Contacts of the strand formed by residues 85 - 91 (chain B) in PDB entry 1UMZ


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 85 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75B  TYR*     3.8    14.5    -      -       +      -
     76B  LEU      3.2    13.7    -      -       -      +
     77B  SER*     4.0     6.0    +      -       -      +
     83B  HIS*     2.7    36.9    +      -       +      +
     84B  ASP*     1.3    78.2    -      -       -      +
     86B  ILE*     1.3    65.7    +      -       -      +
     87B  ASP*     2.4    42.9    -      -       -      +
    105B  VAL*     3.4     6.1    -      -       -      +
    106B  PHE*     2.9    47.6    +      -       +      +
    162B  PRO*     5.3     0.4    -      -       -      +
    167B  MET*     4.1     2.8    -      -       -      +
      3F  BGC      4.9     5.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 86 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75B  TYR*     3.2     4.7    -      -       -      +
     76B  LEU*     2.9    40.6    +      -       +      +
     85B  GLU*     1.3    79.5    -      -       -      +
     87B  ASP*     1.3    58.7    +      -       -      +
     88B  PHE*     5.8     1.0    -      -       +      -
    104B  ASN      3.7     3.8    -      -       -      -
    105B  VAL*     5.3     2.5    -      -       +      -
    132B  VAL*     4.0    28.2    -      -       +      +
    134B  TRP*     4.2    12.8    -      -       +      -
    139B  ILE*     3.6    40.4    -      -       +      -
    141B  PHE*     3.5    29.2    -      -       +      -
    162B  PRO*     4.9     1.6    -      -       +      -
    167B  MET*     3.4    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 87 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75B  TYR*     3.2    16.8    -      -       +      +
     85B  GLU*     2.4    39.6    -      -       -      +
     86B  ILE*     1.3    73.5    -      -       -      +
     88B  PHE*     1.3    59.1    +      -       -      +
     89B  GLU*     3.7    26.0    -      -       +      +
    103B  THR*     3.1    22.9    -      -       -      -
    104B  ASN*     3.0    23.2    +      -       -      +
    106B  PHE*     3.2    24.8    -      -       -      -
    141B  PHE*     3.4    11.8    -      -       -      -
      3F  BGC      3.8     3.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 88 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72B  THR      4.5     0.4    -      -       -      -
     73B  ALA*     3.3     4.9    -      -       -      +
     74B  PHE*     2.9    62.7    +      +       +      +
     75B  TYR*     5.0     0.4    -      -       -      +
     86B  ILE      5.8     0.4    -      -       -      -
     87B  ASP*     1.3    73.9    -      -       -      +
     89B  GLU*     1.3    62.9    +      -       -      +
     90B  PHE*     4.1    10.7    -      -       +      -
    101B  LEU*     3.8    35.2    -      -       +      -
    102B  GLN      3.6     3.4    -      -       -      -
    103B  THR*     4.2     4.3    -      -       +      -
    130B  TYR*     4.2    13.2    -      +       +      -
    131B  SER      3.4    26.0    -      -       -      -
    132B  VAL*     3.6    28.5    -      -       +      -
    141B  PHE*     3.9    17.5    -      +       +      -
    142B  LEU      3.7    15.9    -      -       -      -
    143B  VAL*     4.7     0.2    -      -       +      -
    148B  ILE*     4.2    11.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 89 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71B  VAL*     3.9    11.0    -      -       +      -
     72B  THR      3.5     3.8    -      -       -      -
     73B  ALA*     4.1    13.6    -      -       +      +
     75B  TYR*     6.0     0.9    -      -       +      -
     87B  ASP*     3.7    20.2    -      -       +      +
     88B  PHE*     1.3    79.9    -      -       -      +
     90B  PHE*     1.3    61.8    +      -       -      +
     91B  LEU*     3.7    10.1    +      -       +      +
    101B  LEU*     4.0     1.0    -      -       -      +
    102B  GLN*     2.7    59.2    +      -       +      +
    104B  ASN*     4.6     1.0    -      -       -      +
    174B  TRP*     4.0    12.0    -      -       -      -
    179B  TRP*     4.0     8.3    -      -       -      -
      3F  BGC      2.7    49.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 90 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60B  MET*     3.7    23.8    -      -       +      -
     62B  LEU*     3.4    37.7    -      -       +      -
     70B  THR      3.6     1.7    -      -       -      +
     71B  VAL*     3.3     5.4    -      -       -      -
     72B  THR      2.7    41.5    +      -       -      +
     73B  ALA*     5.3     0.2    -      -       -      -
     74B  PHE*     5.1     0.7    -      -       +      -
     88B  PHE*     4.1    13.7    -      +       +      -
     89B  GLU*     1.3    71.0    -      -       -      +
     91B  LEU*     1.3    61.1    +      -       -      +
     92B  GLY      3.8     0.7    +      -       -      -
     99B  TYR*     3.7    11.7    -      +       +      -
    100B  ILE      3.4     8.1    -      -       -      -
    101B  LEU*     3.6    32.8    -      -       +      -
    119B  LEU*     4.5     7.9    -      -       +      -
    123B  PRO*     5.4     0.7    -      -       +      -
    130B  TYR*     3.5    55.0    -      +       -      -
----------------------------------------------------------
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Residues in contact with LEU 91 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70B  THR      3.7     4.0    -      -       -      -
     71B  VAL*     4.0    12.8    -      -       +      -
     89B  GLU*     3.8    18.8    -      -       +      +
     90B  PHE*     1.3    75.1    -      -       -      +
     92B  GLY*     1.3    64.8    +      -       -      +
     99B  TYR*     3.1     5.9    -      -       -      -
    100B  ILE*     2.8    48.5    +      -       +      +
    102B  GLN*     4.2     4.5    -      -       +      +
    116B  ARG*     3.9    35.4    -      -       -      +
    179B  TRP*     3.7    28.7    -      -       +      -
    180B  ALA*     3.5    26.9    -      -       +      +
      1E  NAG      3.5     8.3    -      -       +      +
----------------------------------------------------------
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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