Contacts of the strand formed by residues 875 - 883 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    870A  PHE*     4.6     7.2    -      -       +      -
    871A  GLU      3.5     4.9    +      -       -      +
    872A  LYS*     3.1    24.4    +      -       +      +
    873A  ARG      5.1     0.2    -      -       -      -
    874A  PHE*     1.3    73.1    -      -       -      +
    876A  LYS*     1.3    66.6    +      -       -      +
    877A  ARG      3.9     2.3    +      -       -      -
    892A  CYS*     4.1    12.2    -      -       +      -
    893A  ARG      4.0     0.4    -      -       -      -
    894A  TYR*     3.6    22.7    -      -       +      -
    905A  VAL*     3.9    26.5    -      -       +      -
    907A  VAL*     4.0    19.5    -      -       +      -
    944A  CYS*     4.1    24.5    -      -       +      -
    953A  LYS*     4.5     5.4    -      -       +      -
    955A  ILE*     3.7    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 876 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    873A  ARG*     3.4    26.7    +      -       -      +
    874A  PHE*     3.7    12.3    -      -       -      +
    875A  LEU*     1.3    76.7    -      -       -      +
    877A  ARG*     1.3    66.7    +      -       -      +
    878A  ILE*     3.6     3.8    +      -       -      +
    892A  CYS*     3.2     4.5    -      -       -      +
    893A  ARG*     2.9    45.7    +      -       +      +
    895A  ASP*     4.7    11.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 877 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    875A  LEU      3.9     4.0    +      -       -      -
    876A  LYS*     1.3    72.9    -      -       -      +
    878A  ILE*     1.3    75.9    +      -       -      +
    879A  ARG*     4.3     7.7    -      -       -      +
    880A  ASP*     3.0    35.5    +      -       -      +
    890A  GLU*     3.3    38.5    +      -       +      +
    891A  LEU      4.5     2.5    -      -       -      +
    892A  CYS*     3.8    10.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 878 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    876A  LYS      3.9     6.7    -      -       -      +
    877A  ARG*     1.3    90.7    +      -       -      +
    879A  ARG*     1.4    70.6    +      -       +      +
    891A  LEU*     2.8    41.6    +      -       +      +
    892A  CYS      4.2     0.9    -      -       -      +
    893A  ARG*     4.0    32.8    -      -       +      +
    904A  GLN*     4.2    15.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 879 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    877A  ARG*     4.3    10.2    -      -       -      +
    878A  ILE*     1.4    86.3    -      -       +      +
    880A  ASP*     1.3    67.1    +      -       -      +
    881A  LEU*     3.6    19.7    -      -       -      +
    890A  GLU*     3.4     3.8    -      -       -      +
    891A  LEU*     2.7    53.7    +      -       +      +
    958A  PHE*     3.9    24.5    -      -       -      -
    960A  PRO      4.9     6.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 880 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    877A  ARG*     3.0    25.4    +      -       -      +
    879A  ARG*     1.3    86.8    +      -       -      +
    881A  LEU*     1.3    65.5    +      -       -      +
    882A  GLY*     4.6     5.2    -      -       -      +
    883A  GLU*     5.7     3.9    -      -       +      +
    888A  LYS*     5.1     7.1    +      -       -      +
    889A  VAL      3.8     5.8    -      -       -      +
    890A  GLU*     3.3    22.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 881 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    879A  ARG*     3.6    26.7    -      -       -      +
    880A  ASP*     1.3    74.5    -      -       -      +
    882A  GLY*     1.3    58.3    +      -       -      +
    889A  VAL*     2.8    14.0    +      -       +      +
    890A  GLU      3.9     4.3    -      -       -      -
    891A  LEU*     3.7    36.3    -      -       +      +
    906A  ALA*     4.1    13.7    -      -       +      -
    958A  PHE*     3.8    35.2    -      -       +      -
    966A  GLU*     4.7     8.4    -      -       -      +
   1201A  0NT      3.5    54.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 882 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    880A  ASP*     3.7     5.2    -      -       -      +
    881A  LEU*     1.3    81.3    -      -       -      +
    883A  GLU*     1.3    58.1    +      -       -      -
    888A  LYS*     3.6     1.4    -      -       -      +
    889A  VAL*     2.8    34.4    +      -       -      +
   1201A  0NT      3.2    29.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 883 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    880A  ASP*     5.7     3.8    -      -       +      +
    882A  GLY*     1.3    73.4    -      -       -      -
    884A  GLY*     1.3    64.2    +      -       -      +
    887A  GLY      4.1     3.4    -      -       -      +
    888A  LYS*     4.3    16.6    -      -       +      +
    911A  LYS*     4.3    18.3    +      -       +      +
   1201A  0NT      2.9    31.9    +      -       +      +
----------------------------------------------------------
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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