Contacts of the strand formed by residues 903 - 910 (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 GLU 903 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    870A  PHE*     4.4    11.1    -      -       -      -
    893A  ARG*     3.5     0.6    -      -       -      -
    894A  TYR*     2.9    35.4    +      -       +      +
    902A  GLY*     1.3    71.6    -      -       -      -
    904A  GLN*     1.3    71.8    +      -       -      +
    905A  VAL*     3.8     8.8    +      -       +      +
    941A  LYS*     3.2    37.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 904 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    878A  ILE*     4.2    17.6    -      -       +      +
    891A  LEU*     4.0    13.1    -      -       +      +
    892A  CYS      3.3     7.0    -      -       -      +
    893A  ARG*     4.3    26.4    +      -       +      +
    902A  GLY      3.8     0.2    +      -       -      -
    903A  GLU*     1.3    78.9    -      -       -      +
    905A  VAL*     1.3    64.6    +      -       -      +
    941A  LYS*     5.4     0.7    -      -       -      -
    957A  GLU*     5.5     0.2    -      -       -      -
    958A  PHE*     3.7    45.8    +      -       +      +
    960A  PRO*     5.1     5.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 905 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    870A  PHE*     4.5     5.8    -      -       +      -
    875A  LEU*     3.9    18.2    -      -       +      -
    891A  LEU*     3.6     4.9    -      -       -      +
    892A  CYS      2.8    39.3    +      -       -      +
    894A  TYR*     4.5     7.6    -      -       +      -
    903A  GLU*     3.8    12.8    -      -       +      +
    904A  GLN*     1.3    78.2    -      -       -      +
    906A  ALA*     1.3    58.0    +      -       -      +
    907A  VAL*     3.8    20.0    -      -       +      -
    941A  LYS*     3.8    32.1    -      -       +      -
    955A  ILE*     3.8    15.7    -      -       +      -
    956A  MET      3.6     7.0    -      -       -      +
    958A  PHE*     3.9     9.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 906 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    881A  LEU*     4.1     7.6    -      -       +      -
    889A  VAL*     3.9     9.9    -      -       +      -
    890A  GLU      3.6     4.9    -      -       -      -
    905A  VAL*     1.3    72.7    -      -       -      +
    907A  VAL*     1.4    58.3    +      -       -      +
    954A  LEU      3.6     1.0    -      -       -      +
    955A  ILE*     3.6     3.5    -      -       -      +
    956A  MET*     2.8    36.7    +      -       +      +
    957A  GLU      3.8     5.6    -      -       -      +
    958A  PHE*     4.0     2.7    -      -       -      +
   1201A  0NT      3.2    44.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 907 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    875A  LEU*     4.0     8.7    -      -       +      -
    888A  LYS      3.5     1.9    -      -       -      +
    889A  VAL*     3.2     4.4    -      -       -      +
    890A  GLU*     2.8    41.3    +      -       +      +
    892A  CYS*     3.7    28.3    -      -       +      -
    905A  VAL*     3.8    17.5    -      -       +      -
    906A  ALA*     1.4    75.9    -      -       -      +
    908A  LYS*     1.4    61.2    +      -       -      +
    909A  SER*     3.9     6.6    +      -       -      +
    953A  LYS*     3.9    28.0    -      -       +      -
    954A  LEU      3.4     1.8    -      -       -      -
    955A  ILE*     3.7    29.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 908 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    884A  GLY*     5.4     6.3    -      -       -      -
    885A  HIS      6.0     0.8    -      -       -      +
    887A  GLY*     4.5    20.4    -      -       -      +
    888A  LYS      3.3     9.4    -      -       -      +
    889A  VAL*     3.8    22.4    -      -       +      -
    906A  ALA      4.2     0.6    -      -       -      -
    907A  VAL*     1.4    72.1    -      -       -      +
    909A  SER*     1.3    62.1    +      -       -      +
    922A  LEU*     4.1    16.0    -      -       +      +
    925A  GLU*     2.7    43.6    +      -       -      +
    953A  LYS*     3.3     5.0    -      -       -      -
    954A  LEU*     2.8    54.6    +      -       +      +
    956A  MET*     4.1     7.3    -      -       +      +
   1021A  ASP*     2.8    33.1    +      -       -      +
   1023A  GLY*     3.7     5.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 909 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    887A  GLY*     3.1     3.3    -      -       -      -
    888A  LYS*     2.9    41.8    +      -       -      +
    890A  GLU*     5.6     4.3    +      -       -      -
    907A  VAL*     3.9     6.5    +      -       -      +
    908A  LYS*     1.3    73.5    -      -       -      +
    910A  LEU*     1.3    68.1    +      -       -      +
    922A  LEU*     4.3     7.0    -      -       -      -
    952A  ILE      4.8     0.9    -      -       -      -
    953A  LYS*     2.9    42.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 910 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    886A  PHE*     3.6    20.0    -      -       +      +
    887A  GLY*     4.2     0.7    -      -       -      -
    888A  LYS*     5.0     4.9    -      -       -      +
    909A  SER*     1.3    80.2    -      -       -      +
    911A  LYS*     1.3    68.1    +      -       -      +
    917A  ASN      4.9     4.0    -      -       -      +
    918A  HIS*     3.5    33.0    -      -       +      +
    919A  ILE*     3.2    42.2    -      -       +      +
    922A  LEU*     4.0    27.0    -      -       +      +
    952A  ILE*     4.9     4.1    +      -       +      +
----------------------------------------------------------
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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