Contacts of the strand formed by residues 440 - 445 (chain A) in PDB entry 5G04


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 LYS 440 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    432A  ILE*     4.1    24.5    -      -       +      -
    433A  THR      3.8     2.0    -      -       -      +
    434A  SER*     4.7    10.5    -      -       -      +
    438A  GLY*     4.7     5.6    -      -       -      -
    439A  GLN*     1.3    99.9    -      -       -      +
    441A  PHE*     1.3    69.0    +      -       -      +
    442A  LEU      3.9     0.4    -      -       -      -
    456A  LYS*     3.5     1.9    -      -       -      -
    457A  PHE*     3.0    46.7    +      -       +      +
    458A  GLN*     3.8    36.2    -      -       -      +
    459A  GLU*     4.6    10.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 441 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    431A  PHE      3.3     0.2    -      -       -      +
    433A  THR*     2.8    43.0    +      -       -      +
    435A  ASP*     3.3    37.2    -      -       -      -
    439A  GLN*     3.6    21.1    -      -       +      -
    440A  LYS*     1.3    75.0    -      -       -      +
    442A  LEU*     1.3    62.6    +      -       -      +
    443A  CYS*     3.1    24.5    -      -       -      -
    454A  CYS*     4.4    14.6    -      -       +      -
    455A  VAL      3.3    20.0    -      -       -      +
    456A  LYS*     3.5    23.3    -      -       +      -
    472A  THR*     5.5     0.2    -      -       -      -
    502A  GLY*     3.9    20.9    -      -       -      +
    503A  VAL*     3.7    29.4    -      -       +      -
----------------------------------------------------------
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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
----------------------------------------------------------
    248A  PHE*     4.0     8.1    -      -       +      -
    255A  ILE*     3.7    43.7    -      -       +      -
    257A  MET*     4.6     7.0    -      -       -      -
    268A  VAL*     5.4     0.4    -      -       +      -
    430A  VAL*     3.6    27.4    -      -       +      +
    431A  PHE      3.6     7.0    -      -       -      +
    432A  ILE*     3.9    16.1    -      -       +      +
    440A  LYS      3.9     1.0    -      -       -      -
    441A  PHE*     1.3    71.3    -      -       -      +
    443A  CYS*     1.3    75.4    +      -       -      +
    444A  PHE*     3.8    13.4    -      -       +      -
    455A  VAL*     2.9    33.5    +      -       -      +
    457A  PHE*     3.6    31.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 443 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    430A  VAL*     3.0    31.4    -      -       -      +
    431A  PHE*     3.4    41.9    +      -       +      -
    433A  THR*     4.7     0.9    -      -       -      -
    441A  PHE*     3.1    23.8    -      -       -      -
    442A  LEU*     1.3    75.2    -      -       -      +
    444A  PHE*     1.3    67.5    +      -       -      +
    445A  LEU*     4.2     0.9    -      -       +      -
    452A  LEU*     5.4     3.6    -      -       +      +
    453A  ARG      3.3    11.9    -      -       -      +
    454A  CYS*     3.9    14.4    -      -       -      -
    479A  ALA*     6.3     0.2    -      -       +      -
    488A  MET*     3.8    16.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 444 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257A  MET*     3.5    28.5    -      -       +      -
    266A  HIS*     3.5    31.6    -      +       +      +
    268A  VAL*     4.6     3.1    -      -       +      -
    414A  THR*     4.0    16.6    -      -       -      -
    415A  GLU      4.1    15.7    -      -       -      -
    427A  ALA*     4.8     0.2    -      -       +      -
    430A  VAL*     3.7    12.8    -      -       +      -
    442A  LEU*     3.8    21.8    -      -       +      -
    443A  CYS*     1.3    79.1    -      -       -      +
    445A  LEU*     1.3    59.9    +      -       -      +
    452A  LEU*     3.2     3.0    -      -       -      -
    453A  ARG*     2.9    72.6    +      -       +      +
    455A  VAL*     3.4    30.7    -      -       +      -
    471A  VAL*     5.2     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 445 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    427A  ALA*     3.3     4.4    -      -       -      -
    428A  SER*     3.0    44.9    +      -       -      +
    429A  LYS*     3.8    32.1    -      -       +      +
    430A  VAL*     5.0     1.6    -      -       -      +
    431A  PHE*     5.7     4.0    -      -       +      -
    443A  CYS*     4.2     1.2    -      -       +      -
    444A  PHE*     1.3    72.7    -      -       -      +
    446A  VAL*     1.3    67.0    +      -       -      +
    447A  GLU*     5.3     0.9    -      -       -      +
    451A  GLN      3.6    18.6    -      -       -      +
    452A  LEU*     3.7    22.7    -      -       +      -
    477A  LYS      3.4    24.7    -      -       -      +
    478A  ASP*     3.8     8.1    -      -       -      +
    479A  ALA*     3.3    30.3    -      -       +      +
----------------------------------------------------------
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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