Contacts of the strand formed by residues 543 - 549 (chain C) in PDB entry 3U1K


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 MET 543 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    511C  ILE*     3.6    15.9    -      -       +      +
    512C  GLY*     3.6    19.6    -      -       -      +
    513C  LEU*     3.8    16.7    +      -       +      -
    529C  LEU*     3.7    30.5    -      -       +      -
    533C  ILE*     3.7     7.4    -      -       -      +
    537C  GLU      5.2     0.9    -      -       -      +
    538C  ASP*     4.1     8.8    -      -       -      +
    541C  GLY      3.7     1.2    -      -       -      -
    542C  ASP*     1.3    82.4    +      -       -      +
    544C  ASP*     1.3    61.5    +      -       -      +
    545C  PHE*     3.5    32.5    -      -       +      -
    560C  ASP      3.1    13.9    -      -       -      +
    561C  ILE*     4.0    11.9    -      -       +      -
    562C  LYS*     4.0     4.6    -      -       -      +
    566C  ILE*     4.0    25.6    -      -       +      -
    570C  ILE*     5.2     1.1    -      -       +      -
    574C  ALA*     4.0     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 544 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1C  CIT      2.5    31.4    -      -       -      +
    510C  ALA*     3.3    25.1    -      -       -      +
    511C  ILE      4.1     1.1    -      -       -      -
    533C  ILE*     3.8     7.0    -      -       -      +
    538C  ASP*     3.3    22.8    -      -       -      +
    543C  MET*     1.3    71.9    -      -       -      +
    545C  PHE*     1.3    58.2    +      -       -      +
    546C  LYS*     3.4     8.5    +      -       -      +
    558C  GLN      3.3     4.0    -      -       -      +
    560C  ASP*     2.8    41.0    +      -       +      +
    562C  LYS*     4.9     0.9    -      -       +      +
    670C  CIT      3.4    23.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 545 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229C  LEU*     4.4     3.4    -      -       +      -
    509C  VAL      3.6     1.7    -      -       -      +
    510C  ALA*     3.2     1.7    -      -       -      -
    511C  ILE*     2.8    49.2    +      -       +      +
    543C  MET*     3.5    29.6    -      -       +      -
    544C  ASP*     1.3    71.1    +      -       -      +
    546C  LYS*     1.3    60.6    +      -       -      +
    547C  ILE*     3.7    14.8    +      -       +      +
    557C  LEU*     3.6    25.4    -      -       +      -
    558C  GLN      3.9     2.9    -      -       -      -
    559C  ALA*     3.5    28.0    -      -       +      +
    561C  ILE*     5.3     0.9    -      -       +      -
    571C  VAL*     4.1    27.4    -      -       +      -
    574C  ALA*     4.1    17.0    -      -       +      -
    575C  ILE*     3.6    33.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 546 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1C  CIT      2.8    26.3    +      -       -      -
    450C  HIS*     4.0     1.2    +      -       -      -
    453C  LEU*     4.2     8.1    -      -       +      +
    482C  SER*     5.8     0.9    -      -       -      -
    484C  SER*     3.6     6.7    -      -       -      +
    485C  MET*     4.0    22.0    -      -       +      +
    509C  VAL      3.6     4.3    -      -       -      -
    510C  ALA*     3.9     9.4    -      -       +      -
    544C  ASP*     3.6    22.2    -      -       -      +
    545C  PHE*     1.3    69.6    -      -       -      +
    547C  ILE*     1.3    61.7    +      -       -      +
    556C  ALA      4.1     0.3    -      -       -      +
    557C  LEU*     3.4     3.4    -      -       -      +
    558C  GLN*     2.8    67.5    +      -       -      +
    560C  ASP*     3.0    21.3    -      -       -      -
    670C  CIT      2.7    37.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 547 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241C  PHE*     4.8     1.3    -      -       +      -
    485C  MET*     3.8     3.1    -      -       -      -
    508C  GLY*     3.4     0.5    -      -       -      -
    509C  VAL*     3.0    35.8    +      -       -      +
    545C  PHE*     4.4     9.6    -      -       +      +
    546C  LYS*     1.3    76.3    -      -       -      +
    548C  ALA*     1.3    65.4    +      -       -      +
    554C  ILE*     3.9    35.4    -      -       +      -
    556C  ALA      3.3    12.3    -      -       -      +
    557C  LEU*     3.9    22.4    -      -       +      -
    575C  ILE*     4.3    23.3    -      -       +      +
    578C  ALA*     3.3    33.0    -      -       +      -
    582C  LYS*     5.7     2.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 548 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    457C  ALA*     3.8    28.3    -      -       +      -
    485C  MET*     4.2     9.4    -      -       +      +
    488C  ALA*     4.8     2.0    -      -       +      -
    506C  VAL*     4.7     2.7    -      -       +      -
    507C  ALA      3.3    14.8    -      -       -      +
    508C  GLY*     3.7     9.4    -      -       -      -
    547C  ILE*     1.3    75.6    -      -       -      +
    549C  GLY*     1.3    59.4    +      -       -      +
    554C  ILE*     3.7     7.7    -      -       -      +
    555C  THR*     2.9    19.9    +      -       -      +
    556C  ALA*     2.9    15.9    +      -       +      +
    582C  LYS*     4.5     4.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 549 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    506C  VAL*     3.3     7.1    -      -       -      +
    507C  ALA      3.0    31.0    +      -       -      +
    548C  ALA*     1.3    77.6    -      -       -      +
    550C  THR*     1.3    64.3    +      -       -      -
    553C  GLY      3.1    13.5    -      -       -      -
    555C  THR*     3.2    16.8    +      -       -      -
    582C  LYS*     3.6     8.4    -      -       -      +
----------------------------------------------------------
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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