Contacts of the strand formed by residues 162 - 165 (chain A) in PDB entry 4UT2


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 ALA 162 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  ILE      3.5     4.1    +      -       -      +
     52A  LEU*     3.4    21.6    -      -       +      -
     53A  LEU*     2.8    30.0    +      -       -      +
    121A  LEU*     3.9     9.3    -      -       -      +
    160A  PRO      3.8     0.6    -      -       -      -
    161A  ILE*     1.3    82.4    -      -       +      +
    163A  ALA*     1.3    57.3    +      -       -      +
    170A  PHE*     4.0    20.0    -      -       +      -
    171A  CYS      3.1    14.8    -      -       -      +
    172A  CYS*     4.3     2.5    -      -       +      -
    186A  ILE*     4.5    10.3    -      -       +      -
    204A  LEU*     5.5     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 163 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52A  LEU*     4.4     0.7    -      -       -      -
     53A  LEU*     3.2    22.4    -      -       +      +
     55A  LEU*     4.2     9.4    -      -       +      -
     88A  LEU*     4.0    31.6    -      -       +      -
    121A  LEU*     4.1     2.9    -      -       +      +
    162A  ALA*     1.3    75.2    -      -       -      +
    164A  ILE*     1.3    65.2    +      -       -      +
    165A  VAL*     4.1     1.3    -      -       +      -
    169A  ILE      3.5     0.9    -      -       -      +
    170A  PHE*     3.6     3.1    -      -       -      -
    171A  CYS*     2.7    40.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 164 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52A  LEU*     4.1    20.2    -      -       +      -
     53A  LEU      2.7    12.2    +      -       -      +
     54A  GLU*     3.4    12.6    -      -       +      +
     55A  LEU      2.9    24.1    +      -       -      +
    163A  ALA*     1.3    77.7    -      -       -      +
    165A  VAL*     1.3    62.3    +      -       -      +
    166A  ASP      3.9     0.5    +      -       -      -
    167A  GLU*     3.7    32.6    +      -       -      +
    168A  LYS      4.1     0.2    -      -       -      +
    169A  ILE      3.1     7.9    -      -       -      +
    170A  PHE*     4.0    14.6    -      -       +      -
    183A  MET*     4.0    34.8    -      -       +      -
    187A  ARG*     5.5     3.1    -      -       -      +
    241A  LEU*     4.2    10.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55A  LEU*     3.3    15.0    -      -       +      +
     57A  ALA*     4.3     6.7    -      -       -      +
     59A  LEU*     4.1    30.5    -      -       +      -
     61A  ILE*     4.6     4.7    -      -       +      -
     88A  LEU*     4.6     4.9    -      -       +      -
    164A  ILE*     1.3    74.9    -      -       -      +
    166A  ASP*     1.3    85.5    +      -       +      +
    167A  GLU      3.2     1.1    -      -       -      -
    168A  LYS*     3.0    12.3    +      -       -      +
    169A  ILE*     2.8    37.8    +      -       +      +
    171A  CYS*     3.9    25.8    -      -       -      -
    285A  VAL*     4.8     9.9    -      -       +      -
    289A  LEU*     4.7     0.4    -      -       +      +
----------------------------------------------------------
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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