Contacts of the strand formed by residues 548 - 554 (chain A) in PDB entry 3U0Z


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 CYS 548 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    483A  GLU      3.7     0.2    -      -       -      +
    484A  VAL*     3.5     8.0    -      -       -      +
    485A  PHE*     3.0    43.2    +      -       +      +
    491A  ILE*     5.1     2.2    -      -       +      -
    504A  ILE*     5.7     1.1    -      -       -      -
    506A  HIS      3.6     1.6    -      -       -      -
    507A  GLY*     4.1     2.9    -      -       -      -
    508A  VAL      3.3    36.8    -      -       -      -
    509A  ALA*     4.6     6.3    -      -       -      -
    544A  ALA*     4.0    10.5    -      -       +      -
    546A  THR      3.8    10.1    -      -       -      +
    547A  TYR*     1.3    74.7    -      -       -      +
    549A  ARG*     1.3    65.1    +      -       -      +
    550A  LEU*     3.7    22.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 549 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    426A  HIS      5.2     6.7    +      -       -      -
    427A  ARG      5.8     0.8    +      -       -      -
    429A  GLN*     4.8    14.8    +      -       -      +
    482A  PHE*     3.4    31.5    -      -       +      -
    483A  GLU      3.9     3.4    -      -       -      -
    484A  VAL*     4.5    12.6    -      -       +      +
    505A  GLN*     2.4    78.8    +      -       -      +
    506A  HIS*     2.7    36.1    +      -       +      +
    547A  TYR*     5.5     4.0    -      -       +      +
    548A  CYS*     1.3    75.8    -      -       -      +
    550A  LEU*     1.3    63.4    +      -       -      +
    551A  TYR*     5.8     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 550 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    482A  PHE*     3.5     8.1    -      -       -      -
    483A  GLU*     2.8    39.6    +      -       +      +
    485A  PHE*     3.5    32.1    -      -       +      -
    491A  ILE*     4.2     9.9    -      -       +      -
    502A  TYR*     3.8    21.8    -      -       +      -
    503A  PHE      3.4     4.7    -      -       -      +
    504A  ILE*     3.6    35.7    -      -       +      +
    505A  GLN      4.5     0.2    -      -       -      +
    527A  PHE*     4.1    17.0    -      -       +      -
    548A  CYS*     4.2    17.0    -      -       +      +
    549A  ARG*     1.3    82.7    -      -       -      +
    551A  TYR*     1.3    65.7    +      -       -      +
    552A  SER      4.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 551 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    455A  CYS*     4.9    18.7    -      -       -      -
    458A  LEU*     5.3     9.4    -      -       +      -
    480A  LEU*     3.8    38.4    -      -       +      -
    481A  ARG      3.5     3.6    -      -       -      -
    482A  PHE*     3.6    50.2    -      +       +      +
    502A  TYR*     3.3     1.7    -      -       -      -
    503A  PHE*     2.5    51.3    +      -       +      +
    505A  GLN*     4.3    34.3    +      -       +      -
    549A  ARG*     5.8     0.5    +      -       -      -
    550A  LEU*     1.3    76.0    -      -       -      +
    552A  SER*     1.3    59.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 552 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    479A  LYS      3.9     1.2    -      -       -      +
    480A  LEU*     3.4     8.2    -      -       -      -
    481A  ARG*     2.9    42.9    +      -       -      +
    483A  GLU*     2.7    29.6    +      -       -      -
    500A  LYS*     4.4    10.5    -      -       -      +
    501A  MET      3.1    10.3    -      -       -      -
    502A  TYR*     3.6    17.0    -      -       -      -
    550A  LEU      4.2     0.2    -      -       -      -
    551A  TYR*     1.3    75.4    -      -       -      +
    553A  LEU*     1.3    63.0    +      -       -      +
    554A  SER      4.2     0.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 553 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    476A  MET*     3.9    37.2    -      -       +      +
    479A  LYS*     3.8    26.5    -      -       +      +
    480A  LEU*     4.2    11.4    -      -       +      -
    500A  LYS*     4.4     1.6    -      -       -      -
    501A  MET*     2.8    43.4    +      -       +      +
    503A  PHE*     4.4     7.4    -      -       +      -
    532A  LEU*     4.6     1.6    -      -       -      +
    552A  SER*     1.3    76.8    -      -       -      +
    554A  SER*     1.3    61.8    +      -       -      +
    557A  ASN*     3.6    27.1    -      -       +      +
    558A  PHE*     3.9    32.8    -      -       +      +
    561A  VAL*     5.8     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 554 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    479A  LYS      5.2     0.8    +      -       -      -
    499A  LYS      3.5    10.1    -      -       -      -
    500A  LYS*     4.4     6.3    -      -       -      +
    552A  SER      4.2     0.4    +      -       -      -
    553A  LEU*     1.3    76.2    -      -       -      +
    555A  VAL*     1.3    67.7    +      -       -      +
    556A  ASP*     3.9     5.2    +      -       -      +
    557A  ASN*     3.0    29.3    +      -       -      +
    558A  PHE*     2.9    19.1    +      -       -      +
----------------------------------------------------------
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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