Contacts of the strand formed by residues 334 - 341 (chain B) 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 CYS 334 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241B  TRP      3.4     2.9    -      -       -      +
    242B  PHE*     3.8     2.1    -      -       -      -
    243B  THR*     2.6    41.6    +      -       +      +
    245B  PRO*     3.5    34.3    -      -       -      +
    248B  SER*     3.6    21.1    -      -       -      +
    305B  ASN*     4.1     2.9    -      -       -      +
    307B  GLY*     3.6    25.6    -      -       -      -
    308B  ASP*     4.1     6.7    -      -       -      -
    332B  VAL      4.0     0.2    +      -       -      -
    333B  PRO*     1.3    74.7    -      -       -      +
    335B  VAL*     1.3    61.3    +      -       -      +
    336B  LEU      3.6     1.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 335 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186B  LEU*     5.1     0.7    -      -       +      -
    190B  LEU*     4.0    21.8    -      -       +      -
    240B  VAL*     3.6    25.8    -      -       +      -
    241B  TRP      3.8     2.7    -      -       -      -
    242B  PHE*     4.3     8.7    -      -       +      -
    305B  ASN*     4.8     1.1    -      -       -      -
    306B  LEU*     3.0    49.9    +      -       +      +
    307B  GLY      2.8    20.8    +      -       -      +
    310B  GLU*     5.4     1.1    -      -       +      +
    311B  LEU*     3.8    35.9    -      -       +      +
    334B  CYS*     1.3    71.6    -      -       -      +
    336B  LEU*     1.3    62.3    +      -       -      +
    337B  SER*     5.0     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 336 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240B  VAL*     3.6     6.9    -      -       -      +
    241B  TRP*     3.0    45.8    +      -       +      +
    243B  THR*     4.1     9.9    -      -       +      -
    248B  SER      3.9     7.4    -      -       -      +
    251B  TRP*     3.6    18.6    -      -       +      -
    252B  LEU*     3.3    55.2    -      -       +      +
    255B  TRP*     4.2     9.9    -      -       +      -
    303B  LEU*     5.2     0.2    -      -       +      -
    304B  TRP      3.3     9.2    -      -       -      +
    305B  ASN*     4.3     9.4    -      -       -      +
    334B  CYS      3.6     2.0    +      -       -      -
    335B  VAL*     1.3    74.9    -      -       -      +
    337B  SER*     1.3    70.9    +      -       -      +
    338B  VAL*     4.3    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 337 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186B  LEU*     3.5    33.1    -      -       -      +
    238B  SER*     5.0     0.3    +      -       -      -
    239B  LEU      3.8     2.9    -      -       -      -
    240B  VAL*     4.6     7.4    -      -       -      +
    302B  THR      3.7     1.6    -      -       -      +
    303B  LEU*     3.4     5.7    -      -       -      -
    304B  TRP*     2.7    40.7    +      -       -      +
    306B  LEU*     4.4    11.4    -      -       -      -
    335B  VAL*     5.0     0.7    -      -       -      -
    336B  LEU*     1.3    78.3    -      -       -      +
    338B  VAL*     1.3    68.6    +      -       -      +
    339B  ASN*     4.7     8.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 338 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114B  TRP*     5.6     4.5    -      -       +      +
    237B  ALA      4.4     0.9    -      -       -      +
    238B  SER*     3.4     8.8    +      -       -      -
    239B  LEU*     2.9    53.8    +      -       +      +
    241B  TRP*     6.2     0.9    -      -       +      -
    255B  TRP*     4.2    20.2    -      -       +      -
    259B  ARG*     3.8    20.6    -      -       +      -
    301B  GLU*     3.4    24.2    -      -       +      +
    302B  THR      3.8     2.7    -      -       -      -
    303B  LEU*     4.0    21.1    -      -       +      +
    336B  LEU*     4.3     8.7    -      -       +      -
    337B  SER*     1.3    75.5    +      -       -      +
    339B  ASN*     1.3    66.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 339 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184B  ASN*     4.8     8.9    -      -       -      +
    185B  LEU      4.7    11.3    -      -       -      +
    186B  LEU*     5.2     3.6    -      -       -      +
    236B  GLU*     3.2    39.6    -      -       -      +
    237B  ALA      3.5     4.8    -      -       -      +
    238B  SER*     3.7    21.0    +      -       -      -
    300B  ILE      4.1     0.2    -      -       -      +
    301B  GLU*     3.1     5.0    -      -       -      -
    302B  THR*     2.8    51.8    +      -       -      +
    337B  SER*     4.7     9.0    +      -       -      +
    338B  VAL*     1.3    76.5    +      -       -      +
    340B  GLY*     1.3    58.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 340 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114B  TRP*     5.9     0.4    -      -       -      -
    236B  GLU*     3.3     8.8    -      -       -      +
    237B  ALA*     3.0    38.6    +      -       -      +
    263B  TRP*     5.0     4.7    -      -       -      -
    300B  ILE      3.3     6.7    -      -       -      -
    301B  GLU*     3.7    18.9    +      -       -      -
    339B  ASN*     1.3    77.6    +      -       -      +
    341B  ASP*     1.3    61.7    +      -       -      -
    342B  LEU*     3.5     3.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 341 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234B  LYS*     3.2    50.4    +      -       -      +
    235B  THR      4.1     1.6    -      -       -      +
    236B  GLU*     4.2    12.2    +      -       -      +
    263B  TRP*     4.0     6.3    -      -       -      -
    299B  LEU      5.2     0.4    -      -       -      +
    300B  ILE*     2.6    22.1    +      -       -      +
    340B  GLY*     1.3    69.7    -      -       -      -
    342B  LEU*     1.3    60.9    +      -       -      +
    343B  ASP*     4.5     2.7    -      -       -      +
    344B  ARG*     3.0    36.8    +      -       +      +
    345B  GLY*     2.9    22.9    +      -       -      -
----------------------------------------------------------
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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