Contacts of the strand formed by residues 112 - 118 (chain B) in PDB entry 6CQX


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 THR 112 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104B  PRO*     5.3     0.7    -      -       +      -
    108B  PRO*     3.2    21.8    -      -       +      +
    110B  SER      3.1    12.8    +      -       -      -
    111B  PRO*     1.3    71.6    -      -       -      +
    113B  PRO*     1.3    72.4    -      -       +      +
    143B  ARG*     3.1    29.2    -      -       +      +
    144B  THR*     3.6    15.0    -      -       -      -
    145B  VAL*     3.7    12.1    -      -       +      +
    191B  GLY      2.9    12.6    +      -       -      -
    192B  GLY*     3.4     4.0    -      -       -      -
    193B  ASP*     2.6    28.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 113 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111B  PRO      4.4     3.6    -      -       -      +
    112B  THR*     1.3    88.1    -      -       +      +
    114B  VAL*     1.3    59.3    +      -       -      +
    143B  ARG      4.4     3.6    -      -       -      +
    144B  THR*     3.5    20.7    -      -       +      -
    145B  VAL      2.9    24.1    +      -       -      -
    193B  ASP*     4.4     0.6    -      -       +      -
    196B  SER*     3.8    27.6    -      -       -      +
    484B  ALA*     4.7    10.8    -      -       +      +
    485B  ARG*     3.7    34.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 114 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112B  THR      3.6    15.0    -      -       -      +
    113B  PRO*     1.3    73.1    -      -       -      +
    115B  LEU*     1.3    72.0    +      -       -      +
    116B  VAL*     3.9    12.1    -      -       +      -
    145B  VAL*     3.2    13.5    -      -       +      +
    147B  VAL*     3.9    20.9    -      -       +      -
    183B  VAL*     4.5     5.8    -      -       +      -
    187B  VAL*     3.7    27.4    -      -       +      -
    192B  GLY*     3.8     2.9    -      -       -      -
    193B  ASP      3.7    17.0    -      -       -      +
    196B  SER      3.0    13.0    +      -       -      +
    197B  VAL*     4.1     7.2    -      -       +      -
    198B  THR*     2.9    28.9    +      -       -      -
    484B  ALA*     5.1     1.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 115 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113B  PRO      4.2     0.2    +      -       -      -
    114B  VAL*     1.3    75.1    -      -       -      +
    116B  VAL*     1.3    56.7    -      -       -      +
    117B  TRP      4.1     0.4    -      -       -      -
    138B  LEU*     4.7    24.5    -      -       +      -
    144B  THR*     4.0    28.7    -      -       +      +
    145B  VAL      2.8    11.5    +      -       -      +
    146B  LEU*     3.3     8.9    -      -       +      +
    147B  VAL      2.7    32.9    +      -       -      +
    198B  THR*     3.5    30.7    -      -       +      +
    200B  PHE*     3.9    28.3    -      -       +      -
    226B  VAL*     5.6     0.7    -      -       +      -
    480B  TRP*     4.9    11.4    -      -       +      +
    481B  ALA*     5.0     7.4    -      -       -      +
    484B  ALA*     4.0    16.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 116 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114B  VAL*     3.9     7.4    -      -       +      -
    115B  LEU*     1.3    76.0    -      -       -      +
    117B  TRP*     1.3    60.9    +      -       -      +
    118B  ILE*     4.7     1.1    -      -       +      +
    147B  VAL*     3.2    28.7    -      -       +      +
    149B  MET*     3.7    29.4    -      -       +      -
    179B  ALA*     6.3     0.2    -      -       +      -
    180B  LEU*     3.9    18.4    -      -       +      -
    183B  VAL*     4.5     7.2    -      -       +      -
    197B  VAL*     3.9    22.9    -      -       +      -
    198B  THR      3.0     7.9    +      -       -      +
    199B  LEU*     3.5    16.3    -      -       +      +
    200B  PHE*     2.9    28.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 117 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116B  VAL*     1.3    72.0    -      -       -      +
    118B  ILE*     1.3    72.4    +      -       -      +
    119B  TYR*     3.6    21.0    +      +       +      +
    120B  GLY      5.1     0.2    -      -       -      -
    128B  SER*     5.6     0.9    -      -       -      -
    133B  TYR*     3.5    54.2    -      +       +      -
    146B  LEU*     4.7     3.8    -      -       +      -
    147B  VAL      2.8    14.4    +      -       -      +
    148B  SER*     3.7    29.3    -      -       -      -
    149B  MET*     3.7    14.2    +      -       -      +
    200B  PHE*     3.3    59.6    -      +       +      -
    201B  GLY*     3.7    13.5    -      -       -      -
    202B  GLU*     3.6    31.0    -      -       +      -
    228B  GLN*     4.1    11.7    -      -       -      -
    451B  ILE*     4.3     5.2    -      -       +      -
    454B  ILE*     6.4     0.2    -      -       +      -
    455B  PHE*     3.6    18.8    -      +       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 118 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116B  VAL*     4.7     4.5    -      -       +      +
    117B  TRP*     1.3    79.4    -      -       -      +
    119B  TYR*     1.3    66.0    +      -       -      +
    149B  MET*     3.8    21.3    -      -       +      -
    151B  TYR*     3.8    10.5    -      -       +      -
    176B  GLN*     3.6    42.0    -      -       +      +
    180B  LEU*     5.5     1.6    -      -       +      -
    199B  LEU*     4.8    11.9    -      -       +      -
    200B  PHE      2.9    14.7    +      -       -      +
    201B  GLY*     3.1    21.4    -      -       -      -
    202B  GLU      3.6     1.0    +      -       -      -
    205B  GLY*     3.3    11.6    -      -       -      +
    208B  SER*     3.9    14.4    -      -       -      -
    209B  VAL*     4.1    19.7    -      -       +      -
    212B  HIS*     4.4    11.9    -      -       +      -
----------------------------------------------------------
 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