Contacts of the strand formed by residues 85 - 91 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  TYR*     3.7    14.5    -      -       +      -
     76A  LEU      3.1    15.0    -      -       -      +
     77A  SER*     4.1     5.5    +      -       -      +
     83A  HIS*     2.8    29.1    +      -       +      +
     84A  ASP*     1.3    78.1    -      -       -      +
     86A  ILE*     1.3    66.5    +      -       -      +
     87A  ASP*     2.3    44.5    -      -       -      +
    105A  VAL*     3.3     5.9    -      -       -      +
    106A  PHE*     2.8    47.1    +      -       +      +
    167A  MET*     4.1     1.7    -      -       -      +
      3D  BGC      4.7     6.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 86 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  PHE      4.5     0.2    -      -       -      +
     75A  TYR*     3.2     4.7    -      -       -      +
     76A  LEU*     2.9    39.2    +      -       +      +
     85A  GLU*     1.3    77.6    -      -       -      +
     87A  ASP*     1.3    60.0    +      -       -      +
     88A  PHE*     5.8     0.6    -      -       -      -
    104A  ASN      3.8     3.8    -      -       -      -
    105A  VAL*     4.8     4.0    -      -       +      +
    132A  VAL*     4.0    31.7    -      -       +      +
    134A  TRP*     4.2    12.3    -      -       +      -
    139A  ILE*     3.6    39.0    -      -       +      -
    141A  PHE*     3.6    28.5    -      -       +      -
    162A  PRO*     4.8     2.7    -      -       +      -
    167A  MET*     3.5    27.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 87 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  TYR*     3.2    16.9    -      -       +      +
     85A  GLU*     2.3    40.7    -      -       -      +
     86A  ILE*     1.3    74.3    -      -       -      +
     88A  PHE*     1.3    61.1    +      -       -      +
     89A  GLU*     3.7    25.1    -      -       +      +
    103A  THR*     3.1    27.4    -      -       -      -
    104A  ASN*     3.0    26.0    +      -       -      +
    106A  PHE*     3.4    22.9    -      -       -      -
    141A  PHE*     3.4     6.2    -      -       -      -
      3D  BGC      3.7     3.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 88 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  THR      3.9     0.6    -      -       -      +
     73A  ALA*     3.3     4.7    -      -       -      +
     74A  PHE*     2.9    63.4    +      +       +      +
     75A  TYR*     5.0     0.3    -      -       -      +
     86A  ILE      5.8     0.2    -      -       -      -
     87A  ASP*     1.3    73.3    -      -       -      +
     89A  GLU*     1.3    63.2    +      -       -      +
     90A  PHE*     4.1    11.0    -      +       +      -
    101A  LEU*     3.7    27.6    -      -       +      -
    102A  GLN      3.5     3.1    -      -       -      -
    103A  THR*     4.3     4.0    -      -       +      -
    130A  TYR*     4.2    13.0    -      +       +      -
    131A  SER      3.4    33.7    -      -       -      -
    132A  VAL*     3.7    20.4    -      -       +      -
    141A  PHE*     4.0    16.6    -      +       +      -
    142A  LEU      3.8    16.2    -      -       -      -
    148A  ILE*     4.1    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 89 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  VAL*     4.0    14.1    -      -       +      +
     72A  THR      3.5     3.4    -      -       -      -
     73A  ALA*     4.1    16.4    -      -       +      +
     75A  TYR*     6.0     0.7    -      -       +      -
     87A  ASP*     3.7    19.4    -      -       +      +
     88A  PHE*     1.3    77.1    -      -       -      +
     90A  PHE*     1.3    62.2    +      -       -      +
     91A  LEU*     3.6    10.8    +      -       +      +
    101A  LEU*     4.0     1.3    -      -       -      +
    102A  GLN*     2.7    56.8    +      -       +      +
    104A  ASN*     4.6     1.0    -      -       -      +
    179A  TRP*     3.9    10.4    -      -       -      -
      3D  BGC      2.6    51.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 90 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  MET*     3.7    29.4    -      -       +      -
     62A  LEU*     3.5    33.7    -      -       +      -
     70A  THR*     3.6     2.1    +      -       -      +
     71A  VAL*     3.3     5.9    -      -       -      -
     72A  THR*     2.7    40.1    +      -       -      +
     74A  PHE*     5.1     0.9    -      -       +      -
     88A  PHE*     4.1    13.9    -      +       +      -
     89A  GLU*     1.3    70.8    -      -       -      +
     91A  LEU*     1.3    61.7    +      -       -      +
     92A  GLY      3.8     0.5    +      -       -      -
     99A  TYR*     3.7    12.3    -      +       +      -
    100A  ILE      3.4     6.3    -      -       -      -
    101A  LEU*     3.6    32.3    -      -       +      -
    119A  LEU*     4.6     7.2    -      -       +      -
    123A  PRO*     5.4     0.7    -      -       +      -
    130A  TYR*     3.5    52.9    -      +       -      -
----------------------------------------------------------
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Residues in contact with LEU 91 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  THR      3.7     3.6    -      -       -      -
     71A  VAL*     3.7    15.9    -      -       +      -
     89A  GLU*     3.8    17.9    -      -       +      +
     90A  PHE*     1.3    74.5    -      -       -      +
     92A  GLY*     1.3    65.9    +      -       -      +
     99A  TYR*     3.2     6.0    -      -       -      -
    100A  ILE*     2.8    57.2    +      -       +      +
    102A  GLN*     4.2     4.3    -      -       +      +
    116A  ARG*     4.0    20.2    -      -       -      +
    179A  TRP*     3.6    37.9    -      -       +      -
    180A  ALA*     3.5    27.1    -      -       -      +
      1C  NAG      3.4     6.6    -      -       +      +
----------------------------------------------------------
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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