Contacts of the strand formed by residues 180 - 183 (chain r) in PDB entry 6QX2


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 180 (chain r).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35r  LEU*     4.4     5.6    -      -       -      -
    174r  GLY      3.2    15.5    -      -       -      +
    175r  ILE*     4.1     7.4    -      -       +      -
    176r  ALA      4.2     0.4    -      -       -      +
    179r  MET*     1.3    72.8    -      -       -      +
    181r  THR*     1.3    62.8    +      -       -      +
    334r  ASN*     3.0    25.5    +      -       -      +
    336r  ILE*     3.3    17.8    -      -       -      +
   2017w    G      3.7    30.5    +      -       -      +
   2018w    C      4.4     6.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 181 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35r  LEU*     3.9    13.0    -      -       -      -
     36r  PRO*     4.6     9.2    -      -       -      -
    172r  ALA      4.8     4.7    -      -       -      -
    173r  SER*     3.3     4.1    -      -       -      -
    174r  GLY*     2.8    33.8    +      -       -      +
    180r  ALA*     1.3    76.8    -      -       -      +
    182r  ASN*     1.3    63.4    +      -       -      +
    183r  ILE*     5.1     3.6    -      -       -      -
    334r  ASN*     3.4     9.4    -      -       -      -
    336r  ILE*     3.1    27.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 182 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172r  ALA      3.5     2.5    -      -       -      -
    173r  SER*     3.4    21.1    -      -       -      -
    181r  THR*     1.3    75.0    -      -       -      +
    183r  ILE*     1.3    60.2    +      -       -      +
    267r  GLN*     4.8     3.6    +      -       -      +
    331r  PHE*     2.9    38.8    -      -       -      -
    332r  GLY      2.9    31.3    +      -       -      +
    333r  VAL*     3.5     8.0    -      -       -      +
    334r  ASN*     2.8    41.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 183 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36r  PRO*     4.9     1.1    -      -       +      -
    167r  LEU*     3.9    43.1    -      -       +      +
    168r  LEU*     4.1    23.6    -      -       +      -
    171r  GLY*     3.2     0.7    -      -       -      -
    172r  ALA*     2.7    44.1    +      -       +      +
    181r  THR*     5.1     1.1    -      -       -      -
    182r  ASN*     1.3    77.0    -      -       -      +
    184r  PRO*     1.3    79.0    -      -       +      +
    185r  PRO*     3.9     1.4    -      -       -      +
    266r  PHE*     5.8     0.3    -      -       -      -
    331r  PHE*     3.8     5.4    -      -       -      -
    334r  ASN      4.4     0.9    -      -       -      +
    335r  MET*     3.8    34.1    -      -       +      -
    336r  ILE      4.2    17.3    -      -       -      +
    337r  ALA*     4.9     0.4    -      -       +      -
    346r  ILE*     5.8     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