Contacts of the strand formed by residues 522 - 526 (chain A) in PDB entry 4ICU


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 CYS 522 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    448A  LEU*     5.6     0.2    -      -       -      -
    449A  LYS*     3.4    14.6    -      -       +      +
    451A  LYS*     3.8    38.6    -      -       -      -
    459A  LYS*     4.8    17.7    -      -       -      -
    493A  TYR*     3.0     9.5    -      -       -      +
    494A  GLU*     2.9    57.1    +      -       +      +
    520A  GLY      5.4     0.2    -      -       -      +
    521A  ASP*     1.3    73.2    -      -       -      +
    523A  LEU*     1.3    61.7    +      -       -      +
    524A  LEU*     4.3     3.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 523 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    448A  LEU*     4.8    18.6    -      -       +      +
    449A  LYS      2.7     9.4    +      -       -      +
    450A  ILE*     3.5    30.5    -      -       +      -
    451A  LYS*     2.9    27.0    +      -       -      +
    465A  LEU*     5.0     1.1    -      -       +      -
    474A  VAL*     3.8    28.3    -      -       +      -
    478A  LEU*     4.2     7.2    -      -       +      -
    491A  LEU*     4.2    11.9    -      -       +      -
    492A  SER      3.4    15.5    -      -       -      +
    493A  TYR*     4.2     5.8    -      -       +      -
    505A  LEU*     3.6    24.7    -      -       +      -
    512A  LEU*     4.9    10.1    -      -       +      -
    517A  VAL*     5.9     0.7    -      -       +      -
    521A  ASP      4.1     1.0    +      -       -      -
    522A  CYS*     1.3    74.3    -      -       -      +
    524A  LEU*     1.3    62.0    +      -       -      +
    525A  VAL*     3.8     6.7    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 524 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    451A  LYS*     3.5    23.3    -      -       +      +
    453A  PRO*     3.8    27.8    -      -       +      -
    490A  LEU      3.7     1.6    -      -       -      +
    491A  LEU*     3.6     8.2    -      -       -      +
    492A  SER*     2.9    44.3    +      -       -      +
    493A  TYR*     3.9     6.5    -      -       -      -
    494A  GLU*     3.7    53.2    -      -       +      +
    502A  GLU*     3.9    23.1    -      -       +      +
    522A  CYS*     3.9     4.5    -      -       -      +
    523A  LEU*     1.3    73.7    -      -       -      +
    525A  VAL*     1.3    61.1    +      -       -      +
    526A  ARG*     4.0     3.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 525 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    450A  ILE*     3.9    24.2    -      -       +      -
    451A  LYS      2.8    12.3    +      -       -      +
    452A  TYR*     3.7    14.4    -      -       +      +
    453A  PRO*     3.6    13.8    -      -       -      +
    454A  HIS*     4.9     1.2    +      -       -      -
    478A  LEU*     3.7    25.8    -      -       +      -
    482A  LEU*     4.3     7.4    -      -       +      -
    489A  LEU*     3.8    27.1    -      -       +      -
    491A  LEU*     3.8    14.6    -      -       +      -
    523A  LEU*     4.1     9.2    -      -       +      +
    524A  LEU*     1.3    75.6    -      -       -      +
    526A  ARG*     1.3    63.2    +      -       -      +
    527A  TRP*     3.7    17.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 526 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    453A  PRO*     3.6    34.7    -      -       +      +
    454A  HIS*     5.0    12.4    -      -       +      +
    489A  LEU*     3.5     4.9    -      -       -      +
    490A  LEU*     2.8    50.1    +      -       +      +
    492A  SER*     3.6     9.7    +      -       -      -
    502A  GLU*     2.7    44.4    +      -       -      -
    524A  LEU*     4.3     4.4    +      -       -      +
    525A  VAL*     1.3    77.1    -      -       -      +
    527A  TRP*     1.3    67.9    +      -       -      +
    514B  PHE*     3.7    55.2    +      -       -      +
    515B  TYR*     4.3    21.9    -      -       -      +
    516B  SER*     5.6     0.9    -      -       -      +
----------------------------------------------------------
 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