Contacts of the helix formed by residues 226 - 243 (chain E) in PDB entry 1GZ0


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 ASN 226 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107D  HIS*     6.1     2.6    -      -       -      -
    111D  ALA*     5.0    11.3    -      -       -      +
    114D  ARG*     3.3    28.4    -      -       -      +
    141D  VAL*     6.0     2.6    -      -       -      +
    228D  SER*     5.6     0.6    -      -       -      -
    108E  ASN*     4.6     6.8    -      -       -      +
    198E  GLU*     3.4    14.6    -      -       -      +
    225E  LEU*     1.3    75.1    -      -       -      +
    227E  VAL*     1.3    63.6    +      -       -      +
    228E  SER*     2.8    27.8    +      -       -      -
    229E  VAL*     3.1    33.8    +      -       -      +
    230E  ALA*     3.1     9.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 227 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103E  VAL*     4.6    17.5    -      -       +      -
    108E  ASN*     4.9    17.0    +      -       +      +
    112E  CYS*     4.1    12.8    -      -       -      -
    195E  MSE      4.8     7.9    -      -       +      -
    196E  GLY      3.8    15.0    -      -       -      +
    197E  ALA*     3.9     2.7    -      -       -      -
    198E  GLU*     3.1    44.0    +      -       +      +
    225E  LEU      3.6     1.8    +      -       -      -
    226E  ASN*     1.3    73.1    +      -       -      +
    228E  SER*     1.3    56.6    +      -       -      +
    230E  ALA*     3.9     6.3    -      -       -      +
    231E  THR*     2.8    44.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 228 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229D  VAL*     3.4    22.7    -      -       -      +
    108E  ASN*     4.5     9.7    +      -       -      -
    111E  ALA*     3.3    36.6    +      -       -      +
    112E  CYS*     4.2    12.6    -      -       -      +
    115E  SER*     4.4     2.6    +      -       -      -
    226E  ASN*     2.8    18.2    +      -       -      -
    227E  VAL*     1.3    70.7    -      -       -      +
    229E  VAL*     1.3    63.8    +      -       -      -
    231E  THR*     3.4     2.8    +      -       -      -
    232E  GLY*     3.1    18.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 229 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111D  ALA*     5.6     2.0    -      -       +      +
    115D  SER*     3.6    24.0    -      -       -      +
    228D  SER*     4.0    29.8    -      -       -      +
    229D  VAL*     4.3    12.8    -      -       +      +
    232D  GLY*     3.9    12.1    -      -       -      -
    225E  LEU*     4.4     9.2    -      -       +      -
    226E  ASN*     3.1    30.9    +      -       -      +
    228E  SER*     1.3    74.4    -      -       -      +
    230E  ALA*     1.3    58.6    +      -       -      +
    232E  GLY*     3.2     1.9    +      -       -      -
    233E  ILE*     2.9    49.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 230 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195E  MSE      3.6    16.6    -      -       +      -
    216E  ILE*     3.9    20.0    -      -       +      -
    225E  LEU*     4.2    13.4    -      -       +      +
    226E  ASN      3.1    15.5    +      -       -      +
    227E  VAL*     3.9     6.1    -      -       -      +
    229E  VAL*     1.3    76.4    -      -       -      +
    231E  THR*     1.3    65.5    +      -       -      +
    233E  ILE*     3.4     6.3    +      -       -      +
    234E  CYS*     2.9    29.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 231 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98E  LEU*     3.8    26.2    -      -       +      -
    100E  LEU*     4.4     0.2    -      -       -      +
    112E  CYS*     3.5    25.9    -      -       +      +
    115E  SER*     5.0     1.6    -      -       -      -
    193E  LEU*     4.4     0.2    -      -       -      +
    195E  MSE      3.3    27.6    -      -       -      +
    227E  VAL*     2.8    23.6    +      -       -      +
    228E  SER      3.7     4.5    -      -       -      -
    230E  ALA*     1.3    74.9    -      -       -      +
    232E  GLY*     1.3    58.7    +      -       -      +
    234E  CYS*     3.8     0.9    -      -       -      +
    235E  LEU*     2.8    53.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 232 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229D  VAL*     3.9    16.2    -      -       -      -
    233D  ILE*     3.9     9.6    -      -       -      -
    115E  SER*     4.2    13.0    -      -       -      -
    228E  SER      3.1    14.5    +      -       -      -
    229E  VAL      3.6     3.1    -      -       -      -
    230E  ALA      3.2     0.4    -      -       -      -
    231E  THR*     1.3    76.7    -      -       -      +
    233E  ILE*     1.3    52.8    +      -       -      +
    235E  LEU*     3.1     3.2    +      -       -      -
    236E  PHE*     2.7    39.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 233 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232D  GLY      3.7    20.6    -      -       -      +
    233D  ILE*     3.9     8.9    -      -       -      +
    236D  PHE*     3.4    49.6    -      -       +      -
    182E  LEU*     4.2    15.3    -      -       +      -
    183E  TYR*     4.4     2.2    -      -       +      +
    216E  ILE*     4.9     8.1    -      -       +      -
    225E  LEU*     3.8    23.3    -      -       +      -
    229E  VAL*     2.9    36.3    +      -       +      +
    230E  ALA*     3.8     5.6    -      -       -      +
    232E  GLY*     1.3    71.4    -      -       -      +
    234E  CYS*     1.3    62.7    +      -       -      +
    236E  PHE*     3.9     2.0    -      -       -      +
    237E  GLU*     3.2    21.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 234 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174E  THR*     3.6    31.0    -      -       -      -
    182E  LEU*     3.9    19.5    -      -       +      -
    187E  MSE      4.2     6.9    -      -       -      +
    193E  LEU*     3.7    24.1    -      -       +      +
    195E  MSE      4.2     3.4    -      -       -      -
    214E  ILE*     4.3     5.4    -      -       +      -
    216E  ILE*     3.6    19.1    -      -       -      -
    230E  ALA      2.9    21.0    +      -       -      +
    231E  THR      3.9     0.7    -      -       -      +
    233E  ILE*     1.3    75.4    -      -       -      +
    235E  LEU*     1.3    64.6    +      -       -      +
    237E  GLU*     3.2    11.8    +      -       -      +
    238E  ALA*     3.3    11.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 235 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96E  PHE*     3.8    13.2    -      -       +      -
     98E  LEU*     4.2    13.5    -      -       +      -
    115E  SER*     4.0     6.5    -      -       -      -
    116E  ALA*     3.7    29.2    -      -       -      +
    119E  ALA*     3.8    18.6    -      -       +      -
    121E  VAL*     4.1    17.0    -      -       +      -
    193E  LEU*     3.4    24.2    -      -       +      -
    231E  THR*     2.8    41.7    +      -       +      +
    232E  GLY*     3.5     4.7    -      -       -      +
    234E  CYS*     1.3    71.9    -      -       -      +
    236E  PHE*     1.3    61.9    +      -       +      +
    238E  ALA*     3.1     9.7    -      -       -      +
    239E  VAL*     3.0    26.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 236 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183D  TYR*     3.2    30.1    +      -       -      +
    216D  ILE*     3.6    18.2    -      -       +      -
    217D  PRO*     3.3    28.0    -      -       +      -
    218D  MSE      3.9    10.5    -      -       +      -
    225D  LEU*     4.3     5.2    -      -       +      -
    233D  ILE*     3.5    28.5    -      -       +      -
    115E  SER*     4.2     8.7    -      -       -      -
    118E  ALA*     3.9    22.9    -      -       +      -
    119E  ALA*     3.9    18.2    -      -       +      -
    232E  GLY*     2.7    25.3    +      -       -      +
    233E  ILE      3.9     2.5    -      -       -      +
    235E  LEU*     1.3    75.0    -      -       +      +
    237E  GLU*     1.3    58.9    +      -       -      +
    238E  ALA      3.1     1.3    -      -       -      -
    239E  VAL*     3.5    20.6    -      -       +      +
    240E  ARG*     3.0    20.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 237 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183D  TYR*     5.3     0.4    -      -       -      -
    237D  GLU*     5.0     0.7    -      -       -      +
    240D  ARG*     3.7     5.1    +      -       -      -
    182E  LEU*     3.7    33.7    -      -       +      +
    183E  TYR*     3.7    28.9    -      -       +      +
    187E  MSE      4.7     5.8    -      -       -      -
    233E  ILE      3.2    14.1    +      -       -      +
    234E  CYS      3.2     9.1    +      -       -      +
    236E  PHE*     1.3    74.7    -      -       -      +
    238E  ALA*     1.3    62.1    +      -       -      +
    240E  ARG*     3.3    32.0    +      -       -      +
    241E  GLN*     2.8    49.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 238 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96E  PHE*     3.6    24.9    -      -       +      -
    187E  MSE      4.0    33.8    -      -       +      +
    191E  LEU*     4.5     2.7    -      -       +      -
    234E  CYS      3.3     8.1    +      -       -      +
    235E  LEU*     3.1    12.5    +      -       -      +
    237E  GLU*     1.3    78.7    -      -       -      +
    239E  VAL*     1.3    66.3    +      -       -      +
    241E  GLN*     3.0     3.5    +      -       -      +
    242E  ARG*     2.8    30.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 239 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183D  TYR*     4.6     1.8    -      -       +      -
    217D  PRO*     4.2    26.7    -      -       +      +
     96E  PHE*     4.5     4.0    -      -       +      -
    119E  ALA*     3.7    38.4    -      -       +      +
    235E  LEU      3.0    19.9    +      -       -      +
    236E  PHE*     3.5    23.1    -      -       +      +
    238E  ALA*     1.3    75.5    -      -       -      +
    240E  ARG*     1.3    57.0    +      -       -      +
    242E  ARG*     3.2     8.2    +      -       -      +
    243E  SER*     2.8    35.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 240 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183D  TYR*     3.6    32.9    -      -       +      +
    237D  GLU*     3.6    19.3    -      -       -      -
    240D  ARG*     3.0    45.1    -      -       -      +
    236E  PHE      3.0    17.3    +      -       -      +
    237E  GLU*     3.3    24.8    +      -       -      +
    239E  VAL*     1.3    73.7    -      -       -      +
    241E  GLN*     1.3    98.9    +      -       -      +
    242E  ARG      3.0     4.5    -      -       -      -
    243E  SER*     3.0    23.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 241 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182E  LEU      3.9     6.9    +      -       -      -
    183E  TYR      5.1     2.4    +      -       -      -
    185E  SER      3.3    22.1    +      -       -      +
    186E  LYS*     3.8     1.4    -      -       -      -
    187E  MSE      2.7    38.6    +      -       -      +
    188E  THR*     3.1    29.4    +      -       +      +
    237E  GLU*     2.8    35.1    +      -       -      +
    238E  ALA      3.0     4.7    +      -       -      +
    240E  ARG*     1.3   100.6    -      -       -      +
    242E  ARG*     1.3    58.3    +      -       -      +
    243E  SER      4.2     3.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 242 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94E  GLN*     3.7    21.4    +      -       +      +
     95E  PRO      3.6     2.2    +      -       -      -
     96E  PHE*     3.1    47.5    -      -       -      +
    187E  MSE      3.0    21.2    +      -       -      +
    188E  THR*     4.2     8.2    -      -       -      +
    189E  GLY      2.7    28.7    +      -       -      +
    191E  LEU*     3.2    34.4    -      -       -      +
    238E  ALA*     2.8    21.8    +      -       -      +
    239E  VAL*     3.5     6.5    -      -       -      +
    241E  GLN*     1.3    77.0    -      -       -      +
    243E  SER*     1.3    65.5    +      -       -      +
     28F  LEU*     5.5     0.7    -      -       -      +
     31F  ARG*     4.7    11.3    -      -       +      +
     32F  GLU*     3.4    19.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 243 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183D  TYR*     5.3     8.9    -      -       -      -
    217D  PRO*     5.4     4.5    -      -       -      +
    239E  VAL*     2.8    23.7    +      -       -      +
    240E  ARG*     3.0    16.8    +      -       -      +
    241E  GLN      4.2     4.0    -      -       -      +
    242E  ARG*     1.3    83.8    -      -       -      +
     28F  LEU*     5.3     3.6    -      -       -      +
     32F  GLU*     4.1    13.4    +      -       -      +
     33F  ASP*     4.3    20.9    -      -       -      +
     34F  LYS*     5.9     3.3    -      -       -      +
----------------------------------------------------------
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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