Contacts of the strand formed by residues 86 - 95 (chain A) in PDB entry 4OE5


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 ASN 86 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83A  SER*     2.9    16.3    +      -       -      +
     85A  PHE*     1.3    95.2    -      -       +      +
     87A  HIS*     1.3    56.9    +      -       -      +
     88A  GLY*     3.1    10.1    +      -       -      -
     89A  HIS*     2.9    42.5    +      -       +      +
    379A  ASP*     5.9     0.4    -      -       -      +
    425A  VAL*     3.6    15.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 87 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82A  VAL*     3.5    28.3    -      -       +      +
     83A  SER      3.2    11.0    -      -       -      +
     86A  ASN*     1.3    72.7    -      -       -      +
     88A  GLY*     1.3    61.6    +      -       -      +
     89A  HIS      3.1     2.6    +      -       -      -
     90A  LYS*     5.5     0.2    -      -       -      +
    423A  ASP      3.0    23.3    +      -       -      -
    424A  SER      3.6    16.4    -      -       -      -
    425A  VAL*     3.0    26.1    +      -       -      -
    426A  GLY*     3.6    13.7    -      -       -      -
    427A  TYR*     3.6    45.2    -      +       +      +
----------------------------------------------------------
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Residues in contact with GLY 88 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  ASN*     3.0     9.5    +      -       -      -
     87A  HIS*     1.3    83.0    +      -       -      +
     89A  HIS*     1.3    57.6    +      -       -      +
     90A  LYS*     3.5    10.9    +      -       -      +
    425A  VAL      4.6     0.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 89 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57A  LEU      3.5    13.7    +      -       -      -
     58A  LYS*     4.6     1.9    -      -       -      -
     59A  GLY*     3.7    24.8    +      -       -      -
     60A  ARG      3.6    26.0    -      -       -      -
     82A  VAL*     3.3     4.0    -      -       -      -
     83A  SER*     3.0    33.9    +      -       -      -
     85A  PHE*     6.2     1.1    -      +       -      -
     86A  ASN*     2.9    33.9    +      -       +      +
     87A  HIS      3.1     0.2    -      -       -      -
     88A  GLY*     1.3    75.9    -      -       -      +
     90A  LYS*     1.3    72.0    +      -       -      +
     91A  VAL*     3.4    21.0    +      -       +      +
    149A  VAL*     4.2    10.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 90 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  ARG      3.6     3.1    -      -       -      +
     61A  MET*     3.5    31.2    -      -       -      +
     80A  TYR*     3.8    37.0    -      -       +      -
     81A  GLN      3.5     8.1    -      -       -      +
     82A  VAL*     4.1    15.9    -      -       +      -
     87A  HIS      5.5     0.2    -      -       -      +
     88A  GLY      3.5     9.6    +      -       -      +
     89A  HIS*     1.3    79.9    +      -       -      +
     91A  VAL*     1.3    61.3    +      -       -      +
     92A  ALA      3.5     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 91 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  ARG      3.9     7.6    -      -       -      +
     61A  MET*     3.6     4.5    -      -       -      -
     62A  GLU      3.2    16.6    +      -       -      -
     81A  GLN*     2.7    50.6    +      -       +      +
     82A  VAL      4.4     2.5    -      -       -      +
     83A  SER*     4.0     8.5    -      -       -      +
     89A  HIS*     3.6    37.9    -      -       +      +
     90A  LYS*     1.3    74.1    -      -       -      +
     92A  ALA*     1.3    60.2    +      -       -      +
    149A  VAL*     3.7    17.5    -      -       +      +
    150A  GLY*     4.5     3.6    -      -       -      -
    240A  LEU*     3.9    26.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 92 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  MET*     3.7     6.2    -      -       -      +
     62A  GLU      3.3    11.7    -      -       -      +
     64A  ILE*     3.9    22.4    -      -       +      -
     80A  TYR*     3.2     7.8    -      -       -      -
     81A  GLN*     2.8    49.7    +      -       +      +
     90A  LYS      3.5     0.2    -      -       -      -
     91A  VAL*     1.3    85.0    -      -       +      +
     93A  LYS*     1.3    61.0    +      -       -      +
     94A  PHE*     4.1     4.5    -      -       +      -
    239A  MET*     4.9     0.4    -      -       +      -
    240A  LEU*     4.5     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 93 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  MET*     3.7    19.8    -      -       +      +
     62A  GLU      2.8     9.4    +      -       -      +
     63A  ALA*     3.5    14.1    -      -       -      +
     64A  ILE*     2.7    27.2    +      -       -      +
     74A  TRP*     3.7    22.0    -      -       +      -
     78A  VAL*     3.6    17.9    -      -       +      -
     79A  GLN      3.4     4.3    -      -       -      -
     80A  TYR*     3.5    38.6    -      -       +      +
     92A  ALA*     1.3    73.0    -      -       -      +
     94A  PHE*     1.3    64.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 94 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  ILE*     3.2    28.5    -      -       +      +
     74A  TRP*     3.7     6.2    -      -       -      -
     78A  VAL*     3.4     7.6    -      -       -      +
     79A  GLN*     2.7    56.6    +      -       +      +
     80A  TYR      3.9     3.6    -      -       -      -
     81A  GLN*     3.8    23.3    -      -       +      -
     92A  ALA      4.5     2.5    -      -       -      -
     93A  LYS*     1.3    75.9    -      -       -      +
     95A  CYS*     1.3    81.3    +      -       -      +
     96A  TYR*     3.9    18.6    -      +       -      -
    236A  ASP*     3.6    31.0    -      -       +      -
    239A  MET*     3.8    36.8    -      -       +      -
    263A  PRO*     3.8    11.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 95 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  ILE      4.0     1.4    +      -       -      -
     66A  CYS*     3.6    19.6    -      -       -      +
     73A  VAL      3.8    14.4    -      -       -      -
     74A  TRP*     3.7    22.0    -      -       +      -
     75A  THR*     3.4    38.6    -      -       -      +
     77A  ASP      3.3    14.8    -      -       -      +
     78A  VAL*     4.2     0.9    -      -       -      -
     79A  GLN      4.2     0.7    -      -       -      +
     94A  PHE*     1.3    85.5    -      -       -      +
     96A  TYR*     1.3    59.7    +      -       -      +
    263A  PRO*     3.5    20.8    -      -       -      +
----------------------------------------------------------
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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