Contacts of the strand formed by residues 1741 - 1747 (chain A) in PDB entry 3AU5


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 MET1741 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1730A  ILE*     6.0     0.2    -      -       -      -
   1740A  ASN*     1.3    77.1    -      -       -      +
   1742A  PHE*     1.3    68.9    +      -       -      +
   1743A  ALA*     5.9     0.2    -      -       -      -
   1788A  LEU*     3.5     5.2    -      -       -      +
   1789A  TYR*     2.6    46.4    +      -       -      -
   1790A  CYS*     3.2    37.3    +      -       +      +
   1792A  LEU*     4.9     4.0    -      -       +      +
   2035A  ALA*     4.5     8.7    -      -       +      +
   2038A  SER*     5.6     0.7    -      -       -      +
   2039A  MET*     3.7    43.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE1742 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1726A  VAL*     4.0     9.4    -      -       -      +
   1730A  ILE*     3.8    24.8    -      -       +      +
   1735A  MET*     3.6    35.7    -      -       +      -
   1738A  SER*     3.3    31.4    -      -       -      -
   1740A  ASN      4.1     5.2    -      -       -      -
   1741A  MET*     1.3    90.3    -      -       -      +
   1743A  ALA*     1.3    66.3    +      -       -      +
   1786A  PHE*     3.4    30.7    -      +       +      -
   1787A  LYS*     3.1    22.4    -      -       -      +
   1788A  LEU*     3.3    35.4    -      -       +      -
   1789A  TYR*     4.0     2.0    -      -       -      -
   1803A  GLU*     4.0     6.5    -      -       +      -
   1806A  PHE*     4.2     6.5    -      +       -      -
----------------------------------------------------------
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Residues in contact with ALA1743 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1726A  VAL*     3.7    16.3    -      -       -      +
   1742A  PHE*     1.3    79.6    -      -       -      +
   1744A  LEU*     1.3    64.0    +      -       -      +
   1745A  PHE*     3.4    14.0    -      -       +      -
   1754A  ALA*     5.3     2.2    -      -       +      -
   1755A  ILE      4.8     8.3    -      -       -      +
   1786A  PHE*     3.6     6.6    -      -       -      -
   1787A  LYS      3.0    27.8    +      -       -      -
   1789A  TYR*     3.9    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU1744 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1704A  VAL*     3.7    28.5    -      -       +      -
   1722A  ALA*     4.3    21.7    -      -       +      +
   1725A  VAL*     4.1    23.3    -      -       +      -
   1726A  VAL*     3.5    17.4    -      -       +      +
   1729A  LEU*     5.1     1.1    -      -       +      -
   1743A  ALA*     1.3    77.0    -      -       -      +
   1745A  PHE*     1.3    66.5    +      -       -      +
   1754A  ALA*     3.8     1.0    -      -       -      -
   1755A  ILE*     2.9    40.7    +      -       +      -
   1761A  VAL*     4.5    11.7    -      -       +      -
   1784A  PHE*     4.0    27.6    -      -       +      -
   1785A  TYR      3.4    15.9    -      -       -      +
   1786A  PHE*     4.5     3.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE1745 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1743A  ALA*     3.4    25.8    -      -       +      -
   1744A  LEU*     1.3    77.3    -      -       -      +
   1746A  GLU*     1.3    63.7    +      -       -      +
   1747A  TYR*     4.3     0.7    -      -       +      -
   1752A  ASP*     3.0    35.7    -      -       -      +
   1753A  LYS      3.3    15.0    -      -       -      -
   1754A  ALA*     3.7    20.0    -      -       +      -
   1755A  ILE*     4.3     3.1    -      -       -      -
   1783A  LYS      3.4     0.2    -      -       -      +
   1784A  PHE*     3.2    11.8    -      -       -      -
   1785A  TYR*     2.8    41.4    +      -       +      +
   1787A  LYS*     3.5    35.9    -      -       +      -
   1788A  LEU      4.3     5.4    -      -       -      -
   1789A  TYR*     3.5    30.3    -      +       +      -
----------------------------------------------------------
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Residues in contact with GLU1746 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1745A  PHE*     1.3    75.5    -      -       -      +
   1747A  TYR*     1.3    60.1    +      -       -      +
   1751A  VAL      3.5     0.9    -      -       -      +
   1752A  ASP*     3.3    10.2    -      -       -      +
   1753A  LYS*     3.1    46.7    +      -       -      +
   1755A  ILE*     3.9    21.8    -      -       +      +
   1764A  VAL*     3.9    24.4    -      -       -      +
   1767A  LYS*     2.8    36.0    +      -       -      -
   1768A  PHE*     3.9    14.7    -      -       +      -
   1782A  TRP*     3.6    18.6    -      -       +      -
   1783A  LYS      3.5     4.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR1747 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1707A  HIS*     3.6    18.4    +      -       -      -
   1745A  PHE*     4.3     0.2    -      -       +      -
   1746A  GLU*     1.3    72.8    -      -       -      +
   1748A  ASN*     1.3    58.7    +      -       -      +
   1749A  GLY*     4.1    26.0    -      -       -      +
   1750A  HIS      5.0     2.5    -      -       -      -
   1751A  VAL      3.4    13.9    -      -       -      -
   1752A  ASP*     3.1    40.0    +      -       +      +
   1781A  PRO      3.6     1.4    -      -       -      +
   1782A  TRP*     3.1     7.9    -      -       -      -
   1783A  LYS*     2.6    41.3    +      -       +      +
   1785A  TYR*     3.4    48.2    -      +       +      -
   1787A  LYS*     3.1    30.6    +      -       +      -
   1813A  GLU*     4.0    11.4    +      -       -      -
   1817A  HIS*     6.0     1.3    -      -       -      -
----------------------------------------------------------
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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