Contacts of the strand formed by residues 97 - 103 (chain A) in PDB entry 5ODS


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 97 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  PHE*     3.5     5.1    -      -       -      -
     92A  ASN*     2.8    33.0    +      -       -      +
     95A  MET*     3.0    24.9    -      -       -      +
     96A  LYS*     1.3    77.9    -      -       -      +
     98A  LYS*     1.3    63.2    +      -       -      +
     99A  MET*     5.6     0.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 98 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89A  GLN*     3.4    38.0    -      -       +      +
     90A  ILE      4.2     0.9    -      -       -      -
     91A  PHE*     3.9    14.1    -      -       +      -
     97A  SER*     1.3    73.7    -      -       -      +
     99A  MET*     1.3    65.8    +      -       -      +
    100A  LYS      3.7    17.0    -      -       -      +
    101A  ALA*     4.2    14.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 99 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  VAL*     3.6    35.4    -      -       +      -
     90A  ILE*     2.9    22.8    +      -       +      +
     92A  ASN*     3.9    33.2    -      -       +      +
     97A  SER*     3.6     1.3    +      -       -      +
     98A  LYS*     1.3    76.5    -      -       -      +
    100A  LYS*     1.3    68.6    +      -       +      +
    132A  MET*     3.7    44.9    -      -       +      +
    133A  GLU*     5.5     1.1    -      -       -      +
    134A  GLY      5.5     0.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 100 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89A  GLN*     3.6     2.8    -      -       -      -
     90A  ILE*     3.1    33.0    +      -       +      +
     98A  LYS*     3.7     9.0    -      -       -      +
     99A  MET*     1.3    83.8    -      -       -      +
    101A  ALA*     1.3    68.4    +      -       -      +
    130A  TRP*     3.3    22.4    -      -       +      +
    131A  SER      3.2    27.4    -      -       -      +
    132A  MET*     3.5    21.3    -      -       -      +
    133A  GLU      3.9     1.1    -      -       -      -
    134A  GLY      3.2    26.9    -      -       -      +
    135A  GLU*     3.8     8.0    +      -       -      +
    136A  SER      2.9    33.7    +      -       -      +
    137A  GLN*     4.5     6.1    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 101 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  THR*     5.9     2.9    -      -       +      -
     88A  LEU      3.4    12.1    -      -       -      +
     89A  GLN*     4.8     0.9    -      -       +      -
     98A  LYS*     4.2    23.6    -      -       +      +
    100A  LYS*     1.3    82.1    +      -       -      +
    102A  HIS*     1.3    67.2    +      -       -      +
    130A  TRP*     3.7     6.7    -      -       -      -
    137A  GLN*     4.4     7.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 102 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  LYS      3.8     0.3    -      -       -      +
     87A  THR*     4.6     1.5    -      -       -      +
     88A  LEU*     2.6    46.8    +      -       +      +
    101A  ALA*     1.3    75.3    -      -       -      +
    103A  THR*     1.3    79.7    +      -       -      +
    104A  MET*     3.6    31.2    -      -       +      +
    121A  LEU*     5.8     0.4    -      -       -      +
    130A  TRP*     3.7    21.4    -      -       +      -
    137A  GLN*     3.3    43.8    +      -       +      +
    138A  PRO*     3.4    19.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 103 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  LYS*     3.3    13.9    -      -       +      +
     87A  THR*     3.8    23.3    +      -       -      +
    102A  HIS*     1.3    89.6    +      -       -      +
    104A  MET*     1.3    68.7    -      -       -      +
    105A  THR*     4.0     1.2    +      -       -      +
----------------------------------------------------------
 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