Contacts of the strand formed by residues 153 - 157 (chain B) in PDB entry 4CY1


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 VAL 153 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145B  VAL*     3.5    29.4    -      -       +      -
    146B  SER      3.2     5.2    -      -       -      +
    152B  SER*     1.3    76.8    -      -       -      +
    154B  ARG*     1.3    64.9    +      -       -      +
    155B  ILE*     5.0     0.9    -      -       +      -
    166B  THR*     3.6     1.7    -      -       -      +
    167B  LEU*     2.7    58.9    +      -       +      +
    169B  ALA*     3.5    24.2    -      -       +      +
    174B  VAL*     4.0     7.6    -      -       +      -
    177B  VAL*     3.9    19.3    -      -       +      -
    186B  ILE*     4.8     5.6    -      -       +      -
    188B  SER*     3.9    13.7    -      -       -      -
    198B  TRP*     5.0     1.3    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 154 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127B  GLY*     3.1    36.2    +      -       -      -
    128B  HIS*     3.5    23.8    +      -       +      +
    145B  VAL*     3.3     6.8    -      -       -      +
    146B  SER*     2.9    35.4    +      -       -      +
    150B  ASP*     4.8     1.6    +      -       -      -
    152B  SER*     4.1     2.4    +      -       -      +
    153B  VAL*     1.3    77.9    -      -       -      +
    155B  ILE*     1.3    64.3    +      -       -      +
    156B  TRP*     3.5    36.6    -      -       +      +
    163B  CYS*     3.2    22.9    -      -       -      +
    165B  LYS      3.4     3.6    -      -       -      +
    166B  THR*     3.1    43.3    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 155 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143B  LEU*     4.1    32.3    -      -       +      -
    144B  ILE      3.3     7.9    -      -       -      +
    145B  VAL*     4.6     4.0    -      -       +      -
    153B  VAL*     5.0     0.2    -      -       +      -
    154B  ARG*     1.3    78.1    -      -       -      +
    156B  TRP*     1.3    58.5    +      -       -      +
    163B  CYS*     3.7     2.1    -      -       -      -
    164B  LEU*     2.7    38.1    +      -       +      +
    165B  LYS*     3.0    33.1    +      -       +      +
    167B  LEU*     4.4    17.5    -      -       +      -
    179B  PHE*     5.0     3.6    -      -       +      -
    186B  ILE*     3.7    29.2    -      -       +      -
    199B  ASP      5.4     0.2    -      -       -      +
    200B  THR*     4.0    20.6    -      -       +      +
    203B  GLY*     5.4     0.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 156 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111B  LEU*     3.8    17.5    -      -       +      +
    125B  LEU*     3.6    29.6    -      -       +      -
    126B  LYS      3.4    46.9    -      -       -      -
    127B  GLY*     3.9     2.9    -      -       -      -
    128B  HIS*     4.0     6.1    -      +       -      -
    143B  LEU*     3.3    10.4    -      -       -      +
    144B  ILE*     2.8    55.8    +      -       +      +
    146B  SER*     2.8    22.8    +      -       -      -
    154B  ARG*     3.5    40.4    -      -       +      +
    155B  ILE*     1.3    75.9    -      -       -      +
    157B  ASP*     1.3    65.1    +      -       -      +
    161B  GLY      3.8     9.0    -      -       -      -
    162B  LYS      3.4     4.3    -      -       -      +
    163B  CYS*     3.6    32.5    -      -       +      -
    164B  LEU*     4.2     4.0    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 157 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113B  ILE*     4.9     0.5    -      -       -      +
    142B  ASN*     3.9     8.1    -      -       -      +
    143B  LEU*     5.6     0.4    -      -       -      -
    156B  TRP*     1.3    71.1    -      -       -      +
    158B  VAL*     1.3    57.6    +      -       -      +
    159B  LYS*     3.1    23.6    +      -       -      +
    160B  THR*     3.2    32.4    +      -       -      +
    161B  GLY*     2.7    35.2    +      -       -      -
    162B  LYS      2.8    13.9    +      -       -      +
    164B  LEU*     3.9    29.4    -      -       +      +
----------------------------------------------------------
 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