Contacts of the strand formed by residues 1059 - 1069 (chain B) in PDB entry 6ZGI


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 GLY1059 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    727B  LEU      3.2    13.0    -      -       -      -
    729B  VAL*     4.0    11.6    -      -       -      +
    782B  PHE*     3.9    12.4    -      -       -      -
    948B  LEU*     4.1     8.1    -      -       -      -
   1056B  ALA*     2.8    30.1    +      -       -      +
   1057B  PRO      3.3     1.0    -      -       -      -
   1058B  HIS*     1.3    81.3    -      -       -      +
   1060B  VAL*     1.3    61.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL1060 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    725B  GLU      3.7     0.9    -      -       -      +
    726B  ILE*     3.6     3.3    -      -       -      +
    727B  LEU*     2.9    47.3    +      -       +      +
    729B  VAL*     4.4     4.9    -      -       +      -
    781B  VAL*     4.9     2.7    -      -       +      -
    782B  PHE*     4.0    24.7    -      -       +      -
    948B  LEU*     5.2     0.4    -      -       -      +
   1025B  ALA*     4.2    11.4    -      -       +      -
   1029B  MET*     4.5     8.7    -      -       +      -
   1053B  PRO*     4.6     0.4    -      -       +      -
   1054B  GLN      3.4    17.5    -      -       -      +
   1056B  ALA*     4.4     0.8    -      -       -      +
   1059B  GLY*     1.3    73.3    -      -       -      +
   1061B  VAL*     1.3    75.4    +      -       -      +
   1062B  PHE*     3.7    33.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL1061 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    724B  THR*     4.4    11.9    -      -       +      -
    725B  GLU      3.2     4.5    -      -       -      +
    726B  ILE*     3.5    35.0    -      -       +      -
    818B  ILE*     6.4     0.4    -      -       +      -
    822B  LEU*     3.7    33.9    -      -       +      -
    938B  LEU*     6.5     0.4    -      -       +      -
    945B  LEU*     4.9     0.7    -      -       +      -
   1052B  PHE      3.9     0.3    -      -       -      +
   1053B  PRO*     3.5     3.6    -      -       -      +
   1054B  GLN*     2.9    41.9    +      -       +      +
   1056B  ALA*     4.1    12.1    -      -       +      -
   1060B  VAL*     1.3    79.9    -      -       -      +
   1062B  PHE*     1.3    71.2    +      -       -      +
   1063B  LEU*     4.6     9.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE1062 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    723B  THR      3.5     1.4    -      -       -      +
    724B  THR*     3.2     8.0    -      -       -      -
    725B  GLU*     2.9    42.4    +      -       -      +
    727B  LEU*     4.3    15.9    -      -       +      -
   1025B  ALA      3.9    18.2    -      -       -      -
   1028B  LYS*     4.0    17.3    -      -       +      -
   1029B  MET*     3.9    31.2    -      -       +      -
   1032B  CYS*     5.7     0.7    -      -       +      -
   1033B  VAL*     4.0    30.1    -      -       +      -
   1051B  SER*     5.0     2.0    -      -       -      -
   1052B  PHE      3.6     1.8    -      -       -      -
   1053B  PRO*     4.3     8.5    -      -       +      -
   1060B  VAL*     3.7    28.0    -      -       +      -
   1061B  VAL*     1.3    76.9    -      -       -      +
   1063B  LEU*     1.3    61.9    +      -       -      +
   1064B  HIS*     3.6    29.9    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU1063 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    722B  VAL*     4.3    13.2    -      -       +      -
    723B  THR      3.4     3.6    -      -       -      +
    724B  THR*     3.6    29.2    -      -       +      -
    805B  ILE*     4.0    27.4    -      -       +      -
    818B  ILE*     4.7    10.1    -      -       +      -
    931B  ILE*     4.7    15.5    -      -       +      -
    934B  ILE*     4.4    12.3    -      -       +      -
   1051B  SER*     3.1     5.8    -      -       -      -
   1052B  PHE*     2.9    58.1    +      -       +      +
   1054B  GLN*     4.6    14.1    -      -       +      -
   1061B  VAL*     4.6     7.6    -      -       +      -
   1062B  PHE*     1.3    73.2    -      -       -      +
   1064B  HIS*     1.3    61.4    +      -       -      +
   1065B  VAL      3.8     0.9    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS1064 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    721B  SER      3.4     2.6    -      -       -      +
    722B  VAL*     3.2     4.0    -      -       -      -
    723B  THR*     2.9    51.8    +      -       +      +
    724B  THR      5.1     0.2    -      -       -      -
    725B  GLU*     3.2    33.8    +      -       +      +
   1028B  LYS*     4.8     1.4    -      -       -      +
   1032B  CYS*     4.3     7.7    -      -       -      -
   1042B  PHE      4.8     0.6    +      -       -      -
   1043B  CYS*     3.4    44.7    -      -       +      +
   1044B  GLY*     4.2     4.9    +      -       -      -
   1048B  HIS*     4.9     0.4    -      -       +      -
   1050B  MET      3.7     3.1    -      -       -      +
   1051B  SER*     3.0    28.9    +      -       -      +
   1062B  PHE*     3.6    30.1    +      +       +      +
   1063B  LEU*     1.3    70.8    -      -       -      +
   1065B  VAL*     1.3    60.4    +      -       -      +
   1066B  THR*     3.9     2.3    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL1065 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    720B  ILE*     3.7    28.5    -      -       +      -
    721B  SER      3.4     5.6    -      -       -      +
    722B  VAL*     4.0    20.2    -      -       +      -
    927B  PHE*     4.2    11.7    -      -       +      -
   1048B  HIS*     4.2     0.5    -      -       -      -
   1049B  LEU*     2.8    39.4    +      -       +      +
   1050B  MET*     2.8    32.8    +      -       +      +
   1052B  PHE*     3.8    29.4    -      -       +      -
   1063B  LEU      4.5     1.1    -      -       -      +
   1064B  HIS*     1.3    72.8    -      -       -      +
   1066B  THR*     1.3    55.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR1066 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    720B  ILE*     3.6     6.6    -      -       -      +
    721B  SER*     2.9    49.1    +      -       -      -
    723B  THR*     5.4     3.4    -      -       +      +
   1043B  CYS      3.7    22.9    -      -       -      +
   1044B  GLY*     4.5     1.8    -      -       -      -
   1045B  LYS      3.0    29.6    +      -       -      +
   1046B  GLY*     4.1     5.4    -      -       -      +
   1047B  TYR      3.3    11.4    -      -       -      -
   1048B  HIS*     3.8    13.2    -      -       -      +
   1049B  LEU*     4.1     6.3    -      -       -      +
   1064B  HIS*     4.6     5.3    +      -       +      +
   1065B  VAL*     1.3    78.9    -      -       -      +
   1067B  TYR*     1.3    59.5    +      -       -      +
   1068B  VAL*     4.5     0.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR1067 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    717B  ASN      4.9     1.6    +      -       -      -
    718B  PHE*     3.5    46.1    -      +       +      +
    719B  THR      3.7     2.9    -      -       -      -
    720B  ILE*     4.3     9.4    -      -       +      -
    906B  PHE*     4.1    27.4    -      +       -      -
    909B  ILE*     3.7    25.8    -      -       +      -
    911B  VAL*     4.3    17.9    -      -       +      +
   1046B  GLY*     3.8     1.9    -      -       -      -
   1047B  TYR*     2.9    51.3    +      +       +      +
   1049B  LEU*     4.3     7.6    -      -       +      -
   1066B  THR*     1.3    71.7    -      -       -      +
   1068B  VAL*     1.3    66.4    +      -       -      +
   1069B  PRO*     4.1    19.5    -      -       +      +
   1108B  ASN*     4.1    17.6    +      -       +      -
   1109B  PHE*     4.2     8.0    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL1068 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    718B  PHE*     3.4     2.4    -      -       -      +
    719B  THR*     2.8    51.3    +      -       +      +
    721B  SER*     3.7    26.7    -      -       -      +
   1045B  LYS      4.5    11.9    -      -       -      +
   1046B  GLY*     4.9     0.2    -      -       -      -
   1066B  THR*     4.5     0.2    -      -       -      +
   1067B  TYR*     1.3    82.1    -      -       -      +
   1069B  PRO*     1.3    79.1    -      -       +      +
   1070B  ALA*     5.7     0.4    -      -       -      -
    890C  ALA      4.3    14.1    -      -       -      +
    891C  GLY*     4.9     6.5    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO1069 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    715B  PRO*     3.7    28.7    -      -       +      -
    717B  ASN      4.0     5.6    -      -       -      +
    718B  PHE*     4.6     0.9    -      -       -      -
   1047B  TYR*     4.1    25.1    -      -       +      +
   1067B  TYR*     4.1    16.8    -      -       +      +
   1068B  VAL*     1.3    96.4    -      -       +      +
   1070B  ALA*     1.3    61.3    +      -       -      +
   1108B  ASN*     5.2     5.6    -      -       -      +
    890C  ALA*     4.7    11.4    -      -       +      +
    891C  GLY*     5.5     2.4    -      -       -      -
    892C  ALA*     5.3     9.5    +      -       -      +
    894C  LEU*     5.4     7.6    -      -       +      -
----------------------------------------------------------
 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