Contacts of the strand formed by residues 509 - 514 (chain C) in PDB entry 5U03


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 509 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    402C  MET*     4.3     4.5    -      -       +      +
    458C  GLN*     3.5    19.7    -      -       -      +
    483C  GLU*     3.6    12.5    +      -       -      +
    484C  VAL*     4.0    27.9    -      -       +      +
    489C  LYS*     3.3    36.1    -      -       +      -
    499C  PHE*     3.6    30.3    -      -       +      -
    501C  GLY      3.5     1.3    -      -       -      +
    502C  GLN*     3.6    20.0    -      -       +      +
    506C  GLY      4.0     8.1    -      -       -      +
    507C  GLU      3.3    24.9    +      -       -      +
    508C  ARG*     1.4    84.6    -      -       -      +
    510C  GLU*     1.3    62.6    +      -       -      +
    524C  GLN*     3.4    18.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 510 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    402C  MET*     3.7     5.1    -      -       -      +
    449C  ARG*     4.0     6.9    +      -       -      -
    455C  THR*     3.6    35.7    -      -       +      +
    478C  HIS*     3.3    26.3    +      -       +      -
    480C  HIS*     2.9    23.2    +      -       -      -
    501C  GLY      2.8     9.6    +      -       -      +
    502C  GLN      4.4     9.2    -      -       -      -
    503C  ASP*     4.4     4.3    -      -       -      +
    508C  ARG*     4.5     7.4    -      -       -      +
    509C  MET*     1.3    80.0    -      -       -      +
    511C  ILE*     1.3    61.7    +      -       -      +
    523C  VAL*     3.2     8.1    -      -       -      +
    524C  GLN*     3.1    28.6    +      -       -      +
    525C  TYR*     3.4    30.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 511 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    402C  MET*     4.2     2.0    -      -       -      -
    455C  THR*     4.6     1.1    -      -       +      -
    457C  PHE*     4.2    23.6    -      -       +      -
    464C  MET*     4.6    14.6    -      -       +      -
    468C  TYR*     5.2     0.4    -      -       +      -
    474C  LEU*     4.4    13.2    -      -       +      -
    499C  PHE*     3.5     7.3    -      -       -      +
    500C  VAL*     2.8    36.5    +      -       +      -
    501C  GLY*     3.1    26.4    +      -       -      +
    510C  GLU*     1.3    86.5    -      -       +      +
    512C  VAL*     1.4    70.3    +      -       -      +
    513C  GLU*     4.3    11.4    -      -       +      +
    521C  VAL*     5.7     0.7    -      -       +      -
    522C  GLY      3.5     6.5    -      -       -      +
    523C  VAL*     4.3     4.5    -      -       +      -
    525C  TYR*     3.6    32.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 512 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    402C  MET*     3.8    24.2    -      -       +      +
    405C  ALA*     6.1     3.1    -      -       +      -
    406C  VAL*     5.1     5.2    -      -       +      -
    497C  LEU*     3.5    37.0    -      -       +      -
    498C  LYS      3.2    20.2    -      -       -      +
    499C  PHE*     4.0    13.0    -      -       +      -
    500C  VAL      4.4     0.2    -      -       -      +
    511C  ILE*     1.4    76.2    -      -       -      +
    513C  GLU*     1.4    62.7    +      -       -      +
    514C  LEU      4.2     0.2    -      -       -      -
    520C  PHE*     5.8     4.3    -      -       +      +
    521C  VAL*     3.3     8.5    -      -       -      +
    522C  GLY*     3.0    40.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 513 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461C  ASN      5.0     0.9    -      -       -      +
    462C  SER*     2.6    30.9    +      -       -      -
    463C  VAL*     3.2    27.6    +      -       -      +
    464C  MET*     3.0    23.5    +      -       +      +
    498C  LYS*     2.8    32.9    +      -       -      +
    500C  VAL*     3.8    19.1    -      -       +      +
    511C  ILE*     4.3     6.7    -      -       +      +
    512C  VAL*     1.4    79.9    -      -       -      +
    514C  LEU*     1.3    65.2    +      -       -      +
    515C  GLU*     3.5    12.6    +      -       -      +
    520C  PHE      3.9     3.8    -      -       -      -
    521C  VAL*     3.8    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 514 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    389C  ARG*     3.6    35.2    -      -       +      +
    392C  LYS*     5.5     2.2    -      -       -      +
    409C  PHE*     3.8    21.8    -      -       +      -
    496C  GLY      3.5    17.9    -      -       -      +
    497C  LEU*     3.7    22.9    -      -       +      +
    512C  VAL*     4.2     0.4    -      -       -      +
    513C  GLU*     1.3    73.1    -      -       -      +
    515C  GLU*     1.3    70.5    +      -       -      +
    517C  HIS*     4.0    26.0    +      -       +      +
    520C  PHE*     3.0    45.5    +      -       +      +
----------------------------------------------------------
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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