Contacts of the strand formed by residues 175 - 180 (chain H) in PDB entry 5A0Q


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 175 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15H  GLY*     3.1     2.1    -      -       -      -
     16H  ALA*     2.9    38.5    +      -       +      +
     17H  ASP      5.1     2.7    -      -       -      +
     18H  SER*     4.9     0.8    -      -       -      -
     30H  VAL*     3.2    45.9    +      -       -      +
     31H  THR      4.3    11.5    +      -       -      -
     32H  ASP*     4.1    27.8    +      -       -      +
     33H  LYS      5.8     0.2    -      -       -      +
     34H  LEU*     3.2    13.2    -      -       +      +
    173H  VAL*     3.4    25.2    +      -       -      +
    174H  ILE*     1.3    75.4    -      -       -      +
    176H  LEU*     1.3    61.0    +      -       -      +
    186H  ARG*     6.4     0.9    -      -       +      +
    187H  GLN      3.7     4.0    -      -       -      +
    188H  VAL*     3.4    36.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 176 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13H  VAL*     3.7    18.4    -      -       +      -
     14H  LEU      3.2    17.9    -      -       -      +
     15H  GLY*     4.9     1.6    -      -       -      -
     34H  LEU*     3.8     3.6    -      -       -      -
    153H  LEU*     4.3    19.1    -      -       +      +
    156H  THR*     3.1    30.7    -      -       -      +
    157H  ALA*     4.6     5.2    -      -       +      +
    160H  LEU*     6.1     0.2    -      -       +      -
    174H  ILE*     5.4     3.4    -      -       +      -
    175H  ARG*     1.3    73.7    -      -       -      +
    177H  ALA*     1.3    78.4    +      -       -      +
    178H  ALA*     4.4     5.8    -      -       +      +
    185H  GLU      4.5     5.2    -      -       -      +
    186H  ARG*     3.0    26.6    -      -       -      +
    187H  GLN*     3.0    48.5    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 177 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12H  VAL      4.7     0.2    -      -       -      -
     13H  VAL*     3.7     0.9    -      -       -      -
     14H  LEU*     2.9    44.9    +      -       +      +
     34H  LEU*     3.5    10.2    -      -       +      +
     42H  PHE*     5.4     2.9    -      -       +      -
    176H  LEU*     1.3    92.5    -      -       -      +
    178H  ALA*     1.3    59.9    +      -       -      +
    179H  ILE*     4.1    19.5    -      -       +      -
    184H  VAL*     4.8     0.7    -      -       +      -
    186H  ARG*     3.5    21.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 178 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12H  VAL      3.6     7.4    -      -       -      -
     13H  VAL*     4.5    12.3    -      -       +      -
    149H  LYS*     6.1     3.8    -      -       -      +
    176H  LEU*     4.6     4.0    -      -       +      -
    177H  ALA*     1.3    73.5    -      -       -      +
    179H  ILE*     1.3    55.5    +      -       -      +
    180H  ALA*     5.3     2.2    -      -       +      -
    183H  GLY      4.5     0.2    -      -       -      -
    184H  VAL*     2.7    37.5    -      -       -      +
    185H  GLU*     2.8    37.4    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 179 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11H  GLY*     3.1    11.9    -      -       -      -
     12H  VAL*     3.0    36.6    +      -       +      +
     14H  LEU*     5.2     2.2    -      -       +      -
     40H  ARG*     3.2    35.7    -      -       -      +
     42H  PHE*     3.7    35.2    -      -       +      +
    101H  ALA*     4.9     1.8    -      -       +      -
    102H  GLY      4.6     6.1    -      -       -      +
    103H  TRP*     4.0    17.3    -      -       +      -
    177H  ALA*     4.2    12.1    -      -       +      -
    178H  ALA*     1.3    78.5    -      -       -      +
    180H  ALA*     1.3    69.9    +      -       -      +
    183H  GLY      3.9     2.2    -      -       -      -
    184H  VAL*     4.0    22.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 180 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10H  GLY*     3.7    19.7    -      -       -      -
     11H  GLY      3.8     1.1    -      -       -      +
     40H  ARG*     4.3     5.1    +      -       -      -
    103H  TRP*     3.7    19.5    -      -       -      -
    149H  LYS*     5.4     7.9    -      -       -      -
    178H  ALA*     5.3     1.8    -      -       +      -
    179H  ILE*     1.3    82.2    -      -       -      +
    181H  GLU*     1.4    72.0    +      -       +      +
    182H  SER      3.1     2.6    +      -       -      -
    183H  GLY      2.8    21.2    +      -       -      +
    184H  VAL*     5.2     0.3    -      -       -      +
----------------------------------------------------------
 Back to top of page


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