Contacts of the strand formed by residues 207 - 211 (chain C) in PDB entry 5M64


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 HIS 207 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80C  ALA*     3.2     7.2    -      -       -      +
     81C  GLU*     3.1    23.6    +      -       -      +
     82C  TYR*     3.1    14.5    +      -       +      +
     84C  TYR*     3.4    29.7    -      +       -      -
    126C  PHE*     3.2    39.1    -      +       +      -
    131C  THR*     3.8    15.3    -      -       +      -
    132C  ILE      3.4     6.3    -      -       -      -
    133C  VAL*     4.8     7.1    -      -       +      +
    134C  LEU*     5.6     0.2    -      -       -      -
    205C  LYS*     3.0    37.2    +      -       -      +
    206C  ALA*     1.3    83.7    -      -       -      +
    208C  CYS*     1.3    59.8    +      -       -      +
    209C  ILE*     5.6     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 208 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78C  VAL*     3.5    24.0    -      -       -      -
     79C  ALA*     3.4    26.2    -      -       -      -
     80C  ALA*     3.6     7.0    -      -       -      +
    106C  LEU*     3.9    21.5    -      -       -      -
    108C  VAL*     5.4     1.6    -      -       -      -
    130C  ASN      4.1     0.7    -      -       -      +
    131C  THR*     3.4    10.0    -      -       -      +
    132C  ILE*     2.8    52.0    +      -       +      +
    134C  LEU*     4.4    11.2    -      -       +      +
    207C  HIS*     1.3    73.4    -      -       -      +
    209C  ILE*     1.3    59.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 209 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78C  VAL*     3.4     6.8    -      -       -      -
     79C  ALA      2.8    36.6    +      -       -      +
     81C  GLU*     3.3    44.6    -      -       +      +
    114C  THR      6.0     0.2    -      -       -      +
    116C  VAL*     3.6    37.2    -      -       +      -
    125C  LYS*     6.0     0.2    -      -       -      -
    126C  PHE*     3.8    22.7    -      -       +      -
    130C  ASN      4.3    11.0    -      -       -      +
    131C  THR*     5.2     0.2    -      -       -      +
    207C  HIS      4.2     0.4    +      -       -      +
    208C  CYS*     1.3    74.3    -      -       -      +
    210C  LEU*     1.3    81.4    -      -       +      +
    219C  PHE*     3.6     5.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 210 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76C  PRO*     5.1    10.8    -      -       +      -
     77C  SER      3.2     8.5    -      -       -      +
     78C  VAL*     3.7    32.1    -      -       +      -
    110C  PRO*     4.9     4.9    -      -       +      -
    111C  ASP*     4.7    13.2    -      -       -      +
    113C  LEU*     3.3    51.8    -      -       +      +
    114C  THR      4.5    10.5    -      -       -      +
    115C  TRP*     4.5    19.8    -      -       +      -
    130C  ASN      4.4     6.1    -      -       -      +
    132C  ILE*     6.2     0.2    -      -       +      -
    209C  ILE*     1.3    99.7    -      -       +      +
    211C  GLY*     1.3    59.9    +      -       -      +
    219C  PHE*     3.4     5.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 211 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76C  PRO*     3.5     4.0    -      -       -      +
     77C  SER      2.9    29.8    +      -       -      +
    115C  TRP*     3.7    16.1    -      -       -      -
    210C  LEU*     1.3    78.9    -      -       -      +
    212C  ILE*     1.3    65.6    +      -       -      -
    219C  PHE*     3.6    16.4    -      -       -      +
----------------------------------------------------------
 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