Contacts of the strand formed by residues 734 - 739 (chain B) in PDB entry 1EGI


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 TYR 734 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    700B  THR*     3.7     1.4    +      -       -      -
    701B  TYR*     2.9    48.5    +      +       +      +
    732B  VAL*     4.9     0.5    -      -       -      +
    733B  GLU*     1.3   104.5    +      -       +      +
    735B  CYS*     1.3    60.7    +      -       -      +
    748B  ASP*     4.4    20.2    -      -       +      +
    749B  ILE*     3.5    18.4    -      -       -      +
    750B  ASN*     4.7    12.1    -      -       +      -
    751B  CYS*     3.2     8.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 735 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    655B  TRP*     3.3    36.8    -      -       +      -
    696B  TRP*     3.6    20.9    -      -       +      -
    699B  LEU      3.4     4.9    -      -       -      +
    700B  THR*     3.9    10.1    -      -       -      +
    732B  VAL*     4.7     0.2    -      -       -      -
    734B  TYR*     1.3    76.7    -      -       -      +
    736B  GLY*     1.3    59.1    +      -       -      +
    748B  ASP*     3.3     4.6    -      -       -      -
    749B  ILE*     2.6    44.1    +      -       -      +
    751B  CYS*     2.0    45.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 736 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    696B  TRP*     3.3     8.6    -      -       -      -
    697B  LEU*     3.2    28.3    +      -       -      +
    699B  LEU*     2.8    40.8    +      -       -      +
    735B  CYS*     1.3    72.4    -      -       -      +
    737B  GLU*     1.3    60.3    +      -       -      -
    747B  ASN      3.4     7.4    -      -       -      -
    748B  ASP*     4.3     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 737 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    694B  LEU*     3.8    25.7    -      -       +      +
    695B  PHE      3.2    12.1    -      -       -      +
    696B  TRP*     4.1     5.6    -      -       +      -
    697B  LEU*     4.6     4.7    -      -       -      +
    735B  CYS      4.1     0.2    +      -       -      -
    736B  GLY*     1.3    75.6    -      -       -      +
    738B  LEU*     1.3    62.1    +      -       -      +
    739B  LYS      4.1     0.2    +      -       -      -
    745B  SER      3.9     0.3    -      -       -      +
    746B  TRP*     3.3     7.0    -      -       -      +
    747B  ASN*     2.9    65.2    +      -       +      +
    749B  ILE*     4.0    18.7    -      -       +      +
    755B  ASN*     2.7    42.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 738 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    672B  ILE*     5.1     5.6    -      -       +      -
    681B  ILE*     4.1    16.2    -      -       +      -
    685B  ILE*     4.5     6.3    -      -       +      -
    694B  LEU*     3.3    10.2    -      -       -      +
    695B  PHE*     2.6    41.5    +      -       +      +
    697B  LEU*     3.9    21.4    -      -       +      +
    737B  GLU*     1.3    73.2    -      -       -      +
    739B  LYS*     1.3    65.8    +      -       -      +
    740B  GLY      3.5     1.4    +      -       -      +
    744B  MET*     3.2    55.6    -      -       +      +
    745B  SER      3.7     3.4    -      -       -      +
    746B  TRP*     3.9    10.3    -      -       +      +
    758B  ILE*     3.9    25.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 739 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    692B  HIS*     5.1    12.2    +      -       -      +
    693B  LYS      5.0     0.4    -      -       -      +
    694B  LEU*     3.8    27.1    -      -       +      +
    737B  GLU      4.1     0.4    +      -       -      -
    738B  LEU*     1.3    69.9    -      -       -      +
    740B  GLY*     1.3    54.6    +      -       -      +
    741B  ASP*     2.7    46.5    +      -       +      +
    743B  THR*     5.0     0.2    -      -       -      +
    744B  MET*     3.4    19.4    -      -       -      +
    745B  SER*     3.0    28.8    +      -       -      +
----------------------------------------------------------
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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