Contacts of the strand formed by residues 206 - 215 (chain C) 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 C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124C  GLN*     3.4    23.8    -      -       +      +
    126C  PHE*     4.8     6.7    -      +       -      -
    193C  TYR*     3.0    54.7    +      +       -      -
    196C  CYS*     3.2    22.6    +      -       +      +
    197C  LEU*     3.6    21.8    -      -       +      -
    200C  VAL*     4.3    15.0    -      -       +      -
    203C  ARG      4.0    17.0    -      -       -      +
    204C  LEU*     4.7     4.7    -      -       +      -
    205C  PRO*     1.3    77.3    -      -       -      +
    207C  GLY*     1.3    63.7    +      -       -      +
    208C  LEU*     3.5    23.8    -      -       +      -
    241C  TRP*     3.2     9.0    -      -       -      -
    242C  PHE*     3.4    28.4    +      +       +      -
----------------------------------------------------------
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Residues in contact with GLY 207 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124C  GLN      3.4     8.9    +      -       -      +
    125C  VAL*     3.3     9.1    -      -       -      -
    126C  PHE      2.9    19.9    +      -       -      -
    206C  TYR*     1.3    77.2    -      -       -      +
    208C  LEU*     1.3    72.5    +      -       -      +
    209C  ALA      4.1     0.2    -      -       -      -
    239C  LEU*     4.2     3.8    -      -       -      -
    240C  VAL      3.3    11.2    -      -       -      -
    241C  TRP*     2.9    21.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 208 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126C  PHE*     3.4    17.0    -      -       +      +
    128C  VAL*     3.9    18.6    -      -       +      +
    189C  ALA*     3.3    38.6    -      -       +      +
    192C  HIS*     3.5    20.0    -      -       +      -
    193C  TYR*     4.1     7.4    -      -       -      +
    196C  CYS*     4.2    13.2    -      -       +      -
    206C  TYR*     3.5    19.7    -      -       +      -
    207C  GLY*     1.3    85.2    -      -       -      +
    209C  ALA*     1.3    62.6    +      -       -      +
    210C  GLN*     4.9     0.5    +      -       -      +
    238C  SER*     3.9     3.6    +      -       -      +
    239C  LEU*     4.2     1.7    -      -       -      +
    240C  VAL*     3.1    31.5    +      -       -      +
    242C  PHE*     3.9    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 209 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114C  TRP*     4.2     5.6    -      -       +      -
    115C  TRP*     3.7    16.0    -      -       +      -
    119C  VAL*     3.6    32.3    -      -       +      -
    125C  VAL*     3.7    11.4    -      -       +      +
    126C  PHE      3.0     8.8    +      -       -      +
    127C  PRO*     3.7     2.6    -      -       -      +
    128C  VAL*     3.1    28.9    +      -       -      +
    208C  LEU*     1.3    72.2    -      -       -      +
    210C  GLN*     1.3    62.2    +      -       -      +
    238C  SER      3.4     8.3    -      -       -      +
    239C  LEU*     4.6     4.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 210 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114C  TRP*     4.4     0.9    -      -       -      -
    115C  TRP*     4.1     6.0    -      -       -      -
    128C  VAL*     3.6    28.6    -      -       +      +
    129C  ASP*     4.2     0.3    -      -       -      -
    130C  ALA*     2.9    41.4    +      -       -      +
    182C  ARG*     4.5     2.1    +      -       -      +
    185C  LEU*     3.7    49.6    +      -       +      +
    189C  ALA*     4.8     4.4    -      -       -      +
    208C  LEU      4.9     0.7    -      -       -      +
    209C  ALA*     1.3    80.0    -      -       -      +
    211C  ILE*     1.3    67.0    +      -       -      +
    212C  GLY*     5.4     0.2    -      -       -      -
    237C  ALA*     3.4     1.0    -      -       -      -
    238C  SER*     2.6    43.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 211 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111C  ALA*     3.7    36.1    -      -       +      +
    114C  TRP*     3.7    28.0    -      -       +      -
    115C  TRP*     4.2    13.0    -      -       +      -
    185C  LEU*     4.3     0.7    -      -       -      -
    210C  GLN*     1.3    78.7    -      -       -      +
    212C  GLY*     1.3    60.3    +      -       -      +
    235C  THR*     4.2     9.2    -      -       +      -
    236C  GLU      3.3     5.2    -      -       -      +
    237C  ALA*     3.6    20.2    -      -       +      -
    342C  LEU*     3.8    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 212 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132C  HIS*     6.0     0.2    -      -       -      -
    182C  ARG*     4.5     4.9    -      -       -      -
    185C  LEU*     3.7    15.5    -      -       -      +
    210C  GLN*     5.4     0.4    -      -       -      -
    211C  ILE*     1.3    77.8    -      -       -      +
    213C  VAL*     1.3    60.7    +      -       -      -
    214C  CYS*     4.3     0.5    -      -       -      -
    235C  THR*     4.0     4.7    -      -       -      -
    236C  GLU*     2.3    55.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 213 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  HIS*     3.4    37.0    -      -       +      +
    107C  ARG*     5.7     0.7    -      -       -      +
    132C  HIS*     4.2     6.8    +      -       -      +
    182C  ARG*     2.5    34.8    +      -       -      +
    212C  GLY*     1.3    73.6    -      -       -      -
    214C  CYS*     1.3    67.3    +      -       -      +
    215C  PHE*     4.2    12.8    -      -       +      -
    233C  GLU*     4.0    23.8    -      -       +      -
    234C  LYS      3.2    11.7    -      -       -      +
    235C  THR*     3.7    22.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 214 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182C  ARG*     3.6    15.5    -      -       -      +
    183C  GLU      3.4    11.2    -      -       -      +
    184C  ASN*     3.7    20.4    -      -       -      -
    185C  LEU*     4.1    11.2    -      -       -      -
    213C  VAL*     1.3    80.1    -      -       -      +
    215C  PHE*     1.3    64.2    +      -       -      +
    216C  HIS*     3.2    27.8    +      -       +      -
    232C  GLY      3.4     0.2    -      -       -      +
    233C  GLU*     3.7     2.1    -      -       -      -
    234C  LYS      2.9    27.7    +      -       -      -
    236C  GLU*     3.1    28.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 215 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  HIS*     3.7    23.6    -      +       +      -
    133A  HIS*     5.5     1.6    -      +       +      -
    181A  LEU*     5.2     2.5    -      -       +      -
    215A  PHE*     5.1     3.8    -      +       -      -
    132C  HIS*     4.4    28.3    -      +       +      -
    145C  PHE*     4.4    12.9    +      -       +      -
    181C  LEU*     3.6    50.9    -      -       +      +
    182C  ARG*     3.0    16.6    +      -       +      +
    183C  GLU*     3.5    14.7    -      -       -      +
    213C  VAL*     4.2    17.3    -      -       +      -
    214C  CYS*     1.3    73.4    -      -       -      +
    216C  HIS*     1.3    61.2    +      -       -      +
    231C  ILE*     4.5    14.6    -      -       +      -
    232C  GLY      3.3     5.8    -      -       -      +
    233C  GLU*     3.3    43.1    -      -       +      -
----------------------------------------------------------
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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