Contacts of the strand formed by residues 19 - 24 (chain C) in PDB entry 1MOX


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 GLY 19 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16C  CYS*     3.3    24.1    +      -       -      +
     17C  PHE      3.9     0.4    -      -       -      -
     18C  HIS*     1.3    75.7    -      -       -      +
     20C  THR*     1.3    64.7    +      -       -      +
     21C  CYS      4.1     0.2    +      -       -      -
     33C  VAL      3.2    16.2    -      -       -      -
     34C  CYS*     3.6     2.5    -      -       -      -
     35C  HIS*     3.6    23.1    +      -       -      -
     43C  CYS*     4.6     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 20 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16C  CYS*     3.8     2.5    -      -       -      -
     19C  GLY*     1.3    77.3    -      -       -      -
     21C  CYS*     1.3    69.0    +      -       -      +
     22C  ARG*     5.6     0.9    -      -       -      +
     32C  CYS*     3.5     3.1    -      -       -      -
     33C  VAL*     3.1    43.1    +      -       -      +
     35C  HIS*     4.6    11.2    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 21 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7C  ASP*     6.1     0.2    -      -       -      -
      8C  CYS*     2.0    51.6    -      -       +      +
     15C  PHE*     4.5    11.2    -      -       +      +
     16C  CYS*     3.6    15.8    -      -       +      +
     19C  GLY      4.1     0.4    +      -       -      -
     20C  THR*     1.3    82.0    +      -       -      +
     22C  ARG*     1.3    90.1    +      -       -      +
     30C  PRO*     3.6    15.3    -      -       -      -
     31C  ALA      3.4     8.3    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 22 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  GLN*     3.1    33.9    +      -       -      +
     20A  PHE*     6.4     0.2    -      -       -      -
     45A  TYR*     3.2    31.9    +      -       -      -
      5C  PHE*     3.3    55.4    -      -       +      -
      6C  ASN      3.9     6.7    -      -       -      +
      7C  ASP*     5.6     0.4    -      -       -      +
      8C  CYS*     4.1     2.5    -      -       -      -
     20C  THR*     5.6     0.9    -      -       -      +
     21C  CYS*     1.3    83.4    -      -       -      +
     23C  PHE*     1.3    60.4    +      -       -      +
     24C  LEU      3.8     0.6    +      -       -      +
     30C  PRO*     3.4     1.6    -      -       -      +
     31C  ALA*     2.9    39.6    +      -       +      +
     32C  CYS      4.4     3.4    +      -       -      -
     33C  VAL*     3.5    27.3    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 23 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5C  PHE*     3.0     3.8    -      -       -      -
      6C  ASN*     2.8    43.2    +      -       +      +
      7C  ASP      3.2    21.4    +      -       -      +
      8C  CYS*     4.3     2.0    -      -       -      +
      9C  PRO*     5.1    13.0    -      -       +      -
     22C  ARG*     1.3    72.5    -      -       -      +
     24C  LEU*     1.3    68.6    +      -       -      +
     25C  VAL*     3.5     5.2    +      -       +      -
     28C  ASP*     3.3    44.9    -      -       -      -
     29C  LYS*     3.4    29.2    -      -       -      -
     30C  PRO*     3.7    15.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 24 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  LEU*     3.5    34.1    -      -       +      -
     45A  TYR*     4.5     2.2    -      -       -      +
     69A  LEU*     4.2    21.3    -      -       +      -
     99A  SER*     5.4     2.5    -      -       -      +
      4C  HIS*     3.1    13.5    -      -       +      +
      5C  PHE*     3.7    15.9    -      -       +      +
     22C  ARG      3.8     2.0    +      -       -      +
     23C  PHE*     1.3    73.7    -      -       -      +
     25C  VAL*     1.3    59.3    +      -       -      +
     26C  GLN*     4.3     6.1    -      -       +      +
     27C  GLU*     3.2    39.0    -      -       +      +
     28C  ASP*     2.9    27.4    +      -       -      -
     29C  LYS*     3.0    16.8    +      -       +      +
     31C  ALA*     4.2    15.3    -      -       +      -
----------------------------------------------------------
 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