Contacts of the strand formed by residues 117 - 122 (chain B) in PDB entry 1D0N


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 VAL 117 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82B  GLN*     6.2     0.4    -      -       +      -
     83B  TYR      2.9    13.3    +      -       -      +
     84B  ASP*     3.6     9.8    -      -       -      +
     85B  LEU      2.8    25.3    +      -       -      +
    115B  ARG      4.8     3.4    -      -       -      +
    116B  ALA*     1.3    75.2    -      -       -      +
    118B  GLN*     1.3    64.4    +      -       -      +
    119B  HIS*     3.6    26.2    -      -       +      +
    351B  SER*     5.1     0.9    -      -       -      -
    352B  VAL      3.7     9.9    -      -       -      +
    353B  LEU*     4.3    19.3    -      -       +      -
    354B  PRO*     4.4     2.9    -      -       +      -
    357B  GLY      3.7    22.2    -      -       -      +
    359B  THR*     4.2    20.2    -      -       +      -
    382B  TYR*     4.3     9.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 118 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85B  LEU*     3.2    10.8    -      -       +      +
     87B  TYR*     6.1     0.2    -      -       +      -
    105B  THR*     3.2    46.8    +      -       +      +
    106B  VAL*     3.7    10.0    -      -       -      +
    109B  ASP*     3.3    25.9    +      -       +      +
    116B  ALA      4.4     6.5    -      -       -      +
    117B  VAL*     1.3    76.5    -      -       -      +
    119B  HIS*     1.3    65.4    +      -       -      +
    319B  LYS*     4.4     6.9    +      -       -      -
    328B  ARG      5.5     1.0    -      -       -      +
    331B  ALA*     5.2     2.6    -      -       -      +
    332B  LEU*     4.7     8.6    -      -       +      +
    351B  SER*     3.2     5.7    -      -       -      -
    352B  VAL*     2.9    65.3    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 119 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84B  ASP*     3.1    22.3    +      -       -      -
     85B  LEU      2.8    15.9    +      -       -      -
     86B  HIS*     3.4    45.8    -      +       +      +
     87B  TYR*     3.2    33.4    +      -       -      -
    117B  VAL*     3.6    25.8    -      -       +      +
    118B  GLN*     1.3    75.8    +      -       -      +
    120B  ARG*     1.3    60.7    +      -       -      +
    121B  GLU*     3.6     8.6    +      -       -      +
    127B  SER*     4.9     5.6    +      -       -      -
    129B  THR*     4.9     9.6    -      -       +      +
    332B  LEU*     5.9     1.6    -      -       -      -
    350B  VAL      3.3     6.5    -      -       -      +
    351B  SER*     2.9    25.6    +      -       -      -
    352B  VAL*     5.6     0.2    -      -       -      -
    359B  THR*     6.0     1.1    -      -       +      -
    382B  TYR*     5.5     1.1    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 120 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87B  TYR*     3.3    36.9    +      -       +      +
     89B  LEU*     4.0    22.3    -      -       +      +
    119B  HIS*     1.3    73.4    -      -       -      +
    121B  GLU*     1.3    66.3    +      -       -      +
    122B  VAL*     4.0    20.0    +      -       +      +
    332B  LEU*     5.5     2.9    -      -       +      -
    335B  ALA*     6.3     0.9    -      -       -      -
    336B  SER*     4.9    13.1    +      -       -      -
    339B  ILE*     4.6    10.4    -      -       -      +
    346B  LYS*     3.0    33.9    +      -       -      +
    347B  GLN      5.7     0.2    -      -       -      +
    348B  THR      3.4    19.7    +      -       -      +
    349B  GLN*     4.3     8.0    -      -       -      +
    350B  VAL*     2.8    45.1    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 121 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86B  HIS*     2.8    44.9    +      -       +      +
     87B  TYR      2.9    10.9    +      -       -      +
     88B  TRP*     3.1    20.4    -      -       +      -
     89B  LEU*     2.8    28.4    +      -       -      +
    119B  HIS*     3.6     5.9    -      -       +      +
    120B  ARG*     1.3    81.3    -      -       -      +
    122B  VAL*     1.3    63.1    +      -       -      +
    125B  PHE      4.6     0.7    -      -       -      +
    126B  GLU*     3.3     7.6    -      -       +      -
    127B  SER*     2.9    41.1    +      -       -      -
    130B  PHE*     3.3    18.8    -      -       +      +
    349B  GLN*     5.6     0.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 122 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88B  TRP*     4.4     0.9    -      -       -      -
     89B  LEU*     3.9    13.7    -      -       +      +
     91B  ASN*     4.2    12.6    -      -       -      +
    120B  ARG*     4.0    38.5    +      -       +      +
    121B  GLU*     1.3    78.9    +      -       -      +
    123B  GLN*     1.3    78.0    +      -       -      +
    124B  GLY      3.2     0.3    +      -       -      -
    125B  PHE*     2.9    21.9    +      -       +      -
    126B  GLU*     3.4    10.9    +      -       -      -
    346B  LYS      4.2     0.9    -      -       -      +
    347B  GLN*     4.1    38.1    +      -       +      +
    348B  THR      5.3     0.2    -      -       -      +
----------------------------------------------------------
 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