Contacts of the strand formed by residues 484 - 488 (chain B) in PDB entry 4HXG


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 ALA 484 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    460B  ILE      4.0     2.2    +      -       -      -
    461B  GLY*     3.1    21.1    -      -       -      -
    462B  ILE*     3.1     8.1    +      -       -      +
    476B  LEU*     4.6     6.3    -      -       -      -
    482B  PHE*     3.4     4.0    +      -       -      +
    483B  LYS*     1.3    81.3    -      -       -      +
    485B  GLY*     1.3    58.8    +      -       -      +
    536B  ALA*     4.2     1.8    -      -       -      -
    537B  PRO*     3.6    12.8    -      -       +      +
    599B  PHE*     4.8     3.4    -      -       +      -
    600B  PHE*     4.7     7.9    -      -       +      -
    603B  LYS*     3.8    29.8    -      -       +      +
    604B  LEU*     4.2    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 485 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    462B  ILE*     3.2    13.7    -      -       -      -
    472B  THR*     4.5     4.9    -      -       -      -
    476B  LEU*     4.5     6.1    -      -       -      +
    484B  ALA*     1.3    78.0    -      -       -      +
    486B  ILE*     1.3    63.7    +      -       -      -
    537B  PRO      3.3     7.5    +      -       -      -
    538B  LEU*     3.2    14.8    -      -       -      +
    539B  LEU      3.1    23.4    +      -       -      -
    599B  PHE*     3.6     5.3    -      -       -      -
    600B  PHE*     4.9     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 486 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    462B  ILE      3.2     7.3    +      -       -      -
    463B  THR*     3.0    35.1    +      -       -      +
    464B  GLY      3.4     5.2    +      -       -      +
    472B  THR*     4.0     2.5    -      -       -      +
    485B  GLY*     1.3    75.1    -      -       -      -
    487B  SER*     1.3    61.5    +      -       -      +
    488B  GLU*     4.2    10.5    -      -       +      +
    539B  LEU*     3.4    17.7    -      -       +      +
    541B  ILE*     4.2    23.6    -      -       +      -
    596B  PHE*     3.8    24.7    -      -       +      +
    599B  PHE*     3.6    28.9    -      -       +      -
    600B  PHE*     3.5    33.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 487 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    464B  GLY      4.0     2.9    -      -       -      -
    469B  GLY*     3.3    12.5    +      -       -      -
    472B  THR*     3.9    15.0    -      -       -      -
    473B  ASN*     2.9    32.0    +      -       -      -
    486B  ILE*     1.3    72.5    -      -       -      +
    488B  GLU*     1.3    63.4    +      -       -      +
    489B  ASN      4.3     0.4    +      -       -      -
    490B  GLY      4.9     2.9    +      -       -      -
    538B  LEU*     4.0     5.1    -      -       -      +
    539B  LEU      3.0     6.9    +      -       -      -
    540B  LEU*     3.4    21.8    -      -       -      +
    541B  ILE      2.9    24.3    +      -       -      +
    554B  SER*     5.6     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 488 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    463B  THR*     4.3     4.0    +      -       -      -
    464B  GLY      3.1    13.2    +      -       -      +
    465B  ILE*     3.2    18.6    -      -       +      +
    466B  ALA      2.8    20.1    +      -       -      -
    469B  GLY*     4.1     1.1    -      -       -      -
    486B  ILE*     4.2     6.7    -      -       +      +
    487B  SER*     1.3    77.1    +      -       -      +
    489B  ASN*     1.3    79.5    +      -       -      +
    490B  GLY*     3.1     4.6    +      -       -      -
    541B  ILE*     3.4    38.9    -      -       +      +
    580B  HIS*     4.9     0.9    -      -       -      -
    581B  SER*     4.8     1.2    -      -       -      -
    592B  ARG*     2.6    45.8    +      -       -      -
    596B  PHE*     3.9    14.7    -      -       -      -
----------------------------------------------------------
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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