Contacts of the strand formed by residues 219 - 224 (chain C) in PDB entry 5U0A


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 219 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218C  THR*     1.3    72.7    -      -       -      +
    220C  SER*     1.3    60.3    +      -       -      +
    221C  TYR*     3.4    44.3    -      -       +      +
    313C  LEU*     3.2    16.0    -      -       -      +
    314C  ILE      4.5     0.9    +      -       -      -
    326C  ARG      4.6     5.4    +      -       -      +
    327C  PRO      5.1     0.4    -      -       -      -
    328C  ALA*     3.5    33.2    -      -       +      +
    329C  GLU      5.3     0.2    -      -       -      +
    339C  ASP*     4.5    10.1    -      -       -      +
    376C  ALA*     3.7    20.9    -      -       +      -
    377C  PHE      3.3     7.9    -      -       -      +
    378C  GLY*     3.7    10.8    -      -       -      +
    391C  PHE*     4.2    10.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 220 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66C  ALA*     3.5    17.9    -      -       -      +
     70C  ARG*     3.2    30.5    -      -       -      -
    191C  TYR*     5.0     1.8    -      -       -      -
    215C  LEU*     6.0     0.4    -      -       -      -
    218C  THR      4.0     1.8    +      -       -      -
    219C  VAL*     1.3    72.0    -      -       -      +
    221C  TYR*     1.3    62.1    +      -       -      +
    222C  HIS*     3.5    19.1    +      -       -      -
    312C  TYR*     4.3     1.1    -      -       -      -
    313C  LEU*     3.7     9.8    -      -       -      +
    376C  ALA*     3.2     4.9    -      -       -      +
    377C  PHE*     2.9    37.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 221 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219C  VAL*     3.4    32.8    -      -       +      +
    220C  SER*     1.3    70.9    -      -       -      +
    222C  HIS*     1.3    61.5    +      -       -      +
    223C  PRO*     3.8     5.7    -      -       -      +
    312C  TYR*     3.0    47.5    +      -       -      +
    314C  ILE*     3.4    36.8    -      -       +      +
    326C  ARG*     4.1     8.5    +      -       -      -
    339C  ASP*     3.7    36.2    +      -       +      +
    342C  LEU*     4.4     9.2    -      -       +      +
    352C  PRO*     4.3     9.6    -      -       +      -
    354C  ILE*     4.2     4.3    -      -       -      +
    355C  LEU*     4.6     5.5    -      -       +      +
    374C  LEU*     4.2    25.5    -      -       +      +
    375C  ARG      3.8     2.0    -      -       -      -
    376C  ALA*     3.7    20.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 222 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66C  ALA*     3.8    11.7    +      -       -      -
     69C  TRP*     3.5    38.7    -      -       +      +
     70C  ARG*     4.2     3.6    -      -       -      -
    220C  SER*     3.5    29.2    +      -       -      -
    221C  TYR*     1.3    71.2    -      -       -      +
    223C  PRO*     1.3    69.1    -      -       +      +
    224C  LEU*     3.6     1.9    +      -       +      +
    235C  ASN*     4.3    11.9    +      -       -      +
    312C  TYR*     3.1    46.9    +      +       -      -
    374C  LEU*     3.6     2.2    -      -       -      -
    375C  ARG*     2.8    43.5    +      -       +      +
    377C  PHE*     4.0    21.3    -      +       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 223 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221C  TYR      3.8     7.9    -      -       -      +
    222C  HIS*     1.3    85.9    -      -       -      +
    224C  LEU*     1.3    63.7    +      -       -      +
    231C  SER*     3.9    10.8    -      -       -      -
    234C  LEU*     3.8    24.9    -      -       +      +
    235C  ASN*     3.1    33.1    +      -       -      +
    343C  HIS*     5.5     2.0    -      -       -      +
    354C  ILE*     4.4    17.0    -      -       +      -
    355C  LEU*     5.5    11.4    -      -       +      +
    358C  CYS*     5.6     3.6    -      -       +      -
    372C  LEU*     4.9    15.5    -      -       +      -
    374C  LEU*     3.7    16.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 224 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55C  SER      5.5     1.1    -      -       -      +
     56C  ASP*     3.3    33.9    -      -       +      +
     69C  TRP*     5.0     1.6    -      -       +      -
    222C  HIS*     3.6     1.3    +      -       +      +
    223C  PRO*     1.3    76.1    -      -       -      +
    225C  GLY*     1.3    62.1    +      -       -      +
    230C  GLU*     6.0     0.2    -      -       -      -
    231C  SER*     3.4    17.5    -      -       -      +
    372C  LEU*     3.2    11.6    -      -       -      +
    373C  ARG*     2.7    58.6    +      -       +      +
    375C  ARG*     3.9    42.6    -      -       +      +
    394C  THR*     4.5    13.9    -      -       +      -
----------------------------------------------------------
 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