Contacts of the strand formed by residues 178 - 187 (chain G) in PDB entry 6XAV


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 178 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139G  THR*     2.5    45.8    +      -       +      +
    140G  GLY      3.3     6.7    -      -       -      +
    141G  VAL*     4.8    13.0    -      -       +      +
    173G  PHE*     5.2     2.3    -      -       -      -
    176G  GLY      5.4     2.2    -      -       -      +
    177G  ASP*     1.3    76.4    -      -       -      +
    179G  VAL*     1.3    62.4    +      -       -      +
    180G  ARG*     4.3     2.9    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 179 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138G  ILE      3.6     0.9    -      -       -      +
    139G  THR*     3.3     6.5    -      -       -      -
    140G  GLY      2.7    35.2    +      -       -      +
    142G  VAL*     3.7    24.2    -      -       +      -
    150G  ILE*     4.8     2.7    -      -       +      -
    152G  LEU*     3.8    12.2    -      -       +      +
    162G  ILE*     3.8    22.0    -      -       +      -
    173G  PHE*     3.6    36.6    -      -       +      -
    177G  ASP      3.8     2.9    -      -       -      +
    178G  ARG*     1.3    77.4    -      -       -      +
    180G  ARG*     1.3    64.7    +      -       -      +
    181G  GLY      3.8     0.5    +      -       -      -
    199G  ARG*     3.4    23.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 180 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137G  ILE*     3.4    45.6    -      -       +      +
    138G  ILE      3.6     5.2    -      -       -      +
    139G  THR*     4.3    20.2    -      -       +      +
    178G  ARG      4.3     2.7    +      -       -      +
    179G  VAL*     1.3    74.6    -      -       -      +
    181G  GLY*     1.3    58.9    +      -       -      +
    199G  ARG*     3.0    28.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 181 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137G  ILE*     4.6     5.6    -      -       -      +
    138G  ILE*     3.3    36.8    +      -       -      +
    152G  LEU*     5.5     3.1    -      -       -      +
    162G  ILE*     5.0     6.2    -      -       -      +
    179G  VAL      3.8     1.8    +      -       -      -
    180G  ARG*     1.3    75.6    -      -       -      +
    182G  VAL*     1.3    60.4    +      -       -      -
    197G  VAL*     3.5    19.7    -      -       -      +
    198G  THR      5.0     2.7    -      -       -      -
    199G  ARG*     5.0     4.5    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 182 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88F  ARG*     6.4     0.2    -      -       -      +
    134G  GLU*     4.1    10.1    -      -       -      +
    135G  GLY*     6.4     0.9    -      -       -      -
    136G  GLU      5.3    11.2    -      -       -      +
    137G  ILE*     5.3    13.5    -      -       +      +
    138G  ILE*     5.4     0.7    -      -       -      -
    181G  GLY*     1.3    72.6    -      -       -      -
    183G  LEU*     1.3    76.3    +      -       +      +
    184G  TYR*     4.0     0.8    +      -       +      +
    197G  VAL*     3.4     5.1    -      -       -      +
    198G  THR*     3.0    33.8    +      -       +      +
    199G  ARG*     5.7     3.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 183 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130G  PHE*     4.5    22.7    -      -       +      -
    131G  ARG*     3.4    35.3    +      -       -      +
    134G  GLU*     3.2    46.8    -      -       +      +
    136G  GLU      5.8     2.5    -      -       -      +
    138G  ILE*     4.6     9.9    -      -       +      -
    181G  GLY      4.1     0.6    +      -       -      -
    182G  VAL*     1.3    81.9    -      -       +      +
    184G  TYR*     1.3    60.5    +      -       -      +
    185G  SER      5.4     0.2    -      -       -      +
    195G  LEU*     3.8    32.8    -      -       +      -
    196G  PHE      3.7    17.0    -      -       -      +
    197G  VAL*     3.7    16.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 184 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84F  SER*     4.8    12.6    +      -       -      -
     85F  GLN*     3.8    19.2    +      -       +      -
     88F  ARG*     5.1    17.7    -      -       -      -
    113F  LEU      5.4     0.4    -      -       -      -
    114F  LEU*     3.1    43.3    +      -       +      +
    131G  ARG*     4.3     8.3    +      -       -      +
    182G  VAL*     4.0     1.5    +      -       +      +
    183G  LEU*     1.3    76.1    -      -       -      +
    185G  SER*     1.3    73.1    +      -       -      +
    196G  PHE      3.8     3.0    +      -       -      -
    198G  THR*     4.3    21.3    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 185 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102F  ARG*     5.3    11.7    -      -       -      -
    131G  ARG*     3.9    10.1    +      -       -      +
    183G  LEU*     5.1     0.2    -      -       -      +
    184G  TYR*     1.3    92.6    -      -       -      +
    186G  VAL*     1.3    64.6    +      -       -      +
    187G  ARG*     4.3    10.2    +      -       -      +
    195G  LEU*     4.3     0.3    -      -       -      -
    196G  PHE*     2.9    34.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 186 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108F  GLU*     3.8    10.9    -      -       -      +
    127G  VAL*     5.1     8.3    -      -       +      -
    131G  ARG*     3.8    18.2    -      -       -      +
    185G  SER*     1.3    76.0    -      -       -      +
    187G  ARG*     1.3    68.5    +      -       -      +
    188G  PRO*     4.1     0.5    -      -       -      +
    193G  ALA*     3.9    15.5    -      -       +      -
    194G  GLN      3.3    27.8    -      -       -      +
    195G  LEU*     3.7    21.5    -      -       +      -
    196G  PHE      4.2     0.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 187 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102F  ARG*     5.8     2.9    -      -       -      +
    105F  LYS*     3.4    45.6    -      -       +      +
    108F  GLU*     4.3     2.0    -      -       -      +
    185G  SER*     5.2     9.6    +      -       -      +
    186G  VAL*     1.3    75.8    -      -       -      +
    188G  PRO*     1.3    69.1    -      -       +      +
    189G  GLU*     2.8    13.6    +      -       -      +
    193G  ALA*     3.5    12.5    -      -       -      +
    194G  GLN      3.7    11.4    +      -       -      +
    196G  PHE*     3.5    37.9    -      -       +      -
----------------------------------------------------------
 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