Contacts of the helix formed by residues 277 - 291 (chain A) in PDB entry 1GZH


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 CYS 277 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  LYS*     3.3    33.9    -      -       -      -
    275A  CYS*     3.5     4.6    -      -       -      -
    276A  ALA*     1.3    80.2    -      -       +      +
    278A  PRO*     1.3    67.9    -      -       -      +
    279A  GLY      3.3     2.0    -      -       -      -
    280A  ARG*     3.2    58.9    +      -       +      +
    281A  ASP*     2.9    23.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 278 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122A  VAL*     3.6    19.5    -      -       +      +
    123A  THR      3.6     9.6    -      -       -      +
    125A  THR*     4.0     7.2    -      -       +      -
    134A  PHE*     3.5    32.7    -      -       +      +
    135A  CYS*     3.5    32.5    -      -       -      +
    136A  GLN*     3.6     6.5    -      -       +      +
    275A  CYS*     3.7     6.8    -      -       -      +
    276A  ALA      3.2    13.0    -      -       -      +
    277A  CYS*     1.3    83.4    -      -       -      +
    279A  GLY*     1.3    57.8    +      -       -      +
    281A  ASP      3.6     0.3    -      -       -      -
    282A  ARG*     2.8    31.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 279 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  THR*     3.4    27.3    -      -       -      +
    119A  ALA      3.6     2.7    +      -       -      -
    122A  VAL*     3.2    26.8    -      -       -      +
    125A  THR*     4.3     4.3    -      -       -      -
    277A  CYS*     3.3     1.2    -      -       -      -
    278A  PRO*     1.3    81.5    -      -       -      +
    280A  ARG*     1.3    62.9    +      -       -      +
    282A  ARG*     3.2     2.3    +      -       -      +
    283A  ARG*     3.2    19.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 280 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120A  LYS*     4.6     9.1    -      -       +      +
    273A  ARG*     5.3     3.0    -      -       -      +
    275A  CYS*     5.5     0.4    -      -       -      +
    276A  ALA*     4.6    10.5    -      -       -      +
    277A  CYS*     3.2    51.9    +      -       -      +
    279A  GLY*     1.3    75.7    -      -       -      +
    281A  ASP*     1.3    87.0    +      -       -      +
    283A  ARG*     3.6    25.7    +      -       -      +
    284A  THR*     3.0    32.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 281 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134A  PHE*     3.9    10.5    -      -       +      -
    273A  ARG*     2.7    44.7    +      -       -      +
    275A  CYS*     3.1    12.9    -      -       -      +
    277A  CYS      2.9    19.7    +      -       -      +
    278A  PRO      3.8     2.5    -      -       -      +
    280A  ARG*     1.3    95.2    +      -       -      +
    282A  ARG*     1.3    67.0    +      -       -      +
    284A  THR*     4.2     7.0    +      -       -      +
    285A  GLU*     2.9    30.9    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 282 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  HIS*     5.6     4.8    +      -       -      -
    116A  SER      3.3    16.8    +      -       -      -
    117A  GLY      3.5     4.2    +      -       -      -
    118A  THR*     3.7    19.4    -      -       -      +
    125A  THR*     3.0    33.9    +      -       +      -
    126A  TYR      3.3    23.4    +      -       -      -
    127A  SER*     3.8     2.8    -      -       -      +
    128A  PRO*     3.8    14.1    -      -       -      +
    134A  PHE*     3.6    31.6    -      -       +      -
    278A  PRO      2.8    21.5    +      -       -      +
    279A  GLY      3.2     3.8    +      -       -      +
    281A  ASP*     1.3    72.5    -      -       -      +
    283A  ARG*     1.3    54.8    +      -       -      +
    285A  GLU*     3.3     1.6    +      -       -      +
    286A  GLU*     2.8    69.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 283 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  THR*     2.9    58.2    +      -       +      -
    119A  ALA*     4.7     0.6    -      -       -      +
    120A  LYS*     3.2    48.2    -      -       -      +
    279A  GLY      3.2     3.0    +      -       -      +
    280A  ARG*     3.7    22.8    +      -       -      +
    282A  ARG*     1.3    80.5    -      -       -      +
    284A  THR*     1.3    57.1    +      -       -      +
    286A  GLU*     3.2     9.0    +      -       -      +
    287A  GLU*     2.9    34.0    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 284 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    280A  ARG*     3.0    21.7    +      -       -      +
    281A  ASP*     3.7    10.1    +      -       -      +
    282A  ARG      3.3     0.2    -      -       -      -
    283A  ARG*     1.3    78.7    +      -       -      +
    285A  GLU*     1.3    56.2    +      -       +      +
    287A  GLU*     3.0     8.5    +      -       -      +
    288A  ASN*     2.7    37.2    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 285 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130A  LEU*     4.0    21.5    -      -       +      +
    132A  LYS*     2.8    34.4    +      -       -      +
    134A  PHE*     3.1    21.9    -      -       +      -
    273A  ARG*     3.9    17.1    +      -       -      -
    281A  ASP*     2.9    18.3    +      -       +      +
    282A  ARG      4.0     2.0    -      -       -      +
    284A  THR*     1.3    80.8    -      -       +      +
    286A  GLU*     1.3    60.7    +      -       -      +
    288A  ASN*     3.2    26.2    -      -       +      +
    289A  LEU*     3.2     9.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 286 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  THR*     4.9     4.0    -      -       -      +
    127A  SER*     2.8    22.9    +      -       -      -
    128A  PRO*     4.8     0.2    -      -       -      +
    129A  ALA*     4.2    14.2    +      -       +      +
    130A  LEU*     3.8    15.9    -      -       +      -
    282A  ARG*     2.8    63.8    +      -       +      +
    283A  ARG*     3.6     9.6    -      -       -      +
    285A  GLU*     1.3    74.5    -      -       -      +
    287A  GLU*     1.3    63.3    +      -       -      +
    289A  LEU*     3.2    19.7    -      -       -      +
    290A  ARG*     3.6     9.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 287 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    283A  ARG*     2.9    14.2    +      -       +      +
    284A  THR*     3.4     9.6    -      -       -      +
    286A  GLU*     1.3    72.2    -      -       -      +
    288A  ASN*     1.3    68.2    +      -       -      +
    289A  LEU      2.8     4.0    +      -       -      -
    290A  ARG*     2.9    59.4    +      -       +      +
    291A  LYS      3.9     1.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 288 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    284A  THR*     2.7    16.9    +      -       +      +
    285A  GLU*     3.2    23.3    -      -       -      +
    287A  GLU*     1.3    77.2    -      -       -      +
    289A  LEU*     1.3    56.1    +      -       -      +
    291A  LYS      2.8    24.6    -      -       -      +
    292A  LYS*     5.2     2.1    -      -       -      +
   1858B  ARG*     6.0     4.8    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 289 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  ALA*     6.0     5.6    -      -       +      -
    130A  LEU*     3.5    31.4    -      -       +      -
    285A  GLU      3.2     6.0    +      -       -      +
    286A  GLU*     3.2    15.5    -      -       -      +
    287A  GLU      2.8     0.8    +      -       -      -
    288A  ASN*     1.3    80.4    -      -       -      +
    290A  ARG*     1.3    56.1    +      -       -      +
    291A  LYS*     2.6    19.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 290 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    286A  GLU      3.7    10.5    -      -       -      +
    287A  GLU*     2.9    49.4    +      -       -      +
    289A  LEU*     1.3    75.5    -      -       -      +
    291A  LYS*     1.3    62.4    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 291 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287A  GLU      3.9     1.4    +      -       -      -
    288A  ASN*     2.8    20.3    +      -       -      +
    289A  LEU      2.6     7.8    +      -       -      +
    290A  ARG*     1.3    80.2    -      -       +      +
    292A  LYS*     1.3   126.1    +      -       +      +
----------------------------------------------------------
 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