Contacts of the strand formed by residues 439 - 443 (chain A) 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 PHE 439 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    382A  LYS      3.6     4.2    +      -       -      -
    383A  VAL*     3.3    14.3    -      -       +      +
    384A  ALA      3.3    21.5    +      -       -      -
    437A  ILE*     3.3     7.2    -      -       -      +
    438A  LEU*     1.3    91.9    -      -       +      +
    440A  THR*     1.3    65.8    +      -       -      +
    441A  VAL*     5.0     0.4    -      -       +      -
    455A  LEU*     4.4    20.0    -      -       +      -
    456A  ARG      3.3    18.2    -      -       -      +
    457A  SER*     3.7    22.2    -      -       -      -
    474A  PHE*     4.2    14.6    -      +       -      -
    475A  LEU*     3.5    30.5    -      -       +      -
    478A  TYR*     3.5    56.3    -      +       -      -
    479A  ILE*     6.1     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 440 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    384A  ALA*     4.1     6.1    -      -       +      -
    385A  LEU      4.9     0.2    -      -       -      +
    386A  ASP*     5.1     3.6    -      -       -      +
    428A  LEU*     5.7     0.4    -      -       +      -
    429A  TYR*     3.6    33.8    +      -       +      -
    432A  TYR*     3.4    44.1    -      -       +      +
    437A  ILE*     5.1     1.0    -      -       -      +
    439A  PHE*     1.3    79.3    +      -       -      +
    441A  VAL*     1.3    68.5    +      -       -      +
    442A  LEU*     3.6     2.9    +      -       +      +
    454A  HIS      3.7     3.5    -      -       -      +
    456A  ARG*     3.2    40.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 441 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    383A  VAL*     4.0    16.2    -      -       +      -
    384A  ALA      3.6     5.4    +      -       -      +
    385A  LEU*     2.9    59.9    -      -       +      -
    386A  ASP      3.4     1.4    +      -       -      -
    402A  LEU*     4.6    11.9    -      -       +      -
    439A  PHE*     4.0     1.5    -      -       +      -
    440A  THR*     1.3    75.0    -      -       -      +
    442A  LEU*     1.3    61.3    +      -       -      +
    443A  VAL*     5.3     3.4    -      -       +      -
    453A  ILE*     4.3     9.0    -      -       +      -
    454A  HIS      4.0     6.3    -      -       -      -
    455A  LEU*     3.7    19.1    -      -       +      +
    471A  LEU*     3.5    32.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 442 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    386A  ASP*     3.8    16.8    -      -       +      +
    387A  VAL      4.0     2.0    -      -       -      +
    388A  GLY*     3.6    12.3    -      -       -      +
    389A  ARG*     4.7    10.1    -      -       -      +
    425A  LEU*     4.0    27.4    -      -       +      -
    428A  LEU*     6.0     2.5    -      -       +      -
    429A  TYR*     4.2    10.8    -      -       +      +
    440A  THR*     3.6     5.1    +      -       +      +
    441A  VAL*     1.3    76.6    -      -       -      +
    443A  VAL*     1.3    77.7    +      -       -      +
    444A  THR*     3.5    21.8    -      -       +      -
    453A  ILE*     3.6     9.5    -      -       -      +
    454A  HIS*     3.0    50.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 443 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    385A  LEU*     5.5     2.2    -      -       +      -
    386A  ASP      3.2    11.3    +      -       -      +
    387A  VAL*     3.2     1.0    -      -       -      -
    388A  GLY      2.8    28.9    +      -       -      -
    395A  LEU*     2.8    29.7    -      -       +      +
    398A  VAL*     3.6    29.4    -      -       +      -
    399A  CYS*     4.5     9.2    -      -       -      -
    402A  LEU*     4.8    11.0    -      -       +      -
    441A  VAL*     5.3     4.7    -      -       +      -
    442A  LEU*     1.3    75.2    -      -       -      +
    444A  THR*     1.3    62.7    +      -       -      +
    447A  THR*     3.8    17.0    -      -       +      +
    448A  LEU*     5.9     1.3    -      -       +      -
    453A  ILE*     3.5    18.6    -      -       +      -
    468A  ILE*     4.3     5.6    -      -       +      -
----------------------------------------------------------
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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