -      +
    586A  VAL*     2.8    12.6    +      -       +      +
    587A  TYR      3.8    16.4    -      -       -      +
    588A  ARG*     3.8    28.0    -      -       +      +
    597A  ALA*     4.0     8.3    -      -       +      -
    644A  LEU*     3.8    25.8    -      -       +      -
   1001A  3E4      3.9    66.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 578 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    576A  VAL*     3.4     8.8    -      -       -      +
    577A  LEU*     1.3    80.6    -      -       -      +
    579A  HIS*     1.3    76.7    +      -       -      -
    585A  ILE*     3.9     2.8    -      -       -      +
    586A  VAL      2.9    24.0    +      -       -      +
   1001A  3E4      4.2     7.9    -      -       -      -
----------------------------------------------------------
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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