Contacts of the strand formed by residues 190 - 198 (chain B) in PDB entry 5UHE


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 ASP 190 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25B  PRO*     3.8     1.4    -      -       -      +
     26B  LEU*     2.7    45.2    +      -       +      +
     27B  GLU      4.4     0.4    -      -       -      +
     28B  PRO*     4.5     0.2    -      -       -      +
     29B  GLY*     2.9    31.8    +      -       -      -
     31B  GLY*     3.2    33.3    +      -       -      +
     32B  TYR*     4.5     6.3    +      -       -      -
    178B  VAL*     4.0    13.0    -      -       +      +
    179B  ASP      3.6     5.7    -      -       -      +
    180B  ALA*     4.8     3.3    -      -       -      +
    181B  THR*     4.0     0.7    -      -       -      -
    188B  ASP      3.1    14.2    -      -       -      +
    189B  PHE*     1.3    72.9    -      -       -      +
    191B  LYS*     1.3    59.6    +      -       -      +
    192B  LEU      4.1     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 191 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  VAL*     3.9    17.9    -      -       +      -
     23B  ILE      3.8     3.6    -      -       -      -
     24B  GLU*     3.3    36.0    +      -       +      +
    178B  VAL*     3.6     3.8    -      -       -      -
    179B  ASP*     2.9    50.7    +      -       +      +
    180B  ALA      5.6     0.7    -      -       -      +
    181B  THR*     4.1    16.2    -      -       +      +
    189B  PHE      3.9     0.6    +      -       -      -
    190B  ASP*     1.3    73.8    -      -       -      +
    192B  LEU*     1.3    60.7    +      -       -      +
    193B  ILE*     3.6    33.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 192 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21B  PHE      3.6     1.4    -      -       -      +
     22B  VAL*     3.5     2.4    -      -       -      -
     23B  ILE*     2.8    58.5    +      -       +      +
     26B  LEU*     4.3    11.7    -      -       +      -
     31B  GLY*     4.0    14.1    -      -       -      +
     34B  LEU*     3.9    39.0    -      -       +      +
     35B  GLY*     4.4     2.2    -      -       -      +
     38B  LEU*     5.2     4.9    -      -       +      -
    176B  TYR*     4.3    15.3    -      -       +      -
    177B  LYS      3.3    18.4    -      -       -      +
    178B  VAL*     3.6    18.8    -      -       +      +
    190B  ASP      4.1     1.2    +      -       -      -
    191B  LYS*     1.3    71.0    -      -       -      +
    193B  ILE*     1.3    69.1    +      -       -      +
    194B  LEU*     4.2     6.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 193 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20B  GLN*     4.5    24.2    -      -       +      +
     21B  PHE      3.4     7.0    -      -       -      +
     22B  VAL*     4.4    14.6    -      -       +      -
    176B  TYR*     3.4     4.2    -      -       -      +
    177B  LYS*     2.9    45.8    +      -       +      +
    179B  ASP*     4.4    14.8    -      -       -      +
    191B  LYS*     3.6    39.0    -      -       +      +
    192B  LEU*     1.3    77.4    -      -       -      +
    194B  LEU*     1.3    66.3    +      -       -      +
    195B  ASP*     6.3     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 194 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  SER      3.9     0.7    -      -       -      +
     20B  GLN*     3.2     6.7    -      -       -      -
     21B  PHE*     2.8    53.4    +      -       +      +
     23B  ILE*     5.7     5.6    -      -       +      -
     35B  GLY      5.8     2.2    -      -       -      +
     38B  LEU*     4.3    25.6    -      -       +      -
     39B  ARG*     5.2     5.4    -      -       +      +
     42B  LEU*     4.5     5.4    -      -       +      -
    174B  VAL*     3.6    19.1    -      -       +      -
    175B  THR      3.3    17.5    -      -       -      +
    176B  TYR*     3.6    16.2    -      -       +      -
    192B  LEU*     5.1     9.6    -      -       +      +
    193B  ILE*     1.3    76.0    -      -       -      +
    195B  ASP*     1.3    58.8    +      -       -      +
    196B  VAL*     3.9    20.4    +      -       +      -
    208B  LEU*     4.3    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 195 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18B  ARG*     3.6    42.6    +      -       -      -
     19B  SER      3.9     4.1    -      -       -      +
     20B  GLN*     3.5    30.3    +      -       +      +
    173B  LYS      4.6     3.6    -      -       -      +
    174B  VAL*     3.2    10.6    -      -       -      +
    175B  THR*     2.7    55.0    +      -       -      +
    176B  TYR*     4.8     0.2    -      -       -      +
    193B  ILE*     6.3     0.4    -      -       +      -
    194B  LEU*     1.3    71.7    -      -       -      +
    196B  VAL*     1.3    66.6    +      -       -      +
    197B  GLU*     4.4     1.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 196 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18B  ARG*     3.2     4.2    -      -       -      +
     19B  SER      3.0    35.3    +      -       -      +
     21B  PHE*     4.2    16.8    -      -       +      -
     42B  LEU*     4.0    15.9    -      -       +      -
    171B  VAL*     4.2     5.8    -      -       +      -
    174B  VAL*     3.7    20.4    -      -       +      -
    194B  LEU*     3.9    26.0    -      -       +      -
    195B  ASP*     1.3    81.4    +      -       -      +
    197B  GLU*     1.3    61.1    +      -       -      +
    198B  THR*     3.9    24.0    -      -       +      -
    204B  PRO*     4.1    12.2    -      -       +      +
    207B  ALA*     5.0     0.2    -      -       +      -
    208B  LEU*     5.5     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 197 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  ASN*     4.3    14.9    +      -       +      +
     18B  ARG*     3.5    41.6    +      -       +      +
    171B  VAL*     3.6     4.3    -      -       -      +
    172B  LEU*     2.7    43.9    +      -       +      +
    173B  LYS*     3.0    29.2    +      -       +      +
    195B  ASP*     4.4     1.8    +      -       -      +
    196B  VAL*     1.3    74.9    -      -       -      +
    198B  THR*     1.3    64.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 198 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  ASN*     3.2    36.2    +      -       -      +
    170B  PRO      3.5    14.6    -      -       -      +
    171B  VAL*     4.0     4.9    -      -       +      -
    172B  LEU*     3.5     9.8    -      -       -      +
    196B  VAL*     3.9     9.8    +      -       +      -
    197B  GLU*     1.3    77.8    -      -       -      +
    199B  LYS*     1.3    68.9    +      -       -      +
    202B  ILE*     2.8    24.4    +      -       +      +
    204B  PRO*     3.3    19.5    -      -       +      +
    207B  ALA*     3.7    29.6    -      -       +      -
----------------------------------------------------------
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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