Contacts of the strand formed by residues 171 - 180 (chain B) in PDB entry 2O6C


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 LEU 171 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  VAL*     3.5    42.4    -      -       +      +
     40B  GLY*     5.1     3.4    -      -       -      -
     41B  PRO*     3.8    11.9    -      -       +      -
     42B  LEU*     3.7    22.4    -      -       +      -
    142B  PHE      3.6     0.9    -      -       -      +
    143B  GLU*     3.5     3.8    -      -       -      -
    144B  ILE*     2.8    45.5    +      -       +      +
    167B  TRP*     3.7    39.3    -      -       +      +
    169B  GLU      4.4     2.2    -      -       -      +
    170B  PRO*     1.3    74.2    -      -       -      +
    172B  VAL*     1.3    60.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 172 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  VAL*     3.2    26.6    -      -       -      +
    141B  ARG*     3.5    57.7    -      -       +      +
    142B  PHE      3.3     2.2    -      -       -      -
    143B  GLU*     4.2    11.9    -      -       +      -
    144B  ILE*     5.5     0.7    -      -       -      -
    170B  PRO      3.9     9.9    -      -       -      +
    171B  LEU*     1.3    79.9    -      -       -      +
    173B  ALA*     1.3    66.0    +      -       -      +
    174B  GLU*     4.1     9.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 173 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  ARG*     4.1    16.6    -      -       +      -
     39B  VAL*     4.6     2.0    -      -       +      -
     44B  VAL*     3.8    34.8    -      -       +      -
    141B  ARG*     3.5     1.4    -      -       -      -
    142B  PHE*     2.7    40.0    +      -       +      +
    144B  ILE*     4.8     2.4    -      -       +      +
    171B  LEU      4.3     0.2    +      -       -      -
    172B  VAL*     1.3    73.8    -      -       -      +
    174B  GLU*     1.3    59.0    +      -       -      +
    175B  TRP*     4.0    16.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 174 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  ARG*     2.9    29.3    +      -       -      +
    139B  LYS*     4.9    12.5    +      -       -      +
    140B  VAL      3.3    13.2    -      -       -      +
    141B  ARG*     3.0    42.7    +      -       +      +
    172B  VAL*     4.1     9.2    +      -       +      +
    173B  ALA*     1.3    74.4    -      -       -      +
    175B  TRP*     1.3    68.4    +      -       -      +
    176B  ASP*     3.8    20.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 175 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  ILE*     3.7    32.1    -      -       +      +
     34B  GLY*     3.3    26.9    -      -       -      -
     35B  GLU      2.6    28.5    +      -       -      -
     37B  ARG*     3.4    33.2    -      -       +      +
     44B  VAL*     4.4     7.0    -      -       +      -
     45B  GLY      4.5     2.0    -      -       -      -
     46B  GLY*     4.1    19.3    -      -       -      -
    138B  TYR      4.0     1.0    -      -       -      +
    139B  LYS*     3.5     1.4    -      -       -      -
    140B  VAL*     2.7    47.5    +      -       +      +
    142B  PHE*     3.7    48.9    -      +       -      -
    173B  ALA*     4.0    16.6    -      -       +      -
    174B  GLU*     1.3    74.2    -      -       -      +
    176B  ASP*     1.3    60.8    +      -       -      +
    177B  ASP      3.6     3.1    -      -       -      +
    178B  PHE*     5.2     2.7    -      -       +      +
    502B  SO4      3.5    11.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 176 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104B  HIS*     2.6    35.0    +      -       -      -
    138B  TYR      3.3     7.8    -      -       -      +
    139B  LYS*     3.6    28.3    +      -       +      +
    174B  GLU*     3.8    22.3    +      -       -      +
    175B  TRP*     1.3    75.4    -      -       -      +
    177B  ASP*     1.3    63.2    +      -       -      +
    502B  SO4      4.4     5.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 177 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  ILE      5.5     0.9    -      -       -      -
    104B  HIS*     3.2    19.8    -      -       -      -
    137B  THR*     3.6    14.5    -      -       +      +
    175B  TRP*     3.6     1.2    -      -       -      +
    176B  ASP*     1.3    88.3    -      -       -      +
    178B  PHE*     1.3    63.3    +      -       -      +
    179B  GLU*     3.4     9.8    +      -       -      +
    502B  SO4      5.3     2.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 178 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32B  PRO      4.4     1.6    -      -       -      -
     33B  ILE*     3.7    41.3    -      -       +      +
     48B  TYR*     3.4    46.9    -      +       +      -
     71B  ILE*     5.6     3.4    -      -       +      -
    131B  PHE*     3.8    29.8    -      +       -      -
    137B  THR*     3.2     1.4    -      -       -      -
    138B  TYR*     2.6    53.7    +      +       +      +
    140B  VAL*     3.7    28.3    -      -       +      -
    175B  TRP*     4.9     3.5    +      -       +      +
    177B  ASP*     1.3    73.0    -      -       -      +
    179B  GLU*     1.3    70.6    +      -       -      +
    180B  TRP*     3.7    15.9    +      +       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 179 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48B  TYR*     4.2     9.2    +      -       -      -
    136B  GLY      3.8     3.1    -      -       -      +
    137B  THR*     3.6    25.9    +      -       +      +
    177B  ASP*     3.4     7.4    +      -       -      +
    178B  PHE*     1.3    87.7    -      -       -      +
    180B  TRP*     1.3    60.1    +      -       -      +
    181B  LYS*     3.7    34.7    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 180 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48B  TYR*     3.9    29.6    -      +       -      -
     68B  ASP*     3.7    45.3    +      -       +      -
     69B  CYS*     4.4     1.3    -      -       +      -
    131B  PHE*     3.4    36.5    -      +       +      +
    134B  GLY*     3.3    29.9    +      -       -      -
    135B  LEU*     3.5    14.7    -      -       -      +
    136B  GLY*     2.9    41.2    +      -       -      +
    138B  TYR*     4.1     8.3    -      -       +      -
    178B  PHE*     3.7    16.9    +      +       +      -
    179B  GLU*     1.3    70.8    -      -       -      +
    181B  LYS*     1.3    58.8    +      -       -      +
    182B  GLY*     3.4    42.2    -      -       -      -
    183B  PRO*     3.6     9.0    -      -       +      -
    185B  TRP*     4.2     4.9    -      +       -      -
----------------------------------------------------------
 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