Contacts of the strand formed by residues 160 - 165 (chain D) in PDB entry 4UN7


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 160 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128D  TRP*     4.1     9.2    -      -       +      -
    129D  ASN      3.6    23.8    -      -       -      +
    130D  LYS*     3.5    16.4    -      -       +      -
    153D  LEU*     3.7     2.1    -      -       -      +
    154D  ASP*     3.1     6.6    +      -       -      +
    155D  ASP*     3.0    37.2    +      -       +      -
    158D  HIS*     3.8    22.4    -      -       +      -
    159D  GLY*     1.3    74.8    -      -       -      +
    161D  TYR*     1.3    69.2    +      -       -      +
     14F    A      4.0     5.4    -      -       +      -
     15F    C      3.6    37.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 161 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128D  TRP*     3.5     4.9    -      -       -      +
    129D  ASN      2.8    33.9    +      -       -      +
    130D  LYS      3.8    19.1    -      -       -      -
    132D  LYS*     3.6    45.8    +      -       +      +
    135D  LEU*     3.8    14.4    -      -       +      -
    151D  ILE*     4.3     7.9    -      -       +      -
    152D  HIS      3.4     8.7    -      -       -      +
    153D  LEU*     3.8    39.0    -      -       +      +
    154D  ASP*     4.1     0.9    -      -       -      +
    159D  GLY*     3.9    14.4    -      -       -      -
    160D  VAL*     1.3    78.1    -      -       -      +
    162D  VAL*     1.3    62.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 162 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126D  ARG*     3.8    25.4    -      -       +      -
    127D  ILE      3.2    13.5    -      -       -      +
    128D  TRP*     3.9    14.8    -      -       +      +
    135D  LEU*     4.2     4.5    -      -       -      -
    150D  THR      3.7     0.6    -      -       -      +
    151D  ILE*     3.2     5.9    -      -       -      +
    152D  HIS*     2.8    47.6    +      -       +      +
    154D  ASP*     3.6    25.4    -      -       +      +
    161D  TYR*     1.3    75.8    -      -       -      +
    163D  LEU*     1.3    74.1    +      -       -      +
    164D  ASN*     4.5     7.2    -      -       +      +
      6E    G      5.7     2.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 163 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    125D  LEU      4.0     0.3    -      -       -      +
    126D  ARG*     3.5     4.9    -      -       -      -
    127D  ILE*     2.9    41.9    +      -       +      +
    135D  LEU*     3.4    43.8    -      -       +      +
    138D  VAL*     4.2    13.7    -      -       +      -
    139D  SER*     3.7    22.0    -      -       -      +
    142D  LEU*     3.7    12.8    -      -       +      -
    149D  ASN*     3.8    15.7    -      -       +      +
    150D  THR      3.4     5.4    -      -       -      +
    151D  ILE*     4.4     4.3    -      -       +      +
    162D  VAL*     1.3    74.1    -      -       -      +
    164D  ASN*     1.3    60.3    +      -       -      +
    165D  ILE*     3.6    32.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 164 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124D  ARG*     5.2     5.0    +      -       -      +
    125D  LEU      3.9     3.7    +      -       -      +
    126D  ARG*     3.3    27.3    -      -       +      +
    149D  ASN*     3.1     6.6    -      -       -      +
    150D  THR*     2.7    49.1    +      -       -      +
    152D  HIS*     5.6     0.2    -      -       +      -
    162D  VAL*     3.9     7.9    -      -       +      -
    163D  LEU*     1.3    73.3    -      -       -      +
    165D  ILE*     1.3    73.5    +      -       -      +
    166D  SER*     3.9     1.3    +      -       -      +
      5E    T      3.9    40.8    +      -       -      +
      6E    G      3.7    12.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 165 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114D  TYR*     4.5     0.7    -      -       +      -
    125D  LEU*     2.9    58.8    +      -       +      +
    127D  ILE*     4.3    13.2    -      -       +      -
    142D  LEU*     4.0    14.1    -      -       +      -
    147D  VAL*     3.8    22.0    -      -       +      -
    148D  ARG      3.9     2.7    -      -       -      -
    149D  ASN*     4.5     1.3    -      -       +      -
    163D  LEU*     3.6    26.7    -      -       +      -
    164D  ASN*     1.3    80.4    +      -       -      +
    166D  SER*     1.3    76.2    +      -       -      +
    167D  LEU*     3.4     7.1    +      -       -      +
    173D  PHE*     3.8    33.9    -      -       +      -
      5E    T      4.0     0.7    +      -       -      -
----------------------------------------------------------
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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