Contacts of the strand formed by residues 206 - 215 (chain D) in PDB entry 2G4C


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 TYR 206 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124D  GLN*     3.3    25.4    -      -       +      +
    126D  PHE*     4.8     6.7    -      +       -      -
    193D  TYR*     2.9    53.1    +      +       -      -
    196D  CYS*     3.2    22.6    +      -       +      +
    197D  LEU*     3.5    22.6    +      -       +      +
    200D  VAL*     4.2    14.4    -      -       +      -
    203D  ARG      4.0    17.5    -      -       -      +
    204D  LEU*     4.7     4.5    -      -       +      -
    205D  PRO*     1.3    77.4    -      -       -      +
    207D  GLY*     1.3    64.1    +      -       -      +
    208D  LEU*     3.5    24.0    -      -       +      -
    241D  TRP*     3.2     8.5    -      -       -      -
    242D  PHE*     3.4    27.5    +      +       +      -
----------------------------------------------------------
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Residues in contact with GLY 207 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124D  GLN      3.4     8.9    +      -       -      +
    125D  VAL*     3.3     8.0    -      -       -      -
    126D  PHE      2.9    20.3    +      -       -      -
    206D  TYR*     1.3    75.8    -      -       -      +
    208D  LEU*     1.3    71.7    +      -       -      +
    209D  ALA      4.0     0.2    -      -       -      -
    239D  LEU*     4.2     4.7    -      -       -      -
    240D  VAL      3.4    11.4    -      -       -      -
    241D  TRP*     2.9    21.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 208 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126D  PHE*     3.4    15.0    -      -       +      +
    127D  PRO      5.8     0.2    -      -       -      +
    128D  VAL*     3.9    18.5    -      -       +      +
    189D  ALA*     3.4    38.3    -      -       +      +
    192D  HIS*     3.5    24.7    -      -       +      -
    193D  TYR*     4.1     2.0    -      -       -      +
    196D  CYS*     4.2    15.5    -      -       +      -
    206D  TYR*     3.5    20.2    -      -       +      -
    207D  GLY*     1.3    84.3    -      -       -      +
    209D  ALA*     1.3    63.4    +      -       -      +
    210D  GLN*     5.0     0.3    -      -       -      +
    238D  SER*     3.9     3.3    +      -       -      +
    239D  LEU*     4.2     2.1    -      -       -      +
    240D  VAL*     3.1    31.2    +      -       -      +
    242D  PHE*     3.9    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 209 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114D  TRP*     4.2     5.6    -      -       +      -
    115D  TRP*     3.7    15.4    -      -       +      -
    119D  VAL*     3.6    32.1    -      -       +      -
    125D  VAL*     3.7    12.7    -      -       +      +
    126D  PHE      3.0     8.4    +      -       -      +
    127D  PRO*     3.8     1.7    -      -       -      +
    128D  VAL*     3.0    29.1    +      -       -      +
    208D  LEU*     1.3    73.4    -      -       -      +
    210D  GLN*     1.3    63.4    +      -       -      +
    238D  SER      3.4     8.1    -      -       -      +
    239D  LEU*     4.6     3.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 210 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114D  TRP*     4.4     0.9    -      -       -      -
    115D  TRP*     4.1     6.0    -      -       -      -
    128D  VAL*     3.7    29.0    -      -       +      +
    129D  ASP*     4.3     0.3    -      -       -      -
    130D  ALA*     2.9    40.5    +      -       -      +
    182D  ARG*     4.5     1.7    +      -       -      -
    185D  LEU*     3.7    48.4    +      -       +      +
    189D  ALA*     4.8     4.6    -      -       -      +
    208D  LEU      5.0     0.4    -      -       -      +
    209D  ALA*     1.3    79.9    -      -       -      +
    211D  ILE*     1.3    68.4    +      -       -      +
    212D  GLY*     5.4     0.2    -      -       -      -
    237D  ALA*     3.4     1.0    -      -       -      -
    238D  SER*     2.6    41.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 211 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111D  ALA*     3.7    35.2    -      -       +      +
    114D  TRP*     3.7    28.0    -      -       +      -
    115D  TRP*     4.2    12.6    -      -       +      -
    185D  LEU*     4.3     0.4    -      -       -      -
    210D  GLN*     1.3    80.8    -      -       -      +
    212D  GLY*     1.3    60.6    +      -       -      +
    235D  THR*     4.2    10.1    -      -       +      -
    236D  GLU      3.3     4.5    -      -       -      +
    237D  ALA*     3.5    20.2    -      -       +      -
    342D  LEU*     3.8    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 212 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132D  HIS*     6.0     0.2    -      -       -      -
    182D  ARG*     4.5     9.2    -      -       -      -
    185D  LEU*     3.7    10.8    -      -       -      +
    210D  GLN*     5.4     0.4    -      -       -      -
    211D  ILE*     1.3    79.1    -      -       -      +
    213D  VAL*     1.3    62.7    +      -       -      -
    214D  CYS*     4.2     0.7    -      -       -      -
    235D  THR*     4.1     3.8    -      -       -      -
    236D  GLU*     2.4    54.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 213 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132B  HIS*     3.4    37.0    -      -       +      +
    107D  ARG*     5.7     0.9    -      -       -      +
    132D  HIS*     4.2     6.8    +      -       -      +
    182D  ARG*     2.5    34.6    +      -       -      +
    212D  GLY*     1.3    74.9    -      -       -      -
    214D  CYS*     1.3    68.1    +      -       -      +
    215D  PHE*     4.2    12.9    -      -       +      -
    233D  GLU*     4.0    24.0    -      -       +      +
    234D  LYS      3.3    10.8    -      -       -      +
    235D  THR*     3.7    20.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 214 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182D  ARG*     3.6    16.2    -      -       -      +
    183D  GLU      3.3    11.2    -      -       -      +
    184D  ASN*     3.7    19.5    -      -       -      -
    185D  LEU*     4.1    11.7    -      -       -      -
    212D  GLY      4.2     0.2    -      -       -      -
    213D  VAL*     1.3    79.0    -      -       -      +
    215D  PHE*     1.3    63.3    +      -       -      +
    216D  HIS*     3.3    26.0    +      -       +      -
    232D  GLY      3.5     0.3    -      -       -      +
    233D  GLU*     3.7     1.7    -      -       -      -
    234D  LYS      2.9    28.9    +      -       -      +
    236D  GLU*     3.1    27.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 215 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132B  HIS*     3.7    24.0    -      +       +      -
    133B  HIS*     5.4     2.0    -      +       +      -
    181B  LEU*     5.2     2.5    -      -       +      -
    215B  PHE*     5.0     4.5    -      +       -      -
    132D  HIS*     4.4    29.2    -      +       +      -
    145D  PHE*     4.3    12.4    +      -       +      -
    181D  LEU*     3.6    48.7    -      -       +      +
    182D  ARG*     3.0    17.2    +      -       +      +
    183D  GLU*     3.5    14.0    -      -       -      +
    213D  VAL*     4.2    16.4    -      -       +      -
    214D  CYS*     1.3    72.9    -      -       -      +
    216D  HIS*     1.3    63.5    +      -       -      +
    231D  ILE*     4.5    15.3    -      -       +      -
    232D  GLY      3.3     5.6    -      -       -      +
    233D  GLU*     3.3    43.5    -      -       +      -
----------------------------------------------------------
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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