Contacts of the strand formed by residues 171 - 180 (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 VAL 171 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42B  LEU*     3.3    35.7    -      -       +      +
     43B  LEU*     4.0    13.6    -      -       +      +
     46B  ILE*     5.1     4.0    -      -       +      -
    167B  ILE*     5.9     0.2    -      -       -      +
    169B  SER*     3.2    18.1    +      -       -      +
    170B  PRO*     1.3    89.4    -      -       +      +
    172B  LEU*     1.3    66.2    +      -       -      +
    173B  LYS      4.5     0.2    -      -       -      +
    174B  VAL*     3.6    28.5    -      -       +      -
    196B  VAL*     4.2     6.7    -      -       +      -
    197B  GLU      3.6    11.4    -      -       -      +
    198B  THR*     4.0    12.8    -      -       +      +
    207B  ALA*     4.1    14.8    -      -       +      -
    620D  MET*     4.3     5.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 172 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  ASN*     4.9     5.8    -      -       -      +
     43B  LEU*     4.3     3.1    -      -       -      +
    167B  ILE*     5.4     7.0    -      -       +      -
    169B  SER      5.2     0.2    -      -       -      +
    171B  VAL*     1.3    75.7    -      -       -      +
    173B  LYS*     1.3    61.1    +      -       +      +
    197B  GLU*     2.7    28.8    +      -       +      +
    198B  THR      3.5    23.8    -      -       -      +
    199B  LYS*     3.6    42.6    -      -       +      +
    616D  ALA*     3.8    24.2    -      -       +      +
    620D  MET*     3.7    21.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 173 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  ARG*     3.0    31.9    -      -       -      +
     43B  LEU*     4.4     5.1    -      -       +      +
    171B  VAL*     3.8     0.6    -      -       -      +
    172B  LEU*     1.3    84.4    -      -       +      +
    174B  VAL*     1.3    81.2    +      -       -      +
    175B  THR*     3.6    20.8    -      -       +      +
    195B  ASP*     4.0     3.6    -      -       -      +
    196B  VAL*     3.9     0.7    -      -       -      -
    197B  GLU*     3.0    38.8    +      -       +      +
    616D  ALA*     4.2    13.0    -      -       +      -
    619D  ILE*     3.3    42.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 174 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  ARG*     2.8    55.0    +      -       +      -
     42B  LEU*     4.4     8.7    -      -       +      -
     43B  LEU*     4.2    11.0    -      -       +      +
    171B  VAL*     3.6    25.8    -      -       +      -
    173B  LYS*     1.3    91.4    +      -       -      +
    175B  THR*     1.3    63.2    +      -       -      +
    194B  LEU*     3.6    22.9    -      -       +      -
    195B  ASP      3.2    11.9    -      -       -      +
    196B  VAL*     3.7    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 175 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39B  ARG*     5.0     0.2    -      -       -      +
    173B  LYS*     3.6    23.3    -      -       +      +
    174B  VAL*     1.3    77.9    -      -       -      +
    176B  TYR*     1.3    62.4    +      -       -      +
    194B  LEU*     3.3     6.0    -      -       -      +
    195B  ASP*     2.7    56.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 176 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32B  TYR*     5.2    12.1    -      +       -      -
     35B  GLY*     3.7    19.7    -      -       -      +
     36B  ASN*     3.3    43.7    +      -       -      +
     39B  ARG*     4.1    28.5    -      -       +      -
    175B  THR*     1.3    81.4    -      -       -      +
    177B  LYS*     1.3    61.4    +      -       -      +
    178B  VAL*     4.5    10.1    -      -       +      -
    192B  LEU*     4.3    11.9    -      -       +      -
    193B  ILE      3.4     8.5    -      -       -      +
    194B  LEU*     3.6    17.5    -      -       +      -
   1015C  SER*     4.4    10.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 177 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176B  TYR*     1.3    75.4    -      -       -      +
    178B  VAL*     1.3    68.7    +      -       -      +
    179B  ASP*     3.6    29.7    +      -       -      +
    191B  LYS      4.0     0.3    -      -       -      +
    192B  LEU*     3.3     4.0    -      -       -      +
    193B  ILE*     2.9    44.0    +      -       +      +
    437D  LYS*     5.7     7.7    -      -       -      +
    718D  ASP*     5.5     7.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 178 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31B  GLY*     3.7    32.8    -      -       -      +
     32B  TYR*     3.5    50.8    +      -       +      +
    176B  TYR*     4.5     9.4    -      -       +      -
    177B  LYS*     1.3    81.1    -      -       -      +
    179B  ASP*     1.3    71.9    +      -       -      +
    190B  ASP*     4.0    10.1    -      -       +      -
    191B  LYS      3.6     6.5    -      -       -      +
    192B  LEU*     3.6    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 179 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177B  LYS*     3.6    31.9    +      -       -      +
    178B  VAL*     1.3    80.3    -      -       -      +
    180B  ALA*     1.3    64.0    +      -       -      +
    190B  ASP*     3.6     6.6    -      -       -      +
    191B  LYS*     2.9    47.0    +      -       +      +
    193B  ILE*     4.4    17.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 180 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179B  ASP*     1.3    80.4    -      -       -      +
    181B  THR*     1.3    61.3    +      -       -      +
    182B  ARG*     4.2     4.5    +      -       -      +
    187B  THR      3.8    17.7    -      -       -      +
    188B  ASP      4.6     5.2    -      -       -      +
    189B  PHE      3.2     9.4    -      -       -      +
    190B  ASP*     4.8     3.1    -      -       -      +
    191B  LYS*     4.7     3.3    -      -       -      +
----------------------------------------------------------
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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