Contacts of the strand formed by residues 359 - 365 (chain A) in PDB entry 3I7O


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 ILE 359 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    356A  LEU*     3.1    26.9    -      -       +      +
    358A  PRO*     1.3    68.4    -      -       -      +
    360A  VAL*     1.3    54.9    +      -       -      +
    361A  ASP      3.6    18.4    -      -       -      +
    362A  MET*     4.0    10.1    -      -       +      -
    377A  THR*     3.9    17.7    -      -       +      -
    378A  CYS      3.5     4.5    -      -       -      -
    379A  SER*     4.5     2.9    -      -       -      +
   1005A  ASN*     2.7    31.2    +      -       -      +
   1006A  VAL*     4.2     1.5    -      -       +      +
   1031A  GLY*     3.8    25.4    -      -       -      +
   1032A  THR      3.1    14.0    +      -       -      +
   1035A  GLY*     4.1     8.5    -      -       -      -
   1036A  MET      4.0     7.0    -      -       -      +
   1037A  ILE*     3.8    31.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 360 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    358A  PRO*     4.2     9.4    -      -       +      +
    359A  ILE*     1.3    76.2    -      -       -      +
    361A  ASP*     1.3    62.9    +      -       -      +
    378A  CYS*     3.0    14.1    +      -       +      +
    380A  GLY      4.8     7.9    -      -       -      +
    721A  PRO      3.7     9.0    -      -       -      +
    722A  ARG*     2.9    43.2    -      -       +      +
    723A  LYS*     4.9     2.4    -      -       -      +
   1005A  ASN*     3.8    16.8    -      -       -      +
   1006A  VAL*     4.5     1.4    -      -       -      +
     18B  SER*     3.9    36.0    -      -       -      +
     19B  LEU*     4.7    12.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 361 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    359A  ILE*     3.5     5.8    -      -       -      +
    360A  VAL*     1.3    79.9    -      -       -      +
    362A  MET*     1.3    91.7    +      -       -      +
    378A  CYS*     3.0    27.8    +      -       -      -
    722A  ARG      3.5    14.6    -      -       -      +
    723A  LYS*     3.0    28.5    -      -       +      +
    724A  ILE*     2.9    31.2    +      -       -      +
   1006A  VAL*     3.7    20.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 362 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    359A  ILE*     4.0     5.8    -      -       +      -
    361A  ASP*     1.3    95.6    +      -       -      +
    363A  CYS*     1.3    67.9    +      -       -      +
    375A  LEU*     3.9    22.4    -      -       +      -
    376A  VAL      3.1    15.3    -      -       -      +
    377A  THR*     3.8    12.6    -      -       +      +
    724A  ILE*     4.2     5.5    -      -       -      +
   1006A  VAL*     3.6    20.9    -      -       +      +
   1008A  CYS*     4.0    17.0    -      -       -      +
   1029A  LEU*     3.6    25.8    -      -       +      +
   1030A  PHE*     3.6    30.7    -      -       -      +
   1031A  GLY*     3.7    21.8    -      -       -      +
   1037A  ILE*     5.4     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 363 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    362A  MET*     1.3    79.7    -      -       -      +
    364A  VAL*     1.3    70.0    +      -       -      +
    375A  LEU*     3.6     6.1    -      -       -      -
    376A  VAL*     2.7    54.1    +      -       -      +
    724A  ILE*     4.3    27.6    -      -       -      +
    725A  CYS*     5.6     0.4    -      -       -      -
    726A  TYR*     4.7     8.3    -      -       +      +
    733A  PHE*     4.3    16.8    -      -       -      -
   1008A  CYS*     4.5     9.0    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 364 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363A  CYS*     1.3    76.9    -      -       -      +
    365A  VAL*     1.3    91.8    +      -       -      +
    366A  ASP*     3.0    18.8    -      -       -      +
    373A  GLY*     3.6    24.0    -      -       -      -
    374A  GLN      3.2     5.8    -      -       -      +
    375A  LEU*     4.3     9.6    -      -       +      -
    726A  TYR*     5.0     2.9    -      -       -      +
    733A  PHE*     4.9     0.2    -      -       -      -
   1008A  CYS*     4.3    11.1    -      -       -      -
   1009A  HIS      3.8     8.3    -      -       -      +
   1010A  GLY*     3.3    34.8    -      -       -      -
   1011A  SER      4.3     4.9    -      -       -      +
   1012A  LEU*     6.2     0.9    -      -       +      -
   1029A  LEU*     4.5     1.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 365 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363A  CYS      4.2     0.9    -      -       -      +
    364A  VAL*     1.3    91.2    -      -       -      +
    366A  ASP*     1.3   112.2    +      -       +      +
    367A  LEU*     2.5    34.8    -      -       +      +
    372A  GLN      3.1     3.4    -      -       -      +
    373A  GLY*     2.7    13.9    -      -       -      -
    374A  GLN*     2.4    43.3    +      -       +      +
    376A  VAL*     3.4    26.5    -      -       +      -
    733A  PHE*     3.5    17.7    -      -       +      -
----------------------------------------------------------
 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