Contacts of the strand formed by residues 924 - 932 (chain A) in PDB entry 3PT6


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 ARG 924 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    920A  GLU*     4.7     1.2    -      -       -      +
    921A  VAL      2.7    29.0    +      -       -      +
    922A  ASP*     4.1     6.7    -      -       +      +
    923A  GLY*     1.3    81.6    +      -       -      +
    925A  VAL*     1.3    64.9    +      -       -      +
    926A  TYR*     3.1    24.6    -      -       +      +
   1004A  HIS*     2.9    47.9    +      -       +      -
   1005A  CYS      3.0    16.0    -      -       -      -
   1006A  GLY*     3.4    13.3    -      -       -      +
   1016A  ASP*     2.9    36.4    +      -       -      -
   1018A  LYS*     4.0    21.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 925 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    917A  GLN*     3.3    30.5    -      -       +      +
    919A  GLU      3.6    10.3    -      -       -      +
    920A  GLU*     4.0    29.2    -      -       +      +
    923A  GLY      4.2     0.6    -      -       -      -
    924A  ARG*     1.3    70.3    -      -       -      +
    926A  TYR*     1.3    73.6    +      -       -      +
    927A  CYS*     4.3     6.5    -      -       -      -
   1004A  HIS*     3.1     3.3    -      -       -      -
   1005A  CYS*     2.7    39.8    +      -       -      +
   1006A  GLY      5.1     3.3    +      -       -      +
   1007A  LYS*     5.7     5.6    -      -       +      -
   1012A  VAL*     4.0    27.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 926 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    917A  GLN*     3.5     4.5    -      -       -      -
    918A  ILE*     2.6    35.9    +      -       +      -
    919A  GLU*     2.7    24.5    +      -       +      +
    921A  VAL*     4.5    21.4    -      -       +      +
    924A  ARG*     3.1    27.1    -      -       +      +
    925A  VAL*     1.3    73.7    -      -       -      +
    927A  CYS*     1.3    57.1    +      -       -      +
   1002A  GLU*     3.7    30.8    +      -       +      -
   1003A  ILE      3.4     9.6    -      -       -      -
   1004A  HIS*     3.5    32.0    +      +       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 927 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    914A  VAL*     3.5    30.3    -      -       +      -
    916A  GLU      3.3    10.8    -      -       -      +
    917A  GLN*     4.3     6.1    -      -       -      -
    918A  ILE*     4.0     6.1    -      -       -      +
    925A  VAL*     4.3    15.5    -      -       -      -
    926A  TYR*     1.3    80.4    -      -       -      +
    928A  SER*     1.3    61.3    +      -       -      +
    929A  SER      4.3     0.4    -      -       -      +
    930A  ILE*     4.3     7.2    -      -       +      -
    939A  LEU*     3.7    13.7    -      -       -      +
   1003A  ILE*     2.7    42.3    +      -       +      +
   1005A  CYS*     5.0    12.6    -      -       -      -
   1012A  VAL*     5.5     1.6    -      -       -      -
   1017A  ILE*     6.3     0.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 928 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    916A  GLU*     3.0    37.2    +      -       -      +
    917A  GLN      5.2     0.5    -      -       -      -
    918A  ILE*     4.6     9.4    +      -       -      +
    927A  CYS*     1.3    74.5    -      -       -      +
    929A  SER*     1.3    59.7    +      -       -      +
    938A  ARG*     3.3     5.2    -      -       -      +
    939A  LEU*     3.0    46.9    +      -       -      +
   1003A  ILE*     4.1     5.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 929 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    914A  VAL*     3.7     2.6    -      -       -      +
    915A  LEU*     2.7    47.6    +      -       -      +
    916A  GLU*     3.0    38.9    +      -       -      -
    927A  CYS*     3.8     1.2    -      -       -      +
    928A  SER*     1.3    80.3    +      -       -      +
    930A  ILE*     1.3    56.1    +      -       -      +
    936A  VAL*     4.2     5.4    -      -       -      +
    937A  TYR      3.4     5.6    +      -       -      -
    938A  ARG*     3.8    18.7    -      -       -      +
   1003A  ILE*     4.4     0.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 930 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    913A  LYS      3.8     7.2    -      -       -      +
    914A  VAL*     3.7    28.3    -      -       +      +
    915A  LEU*     3.2    10.6    -      -       -      +
    927A  CYS*     4.3     5.2    -      -       +      -
    929A  SER*     1.3    76.5    -      -       -      +
    931A  THR*     1.3    59.4    +      -       -      +
    936A  VAL*     3.9     0.2    -      -       -      +
    937A  TYR*     2.8    37.2    +      -       +      +
   1003A  ILE*     3.7    30.7    -      -       +      -
   1017A  ILE*     3.7    28.9    -      -       +      -
   1019A  LEU*     4.4     4.5    -      -       +      -
   1056A  PHE*     3.6    38.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 931 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    911A  MET      5.8     0.9    -      -       -      +
    912A  PRO*     3.6     1.2    -      -       -      +
    913A  LYS*     3.2    39.6    +      -       +      +
    915A  LEU*     3.3    30.7    -      -       +      +
    930A  ILE*     1.3    76.6    -      -       -      +
    932A  LYS*     1.3    63.8    +      -       -      +
    934A  GLY*     4.4     7.3    +      -       -      -
    935A  VAL      2.8    22.5    +      -       -      -
    936A  VAL*     3.8    11.1    -      -       -      +
    937A  TYR*     4.7     0.4    -      -       -      -
   1056A  PHE*     3.9     4.5    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 932 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    909A  LYS      4.6     0.9    -      -       -      -
    910A  GLU      4.0    12.6    -      -       -      +
    911A  MET      4.7     1.1    -      -       -      -
    912A  PRO*     4.4    17.9    -      -       +      -
    931A  THR*     1.3    76.6    +      -       -      +
    933A  ASN*     1.3    82.1    +      -       +      +
    934A  GLY      3.1     3.9    +      -       -      -
    935A  VAL*     3.0    23.8    +      -       -      +
    937A  TYR*     4.2    10.3    +      -       +      -
   1056A  PHE*     2.7    55.4    +      -       +      +
   1057A  SER*     3.6    14.6    +      -       -      +
   1059A  VAL*     2.9    31.5    +      -       -      +
   1060A  GLN      6.2     0.2    -      -       -      -
----------------------------------------------------------
 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