Contacts of the strand formed by residues 22 - 28 (chain C) in PDB entry 4IHB


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 ALA 22 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12C  VAL*     4.1    19.3    -      -       +      -
     20C  SER*     3.6     4.0    +      -       -      -
     21C  ASP*     1.3    75.0    -      -       -      +
     23C  TYR*     1.3    58.7    +      -       -      +
     37C  VAL*     4.4     0.4    -      -       -      -
     38C  ILE*     3.1    29.5    +      -       -      +
     41C  SER      5.2     0.6    +      -       -      +
     44C  PRO*     4.1    10.1    -      -       +      +
     46C  TRP*     3.1    19.6    +      -       +      -
     69C  VAL*     3.9    19.7    -      -       +      -
     70C  LYS      3.2    11.9    -      -       -      +
     71C  ASP*     4.6     0.2    -      -       -      +
     81C  LEU*     4.7     1.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 23 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22C  ALA*     1.3    72.3    -      -       -      +
     24C  CYS*     1.3    74.8    +      -       -      +
     25C  SER*     4.5     7.0    -      -       -      -
     34C  ARG*     4.0    27.7    +      -       +      -
     35C  THR*     3.4    17.3    -      -       -      +
     36C  LYS      3.4    21.1    -      -       -      +
     37C  VAL*     4.0     6.5    -      -       +      -
     46C  TRP*     3.6     4.0    -      -       -      +
     69C  VAL*     3.4     4.7    -      -       -      +
     70C  LYS*     3.0    74.1    +      -       +      +
     72C  HIS*     3.7    20.0    -      +       +      -
     79C  ARG*     3.1    39.8    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 24 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6C  ILE*     3.8    34.1    -      -       +      +
     23C  TYR*     1.3    78.1    -      -       -      +
     25C  SER*     1.3    60.7    +      -       -      +
     26C  ALA      4.0     0.2    -      -       -      -
     33C  LYS      3.9     0.3    -      -       -      +
     34C  ARG*     3.3     5.4    -      -       -      -
     35C  THR*     2.9    32.8    +      -       +      +
     46C  TRP*     3.4    37.0    -      -       -      -
     67C  VAL*     4.3     7.9    -      -       +      -
     68C  VAL      3.3     4.5    -      -       -      +
     69C  VAL*     3.9    17.0    -      -       -      -
    117C  LEU*     3.9     5.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 25 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23C  TYR*     4.1    10.7    +      -       -      -
     24C  CYS*     1.3    74.5    -      -       -      +
     26C  ALA*     1.3    58.8    +      -       -      +
     27C  VAL*     4.2     3.4    -      -       -      +
     32C  LYS*     3.4    36.6    +      -       -      +
     33C  LYS      3.6     4.0    +      -       -      -
     34C  ARG*     4.3     9.7    +      -       -      +
     66C  HIS      3.6     1.2    -      -       -      +
     67C  VAL*     3.3     2.1    -      -       -      -
     68C  VAL*     2.7    50.9    +      -       -      +
     70C  LYS*     4.9    11.0    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 26 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4C  VAL*     5.9     1.1    -      -       +      -
      6C  ILE*     4.2    17.3    -      -       +      -
     24C  CYS      4.0     0.6    -      -       -      -
     25C  SER*     1.3    75.1    +      -       -      +
     27C  VAL*     1.3    62.4    +      -       -      +
     32C  LYS*     3.4     0.9    -      -       -      -
     33C  LYS*     2.8    43.4    +      -       +      +
     50C  PHE*     5.5     2.2    -      -       +      -
     52C  TRP*     3.7    23.3    -      -       +      -
     65C  LEU*     4.4     4.7    -      -       +      -
     66C  HIS      3.3     4.3    -      -       -      +
     67C  VAL*     4.0    18.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 27 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25C  SER*     4.4     4.5    -      -       -      +
     26C  ALA*     1.3    78.9    -      -       -      +
     28C  PHE*     1.3    64.5    +      -       -      +
     29C  ALA      5.0     0.2    -      -       -      +
     30C  GLY*     4.1    24.5    -      -       -      +
     31C  VAL      3.4     7.6    -      -       -      +
     32C  LYS*     3.7    35.2    -      -       +      -
     64C  GLU      3.9     2.1    -      -       -      +
     65C  LEU*     3.8     3.5    -      -       -      +
     66C  HIS*     2.7    50.3    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 28 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2C  LEU*     3.7    19.1    -      -       +      -
     27C  VAL*     1.3    75.1    -      -       -      +
     29C  ALA*     1.3    76.5    -      -       +      +
     30C  GLY      3.1     1.3    -      -       -      -
     31C  VAL*     2.8    36.7    +      -       -      +
     52C  TRP*     3.6    37.0    +      +       +      +
     53C  ASP      5.5     1.6    -      -       -      -
     54C  LEU*     3.4    33.7    -      -       +      -
     57C  ILE*     5.0     6.1    -      -       +      -
     59C  LEU*     4.8     9.0    -      -       +      -
     63C  SER*     3.5    25.4    -      -       -      -
     64C  GLU      3.6    17.0    -      -       -      -
     65C  LEU*     4.2     8.3    -      -       +      -
     88C  LEU*     3.5    19.7    -      -       +      -
    123C  TYR*     5.5     1.3    -      -       -      -
----------------------------------------------------------
 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