Contacts of the strand formed by residues 551 - 558 (chain C) in PDB entry 1UEX


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 551 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    509C  CYS*     3.8    24.5    -      -       -      +
    511C  ARG      3.3    20.6    -      -       -      +
    513C  LEU*     3.2    28.3    -      -       +      +
    515C  LEU*     5.0     0.9    -      -       +      -
    544C  LEU*     3.7    32.5    -      -       +      -
    545C  ARG      3.2    18.8    +      -       -      +
    546C  ILE*     3.0    26.2    -      -       -      +
    547C  SER      3.1     6.4    +      -       -      -
    550C  TRP*     1.3    78.4    -      -       +      +
    552C  ARG*     1.3    66.9    +      -       -      +
    553C  VAL*     4.2     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 552 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    513C  LEU      2.9     6.6    +      -       -      +
    514C  ASP*     2.6    41.6    +      -       -      +
    515C  LEU      3.3    23.4    +      -       -      -
    546C  ILE*     4.9     1.6    -      -       -      -
    547C  SER      3.7    14.4    -      -       -      +
    548C  GLN*     2.9    44.8    +      -       -      +
    550C  TRP      4.0     0.2    -      -       -      -
    551C  VAL*     1.3    76.2    -      -       -      +
    553C  VAL*     1.3    62.5    +      -       -      +
    568C  LEU*     3.0    34.8    +      -       +      +
    569C  LYS*     3.7    25.5    -      -       -      +
    606C  PHE*     5.5     0.4    -      -       -      -
    610C  ASP*     3.8    14.8    +      -       -      -
    611C  ARG*     3.7    30.8    -      -       -      +
    616C  ARG*     4.5     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 553 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    515C  LEU*     3.6     5.6    -      -       +      +
    517C  PHE*     3.7    28.5    -      -       +      -
    541C  MET*     3.8    22.2    -      -       +      -
    544C  LEU*     4.0    18.6    -      -       +      -
    546C  ILE*     3.9    38.4    -      -       +      +
    551C  VAL*     4.0     2.6    +      -       +      -
    552C  ARG*     1.3    81.6    -      -       -      +
    554C  ALA*     1.3    68.0    +      -       -      +
    555C  VAL*     4.4     2.5    -      -       +      -
    566C  ILE*     3.4    10.0    -      -       +      +
    567C  GLY      3.3    22.0    -      -       -      +
    568C  LEU*     3.7     3.4    +      -       -      +
    577C  LEU*     5.1     4.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 554 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    515C  LEU      3.0     7.9    +      -       -      +
    516C  VAL*     3.9    26.5    -      -       +      -
    517C  PHE*     2.6    38.3    +      -       -      -
    553C  VAL*     1.3    77.0    -      -       -      +
    555C  VAL*     1.3    59.6    +      -       -      +
    556C  VAL*     5.4     0.4    -      -       +      -
    566C  ILE*     3.3    14.1    -      -       -      +
    567C  GLY*     4.3     0.9    -      -       -      -
    568C  LEU*     4.0    16.2    -      -       +      +
    605C  ILE*     4.9     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 555 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    517C  PHE*     3.3     9.9    -      -       +      -
    519C  LEU*     3.9    18.8    -      -       +      -
    537C  VAL*     3.9    25.6    -      -       +      -
    541C  MET*     4.8     0.7    -      -       -      -
    553C  VAL*     4.4     5.4    -      -       +      -
    554C  ALA*     1.3    78.7    -      -       -      +
    556C  VAL*     1.3    72.1    +      -       -      +
    557C  GLU      5.2     0.4    -      -       -      +
    565C  TYR*     3.0    30.3    +      -       +      +
    566C  ILE*     3.1    38.5    +      -       +      +
    581C  ALA*     4.7     3.6    -      -       +      -
    584C  VAL*     4.4    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 556 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    516C  VAL*     4.7     0.2    -      -       +      -
    517C  PHE      2.6     9.5    +      -       -      +
    518C  LEU*     3.1    15.5    -      -       +      +
    519C  LEU*     2.6    36.2    +      -       -      +
    554C  ALA*     5.2     0.4    -      -       +      -
    555C  VAL*     1.3    86.7    -      -       -      +
    557C  GLU*     1.3    58.6    +      -       -      +
    558C  TYR      3.8     0.5    +      -       -      -
    562C  SER*     3.8    28.7    -      -       -      -
    563C  HIS      3.6    12.3    -      -       -      +
    564C  ALA*     3.9    17.9    -      -       +      +
    566C  ILE      4.9     2.0    -      -       -      +
    597C  VAL*     4.3    10.8    -      -       +      -
    600C  TYR*     4.3     6.5    -      -       +      -
    605C  ILE*     4.1    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 557 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    519C  LEU*     3.4    17.7    -      -       +      +
    521C  GLY*     4.3     5.3    -      -       -      -
    530C  PHE*     4.1    18.6    -      -       +      -
    555C  VAL*     6.1     0.4    -      -       +      -
    556C  VAL*     1.3    72.8    -      -       -      +
    558C  TYR*     1.3    60.1    +      -       -      +
    559C  HIS*     2.6    37.6    +      -       -      -
    563C  HIS*     3.1    31.7    +      -       -      +
    565C  TYR*     3.9    32.5    +      -       +      -
    584C  VAL*     4.3     7.4    -      -       +      -
    585C  LYS*     4.0     8.1    -      -       -      +
    587C  ALA*     3.6    20.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 558 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    518C  LEU*     3.7    18.6    -      -       +      -
    519C  LEU      3.2    15.4    +      -       -      -
    520C  ASP*     3.4    22.7    +      -       -      +
    521C  GLY*     2.8    29.8    +      -       -      -
    557C  GLU*     1.3    72.3    -      -       -      +
    559C  HIS*     1.3    64.3    +      -       -      +
    561C  GLY      3.4     9.2    -      -       -      +
    562C  SER*     4.2     4.5    -      -       -      +
    592C  ALA*     3.5    31.5    -      -       +      +
    593C  SER      3.6    17.7    -      -       -      +
    594C  THR*     3.8    14.6    -      -       +      +
    596C  GLU*     6.2     0.2    -      -       +      -
    597C  VAL*     3.5    35.4    -      -       +      +
    620C  LEU*     3.8    10.2    -      -       +      +
    621C  LEU      3.3    14.7    +      -       -      -
    622C  MET*     3.4    21.7    -      -       -      +
----------------------------------------------------------
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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