Contacts of the strand formed by residues 233 - 243 (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 GLU 233 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130B  ALA      4.9     0.2    -      -       -      +
    131B  LEU*     3.6    23.0    -      -       +      +
    132B  HIS*     2.8    48.9    +      -       -      +
    133B  HIS*     3.0    25.6    +      -       +      +
     94D  GLY*     3.0    23.5    +      -       -      +
     96D  HIS*     5.2     3.8    +      -       -      -
    213D  VAL*     4.0     7.9    -      -       +      +
    214D  CYS      3.7     2.7    -      -       -      -
    215D  PHE*     3.3    32.3    -      -       +      -
    231D  ILE*     4.4     4.9    -      -       +      +
    232D  GLY*     1.3    72.3    -      -       -      -
    234D  LYS*     1.3    64.0    +      -       -      +
    343D  ASP*     4.6     2.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 234 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91D  LEU      4.6     4.1    +      -       -      -
     92D  LEU*     3.4    26.5    +      -       -      +
     93D  SER      4.7     4.0    -      -       -      +
     94D  GLY*     4.1    14.6    -      -       -      -
     96D  HIS*     5.9     0.4    -      -       -      -
    213D  VAL*     3.3     3.7    -      -       -      -
    214D  CYS      2.9    33.0    +      -       -      +
    216D  HIS*     4.6     9.2    -      -       +      +
    232D  GLY      4.6     5.4    -      -       -      +
    233D  GLU*     1.3    78.0    -      -       -      +
    235D  THR*     1.3    63.2    +      -       -      +
    236D  GLU*     3.5    17.3    +      -       +      +
    341D  ASP*     2.7    42.5    +      -       -      +
    343D  ASP*     3.6    15.7    -      -       -      +
    344D  ARG*     3.6    25.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 235 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107D  ARG*     2.9    33.5    +      -       -      +
    211D  ILE*     4.2    20.4    -      -       +      -
    212D  GLY*     3.4    16.4    -      -       -      +
    213D  VAL*     3.7    14.5    -      -       +      +
    234D  LYS*     1.3    71.5    -      -       -      +
    236D  GLU*     1.3    63.0    +      -       -      +
    341D  ASP*     4.1     1.0    -      -       -      +
    342D  LEU*     3.2    35.4    +      -       +      +
    343D  ASP*     2.7    23.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 236 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183D  GLU      4.2     4.7    -      -       -      +
    184D  ASN*     4.3     2.8    -      -       -      +
    185D  LEU*     3.3     7.1    -      -       +      +
    211D  ILE*     3.3     1.6    -      -       -      -
    212D  GLY      2.4    56.0    +      -       -      +
    214D  CYS*     3.1    28.1    -      -       -      +
    216D  HIS*     3.3    24.7    +      -       -      -
    234D  LYS*     3.5    14.7    +      -       +      +
    235D  THR*     1.3    76.2    -      -       -      +
    237D  ALA*     1.3    58.2    +      -       -      +
    339D  ASN*     3.6    35.5    +      -       -      +
    340D  GLY      3.6     5.8    -      -       -      +
    341D  ASP*     4.7     9.5    -      -       +      +
    342D  LEU*     5.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 237 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114D  TRP*     3.7    28.8    +      -       +      +
    210D  GLN      3.4     5.4    -      -       -      -
    211D  ILE*     3.5    27.4    -      -       +      -
    235D  THR      4.1     1.0    +      -       -      -
    236D  GLU*     1.3    72.3    -      -       -      +
    238D  SER*     1.3    62.0    +      -       -      +
    338D  VAL      4.8     0.2    -      -       -      -
    339D  ASN*     3.7     1.0    -      -       -      -
    340D  GLY*     3.1    32.2    +      -       -      +
    342D  LEU*     4.2    14.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 238 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114D  TRP*     3.7     7.9    -      -       -      -
    185D  LEU*     3.9    25.3    +      -       -      +
    186D  LEU      4.9     0.8    +      -       -      -
    189D  ALA*     5.9     0.3    -      -       -      +
    208D  LEU      3.9     1.2    +      -       -      +
    209D  ALA*     3.4     4.2    -      -       -      -
    210D  GLN*     2.6    38.0    +      -       -      +
    236D  GLU      4.1     0.4    -      -       -      -
    237D  ALA*     1.3    76.3    -      -       -      +
    239D  LEU*     1.3    60.6    +      -       -      +
    240D  VAL*     4.3    13.7    -      -       -      +
    337D  SER*     5.7     1.1    -      -       -      -
    338D  VAL      3.3    13.0    -      -       -      -
    339D  ASN*     3.7    17.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 239 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114D  TRP*     4.4     7.3    -      -       +      -
    118D  VAL*     3.4    21.5    -      -       +      +
    125D  VAL*     4.4    15.9    -      -       +      -
    207D  GLY*     4.2    15.3    -      -       -      -
    208D  LEU      4.1     6.5    -      -       -      +
    209D  ALA*     4.6     1.1    -      -       -      +
    238D  SER*     1.3    74.0    -      -       -      +
    240D  VAL*     1.3    77.9    +      -       -      +
    241D  TRP*     4.2    11.9    -      -       +      +
    255D  TRP*     3.4    49.6    -      -       +      -
    259D  ARG*     6.0     1.6    -      -       -      -
    336D  LEU      3.6     1.9    -      -       -      +
    337D  SER*     3.6     1.2    -      -       -      -
    338D  VAL*     2.7    51.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 240 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186D  LEU*     3.4    31.0    -      -       +      -
    189D  ALA*     3.7    20.9    -      -       +      -
    190D  LEU*     4.1    10.1    -      -       +      -
    207D  GLY*     3.4     2.9    -      -       -      -
    208D  LEU*     3.1    31.1    +      -       +      +
    238D  SER*     4.3    12.3    -      -       -      +
    239D  LEU*     1.3    79.7    -      -       -      +
    241D  TRP*     1.3    59.7    +      -       -      +
    242D  PHE*     3.5    37.6    +      -       +      -
    335D  VAL*     4.9     5.2    -      -       +      -
    336D  LEU      3.8     4.7    -      -       -      +
    337D  SER*     4.7     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 241 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122D  ARG*     5.1     2.7    -      -       -      -
    124D  GLN*     3.7    30.1    -      -       +      -
    125D  VAL*     3.9    15.3    -      -       +      -
    205D  PRO*     3.8    21.5    -      -       +      -
    206D  TYR*     3.2     9.0    -      -       -      -
    207D  GLY*     2.9    36.1    -      -       -      -
    239D  LEU*     3.8    12.7    -      -       +      -
    240D  VAL*     1.3    70.6    -      -       -      +
    242D  PHE*     1.3    63.0    +      -       -      +
    243D  THR*     3.5    17.1    +      -       +      +
    251D  TRP*     3.1    40.0    -      +       +      -
    255D  TRP*     2.9    46.4    -      +       -      +
    334D  CYS      3.1     3.6    -      -       -      +
    336D  LEU*     3.0    48.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 242 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190D  LEU*     3.4    17.7    -      -       +      -
    193D  TYR*     3.5    52.7    -      +       +      -
    204D  LEU*     4.9     2.7    -      -       +      -
    205D  PRO*     3.0    21.9    -      -       -      +
    206D  TYR*     3.4    32.0    +      +       +      +
    208D  LEU*     3.9    26.0    -      -       +      -
    240D  VAL*     3.5    25.4    -      -       +      -
    241D  TRP*     1.3    68.6    -      -       -      +
    243D  THR*     1.3    68.4    +      -       -      +
    311D  LEU*     4.4     2.5    -      -       +      -
    333D  PRO*     4.0    12.6    -      -       +      -
    334D  CYS      3.5     3.4    -      -       -      -
    335D  VAL*     3.4    34.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 243 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204D  LEU*     4.0     2.9    -      -       -      -
    205D  PRO*     3.4    15.0    -      -       +      -
    241D  TRP*     3.5    22.9    -      -       +      +
    242D  PHE*     1.3    82.4    -      -       -      +
    244D  PRO*     1.3    80.7    +      -       -      +
    248D  SER*     3.8    15.1    -      -       -      -
    251D  TRP*     3.4    23.5    -      -       +      +
    333D  PRO*     2.9    12.0    -      -       -      +
    334D  CYS*     2.6    41.5    +      -       -      +
    336D  LEU*     5.2     4.4    -      -       +      +
----------------------------------------------------------
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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