Contacts of the strand formed by residues 96 - 102 (chain R) in PDB entry 1D0G


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 SER 96 (chain R).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203D  ASP      6.1     0.2    -      -       -      -
    205D  GLN*     3.3    22.4    -      -       -      +
     92R  ARG*     3.2    21.7    -      -       -      +
     93R  GLU*     2.7    42.0    +      -       -      +
     95R  ASP*     1.3    75.8    -      -       -      +
     97R  PRO*     1.3    57.6    -      -       -      +
     98R  GLU      3.6     0.7    +      -       -      -
     99R  MET      3.9     2.4    -      -       -      +
    101R  ARG*     3.0    39.9    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 97 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147D  LEU*     4.1    27.7    -      -       +      +
    148D  GLY      5.0     0.9    -      -       -      +
    205D  GLN*     4.1     1.8    -      -       -      +
    207D  VAL*     4.9     3.4    -      -       +      -
    209D  TYR*     3.7    19.5    -      -       +      +
    261D  THR*     3.8    15.3    -      -       +      -
     92R  ARG*     3.0    32.9    +      -       +      +
     93R  GLU      4.0     4.3    -      -       -      +
     94R  GLU*     3.5    18.8    -      -       -      +
     95R  ASP      3.4     5.8    -      -       -      +
     96R  SER*     1.3    85.4    -      -       -      +
     98R  GLU*     1.3    64.4    +      -       -      +
     99R  MET      3.7     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 98 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189A  TYR*     2.8    32.6    +      -       -      +
    191A  ARG*     3.3    31.9    +      -       -      -
    239A  LEU*     4.3    10.5    -      -       +      -
    147D  LEU*     5.1     2.9    -      -       -      +
    205D  GLN*     3.1    11.0    +      -       -      +
    207D  VAL*     3.7    27.4    -      -       +      -
    209D  TYR*     3.5    16.1    +      -       -      +
    224D  LYS*     2.9    41.4    +      -       -      +
    226D  ALA*     4.1     4.5    -      -       +      -
     67R  ASP*     4.7     1.0    -      -       -      +
     92R  ARG*     4.8     4.9    +      -       -      -
     97R  PRO*     1.3    82.4    -      -       -      +
     99R  MET*     1.3    61.5    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 99 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191A  ARG*     3.1    38.6    -      -       +      +
    192A  PHE      4.0    17.9    -      -       -      +
    193A  GLN*     3.4    32.3    -      -       -      +
    237A  TYR*     3.7    22.7    -      -       +      -
    239A  LEU*     3.5    30.1    -      -       +      -
    205D  GLN*     3.0    28.4    +      -       -      +
     67R  ASP*     5.4     2.5    -      -       -      +
     92R  ARG*     4.2     6.3    -      -       -      +
     96R  SER      3.9     5.9    -      -       -      +
     97R  PRO      3.7     0.4    -      -       -      -
     98R  GLU*     1.3    79.7    -      -       -      +
    100R  CYS*     1.3    75.1    +      -       -      +
    101R  ARG*     3.4     3.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 100 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193A  GLN*     3.9    19.8    +      -       -      +
    237A  TYR*     4.4     3.8    -      -       -      -
     67R  ASP*     5.1     3.5    +      -       -      -
     69R  GLY      3.7     8.5    -      -       -      +
     70R  GLU*     3.7    20.6    -      -       -      -
     86R  CYS*     2.0    57.9    -      -       -      -
     90R  THR*     3.5    16.8    -      -       -      +
     91R  PHE      3.6     2.5    -      -       -      -
     92R  ARG*     3.8     4.2    -      -       -      +
     99R  MET*     1.3    89.3    -      -       -      +
    101R  ARG*     1.3    58.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 101 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    237A  TYR*     4.0     8.5    -      -       +      -
    200D  THR*     5.5     3.4    -      -       -      +
    201D  LYS*     3.0    39.7    +      -       -      +
    203D  ASP*     3.0    49.9    +      -       -      +
    205D  GLN*     3.6     7.4    -      -       -      +
     90R  THR*     3.0     9.2    -      -       -      -
     91R  PHE*     2.8    63.4    +      -       +      +
     93R  GLU*     3.7    11.9    +      -       -      -
     96R  SER*     3.0    40.8    +      -       -      -
     99R  MET      3.5    11.9    -      -       -      +
    100R  CYS*     1.3    73.9    -      -       -      +
    102R  LYS*     1.3    61.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 102 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193A  GLN*     6.2     1.6    -      -       -      +
    195A  GLU*     3.4    28.6    +      -       -      -
    236A  GLU*     3.8    42.0    +      -       +      +
    237A  TYR*     6.1     0.2    -      -       -      -
    201D  LYS*     2.7    28.3    +      -       -      +
     89R  GLY      4.0     4.0    -      -       -      +
     90R  THR*     4.5    13.0    -      -       +      -
     91R  PHE*     4.1     0.4    -      -       -      -
    101R  ARG*     1.3    73.3    -      -       -      +
    103R  CYS*     1.3    68.0    +      -       -      +
----------------------------------------------------------
 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