Contacts of the strand formed by residues 875 - 883 (chain B) in PDB entry 4E5W


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 LEU 875 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    870B  PHE*     4.8     3.6    -      -       +      -
    871B  GLU      3.6     4.2    +      -       -      +
    872B  LYS*     3.1    20.6    +      -       +      +
    873B  ARG      5.0     1.4    -      -       -      +
    874B  PHE*     1.3    75.3    -      -       -      +
    876B  LYS*     1.3    61.2    +      -       -      +
    877B  ARG      3.9     2.1    +      -       -      -
    892B  CYS*     3.9    26.9    -      -       +      -
    893B  ARG      3.7     0.7    -      -       -      -
    894B  TYR*     3.9    24.7    -      -       +      -
    905B  VAL*     3.9    18.2    -      -       +      -
    907B  VAL*     3.9    12.6    -      -       +      -
    944B  CYS*     4.2    24.0    -      -       +      -
    953B  LYS*     4.5     6.3    -      -       +      -
    955B  ILE*     4.0    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 876 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    873B  ARG      6.1     0.2    -      -       -      +
    874B  PHE      4.5     6.1    -      -       -      +
    875B  LEU*     1.3    72.3    -      -       -      +
    877B  ARG*     1.4    66.0    +      -       -      +
    878B  ILE*     3.5     5.1    +      -       +      +
    892B  CYS*     3.1     6.1    -      -       -      -
    893B  ARG*     2.9    44.7    +      -       +      +
    895B  ASP*     2.8    36.1    +      -       +      +
    898B  GLY*     4.2    13.5    +      -       -      -
    900B  ASN*     4.1    22.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 877 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    875B  LEU      3.9     3.8    +      -       -      -
    876B  LYS*     1.4    72.4    -      -       -      +
    878B  ILE*     1.3    76.7    +      -       -      +
    879B  ARG*     4.3     7.4    -      -       -      +
    880B  ASP*     3.0    35.7    +      -       -      +
    890B  GLU*     3.2    37.5    +      -       +      +
    891B  LEU      4.6     2.0    -      -       -      +
    892B  CYS*     3.8    11.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 878 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    876B  LYS*     3.8     9.6    -      -       +      +
    877B  ARG*     1.3    90.2    +      -       -      +
    879B  ARG*     1.4    70.0    +      -       +      +
    891B  LEU*     2.8    35.1    +      -       +      +
    893B  ARG*     4.0    33.4    -      -       +      +
    904B  GLN*     3.9    23.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 879 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    877B  ARG*     4.3    10.0    -      -       -      +
    878B  ILE*     1.4    86.4    -      -       +      +
    880B  ASP*     1.3    67.9    +      -       -      +
    881B  LEU*     3.6    20.3    -      -       -      +
    890B  GLU*     3.4     4.3    -      -       -      +
    891B  LEU*     2.7    52.2    +      -       +      +
    958B  PHE*     3.9    24.5    -      -       -      -
    960B  PRO      5.0     6.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 880 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    877B  ARG*     3.0    25.7    +      -       -      +
    879B  ARG*     1.3    87.7    +      -       -      +
    881B  LEU*     1.3    64.9    +      -       -      +
    882B  GLY*     4.6     4.9    -      -       -      +
    883B  GLU*     5.7     3.1    -      -       +      +
    888B  LYS*     5.1     8.3    -      -       -      +
    889B  VAL      3.8     5.8    -      -       -      +
    890B  GLU*     3.3    22.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 881 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    879B  ARG*     3.6    27.4    -      -       -      +
    880B  ASP*     1.3    73.7    -      -       -      +
    882B  GLY*     1.3    58.2    +      -       -      +
    889B  VAL*     2.8    14.4    +      -       +      +
    890B  GLU      3.9     3.4    -      -       -      -
    891B  LEU*     3.7    33.0    -      -       +      +
    906B  ALA*     4.1    13.7    -      -       +      -
    958B  PHE*     3.8    37.7    -      -       +      -
    966B  GLU*     4.7     7.6    -      -       -      +
   1202B  0NT      3.4    55.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 882 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    880B  ASP*     3.7     4.8    -      -       -      +
    881B  LEU*     1.3    81.7    -      -       -      +
    883B  GLU*     1.3    58.9    +      -       -      -
    888B  LYS*     3.6     1.9    -      -       -      +
    889B  VAL*     2.8    33.5    +      -       -      +
   1202B  0NT      3.2    31.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 883 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    880B  ASP*     5.7     3.6    -      -       +      +
    882B  GLY*     1.3    70.6    -      -       -      -
    884B  GLY*     1.3    63.1    +      -       -      +
    887B  GLY      4.1     3.4    -      -       -      +
    888B  LYS*     4.3    16.8    -      -       +      +
    911B  LYS*     4.3    18.5    +      -       +      -
   1202B  0NT      2.9    35.7    +      -       +      +
----------------------------------------------------------
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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