Contacts of the strand formed by residues 724 - 731 (chain B) in PDB entry 3H44


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 HIS 724 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    553B  ASP*     5.6     0.2    -      -       -      -
    554B  THR      4.4     3.1    -      -       -      -
    555B  ALA      3.2    23.4    +      -       -      +
    556B  MET      3.3     4.0    +      -       -      -
    557B  SER*     3.8     2.0    -      -       -      -
    558B  LYS*     3.5    47.0    -      -       +      +
    578B  PHE*     3.4     5.0    -      -       -      +
    579B  PHE*     2.9    58.7    +      +       +      -
    723B  LEU*     1.3    75.8    -      -       -      +
    725B  ILE*     1.3    71.8    +      -       -      +
    726B  GLU*     4.7     4.5    +      -       -      -
    758B  LEU*     4.3     4.9    -      -       +      +
    763B  LEU*     3.9    40.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 725 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    556B  MET*     3.0    18.1    +      -       +      +
    557B  SER*     3.2     5.8    -      -       -      -
    558B  LYS      2.9    26.3    +      -       -      +
    576B  PHE*     3.9    15.7    -      -       +      -
    577B  GLU      3.4     9.6    -      -       -      +
    578B  PHE*     3.5    33.9    -      -       +      -
    723B  LEU*     4.9     6.3    -      -       +      -
    724B  HIS*     1.3    83.9    -      -       -      +
    726B  GLU*     1.3    70.1    +      -       -      +
    742B  MET*     3.8    31.9    -      -       +      -
    745B  VAL*     4.4     5.8    -      -       +      -
    746B  GLU*     4.8    10.1    -      -       +      -
    749B  LEU*     4.0    17.3    -      -       +      -
    755B  THR*     6.5     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 726 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    558B  LYS*     3.4    27.5    -      -       +      +
    560B  TRP*     3.1    20.8    +      -       -      +
    576B  PHE*     3.2     4.7    -      -       -      -
    577B  GLU*     2.8    38.8    +      -       +      +
    579B  PHE*     4.1    27.1    -      -       +      -
    724B  HIS*     4.1     4.1    +      -       -      +
    725B  ILE*     1.3    76.3    -      -       -      +
    727B  ALA*     1.3    63.1    +      -       -      +
    908B  TRP*     4.1     3.7    -      -       +      -
    911B  ILE*     3.9    22.3    -      -       +      +
    912B  ILE*     6.0     0.2    -      -       -      -
    914B  GLN*     4.9     4.7    +      -       -      +
    916B  TYR*     2.5    30.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 727 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    558B  LYS      3.2     6.4    +      -       -      +
    559B  LEU*     3.9    18.2    -      -       +      -
    560B  TRP*     2.9    36.1    +      -       -      +
    575B  ASN      3.0    13.5    -      -       -      +
    576B  PHE*     3.8    22.2    -      -       +      -
    726B  GLU*     1.3    76.9    -      -       -      +
    728B  LEU*     1.3    60.7    +      -       -      +
    729B  LEU*     4.4     2.9    -      -       +      -
    742B  MET*     4.0    10.5    -      -       -      -
    908B  TRP*     4.3     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 728 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    548B  PRO*     4.3    18.2    -      -       +      -
    560B  TRP*     3.3    17.5    -      -       +      +
    561B  PHE*     4.6     1.1    -      -       -      +
    562B  LYS*     4.9     1.6    -      -       +      +
    573B  ASN*     3.9     1.5    -      -       +      +
    574B  LEU*     3.6     0.5    -      -       -      -
    575B  ASN*     2.7    40.7    +      -       +      +
    727B  ALA*     1.3    74.1    -      -       -      +
    729B  LEU*     1.3    68.1    +      -       -      +
    730B  HIS*     3.9    26.9    -      -       +      -
    904B  SER*     3.9    20.2    -      -       -      +
    907B  TYR*     3.9    21.8    -      -       +      -
    908B  TRP*     3.9    21.4    -      -       +      +
    911B  ILE*     3.9    16.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 729 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    559B  LEU*     3.8    22.4    -      -       +      -
    560B  TRP      2.9     9.7    +      -       -      +
    561B  PHE*     3.5     8.4    -      -       +      -
    562B  LYS      3.2    23.4    +      -       -      +
    573B  ASN      3.5     4.3    -      -       -      -
    574B  LEU*     3.7    27.6    -      -       +      -
    575B  ASN      4.4     1.6    -      -       -      +
    576B  PHE*     3.7    28.5    -      -       +      -
    727B  ALA*     4.4     2.0    -      -       +      -
    728B  LEU*     1.3    86.1    -      -       -      +
    730B  HIS*     1.3    59.4    +      -       -      +
    733B  ILE*     4.2    10.5    -      -       +      +
    738B  ALA*     3.7    37.0    -      -       +      +
    741B  ILE*     4.2    14.4    -      -       +      -
    742B  MET*     4.7     3.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 730 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    562B  LYS*     3.3    38.1    +      -       +      +
    564B  ASP*     4.2    11.7    -      -       -      -
    572B  ALA*     3.6     0.9    -      -       -      +
    573B  ASN*     2.7    40.2    +      -       +      +
    728B  LEU*     3.9    19.2    -      -       +      -
    729B  LEU*     1.3    73.0    -      -       -      +
    731B  GLY*     1.3    63.7    +      -       -      +
    733B  ILE*     4.6     2.7    -      -       -      -
    900B  LEU*     3.5    24.5    -      -       +      +
    903B  GLU*     3.4    27.9    +      -       -      +
    904B  SER*     2.9    39.7    -      -       -      +
    907B  TYR*     4.2     9.2    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLY 731 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    562B  LYS      3.2     3.3    +      -       -      +
    563B  GLN*     3.4     7.8    -      -       -      +
    564B  ASP*     2.8    36.8    +      -       -      -
    571B  LYS      3.8     8.7    -      -       -      -
    572B  ALA*     4.2     1.6    -      -       -      -
    730B  HIS*     1.3    83.4    +      -       -      +
    732B  ASN*     1.3    58.0    +      -       -      -
    733B  ILE*     3.0    15.4    +      -       -      +
    900B  LEU*     3.9     7.9    -      -       -      -
----------------------------------------------------------
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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