Contacts of the strand formed by residues 168 - 172 (chain D) in PDB entry 4XQ2


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 ARG 168 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83D  LEU*     4.3    13.2    +      -       -      +
     86D  LEU*     3.8    40.0    -      -       -      +
     87D  VAL*     5.9     2.6    -      -       -      +
    138D  ALA      2.7    19.1    +      -       -      +
    139D  LEU*     3.2    22.8    -      -       +      +
    140D  VAL*     2.4    37.2    +      -       -      +
    167D  ALA*     1.3    73.7    -      -       -      +
    169D  VAL*     1.3    59.8    +      -       -      +
    170D  VAL      4.1     0.2    -      -       -      -
    189D  ASP*     3.5    17.4    -      -       +      +
    190D  VAL*     4.1    18.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 169 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140D  VAL*     3.3     9.4    -      -       +      +
    142D  ILE*     3.7    26.7    -      -       +      -
    159D  SER*     3.6    24.0    -      -       -      +
    162D  ALA*     3.6    31.0    -      -       +      -
    163D  HIS*     3.9    11.7    -      -       +      +
    168D  ARG*     1.3    81.0    -      -       -      +
    170D  VAL*     1.3    63.2    +      -       -      +
    188D  ALA*     3.8    13.8    -      -       +      +
    189D  ASP*     2.7    44.5    +      -       -      +
    190D  VAL*     3.1     8.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 170 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83D  LEU*     3.5    24.7    -      -       +      -
    139D  LEU*     3.7    15.3    -      -       +      -
    140D  VAL      2.8    12.4    +      -       -      +
    141D  TRP*     3.5    38.8    -      -       +      -
    142D  ILE*     2.7    35.3    +      -       -      +
    168D  ARG      4.1     0.6    -      -       -      -
    169D  VAL*     1.3    76.4    -      -       -      +
    171D  VAL*     1.3    62.8    +      -       -      +
    172D  ASP      4.5     0.7    -      -       -      +
    190D  VAL*     3.3    18.6    -      -       +      +
    192D  LEU*     3.9    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 171 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142D  ILE*     3.0    17.7    -      -       +      +
    144D  THR*     4.1    20.2    -      -       +      -
    155D  VAL*     3.8    35.2    -      -       +      -
    170D  VAL*     1.3    80.3    -      -       -      +
    172D  ASP*     1.3    75.1    +      -       -      +
    173D  ASN*     3.3     8.3    +      -       +      +
    181D  GLN*     4.4     0.9    -      -       -      +
    183D  PRO*     3.8    25.4    -      -       +      -
    188D  ALA*     3.9    10.8    -      -       +      -
    190D  VAL      3.0     6.1    +      -       -      -
    191D  SER*     3.6     3.1    -      -       -      -
    192D  LEU      2.8    25.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 172 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103D  THR*     4.6     5.7    +      -       -      -
    141D  TRP*     4.4    10.2    -      -       -      +
    142D  ILE      2.6     9.8    +      -       -      +
    143D  GLU*     3.5    23.0    -      -       +      +
    144D  THR      3.5    23.6    +      -       -      +
    170D  VAL*     4.1     1.8    -      -       -      +
    171D  VAL*     1.3    69.9    -      -       -      +
    173D  ASN*     1.3    59.3    +      -       -      +
    174D  THR*     2.6    29.5    +      -       -      -
    175D  PHE*     5.2     1.6    +      -       -      +
    192D  LEU*     3.3    31.0    -      -       +      +
    197D  LLP      2.7    35.5    +      -       -      +
----------------------------------------------------------
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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