Contacts of the strand formed by residues 537 - 541 (chain A) in PDB entry 5IVI


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 LYS 537 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    443A  LEU*     3.6    19.1    +      -       -      +
    525A  SER      6.1     0.7    -      -       -      +
    526A  TRP*     5.4     0.7    +      -       -      -
    527A  ASP*     5.1    17.2    -      -       +      +
    529A  ILE*     5.0     7.6    -      -       -      +
    533A  ASP*     5.6     4.6    +      -       -      +
    535A  VAL*     3.6     7.7    +      -       -      +
    536A  TYR*     1.3    74.0    -      -       -      +
    538A  CYS*     1.3    63.0    +      -       -      +
    547A  MET*     4.2    20.0    -      -       +      +
    548A  ILE      3.5     8.3    -      -       -      +
    549A  ASP*     2.9    28.1    +      -       -      +
    550A  VAL*     4.5     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 538 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    422A  TRP*     6.3     0.2    -      -       +      -
    443A  LEU*     3.3    21.1    -      -       +      +
    444A  TYR      4.3     6.7    -      -       -      +
    445A  ARG*     3.8    27.1    -      -       +      -
    537A  LYS*     1.3    76.1    -      -       -      +
    539A  LEU*     1.3    60.3    +      -       -      +
    540A  ASN      3.4     2.0    +      -       -      -
    547A  MET*     3.4    10.3    -      -       -      -
    548A  ILE*     2.9    53.6    +      -       -      -
    550A  VAL*     3.8    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 539 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    443A  LEU      3.0     9.7    +      -       -      -
    444A  TYR*     3.4     3.6    -      -       -      +
    445A  ARG      2.8    25.0    +      -       -      +
    503A  ILE*     5.2     4.3    -      -       +      -
    521A  MET*     3.7    11.7    -      -       +      -
    524A  VAL*     4.0    12.8    -      -       +      -
    526A  TRP*     3.4    50.0    -      -       +      +
    538A  CYS*     1.3    70.3    -      -       -      +
    540A  ASN*     1.3    58.8    +      -       -      +
    541A  ILE*     3.5    23.0    +      -       +      +
    545A  LEU*     4.0    17.7    -      -       +      -
    546A  LYS      3.7    30.3    -      -       -      +
    547A  MET*     3.7    16.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 540 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    445A  ARG*     2.9    44.2    +      -       +      +
    447A  ASP*     3.0    29.2    +      -       -      +
    538A  CYS      3.4     2.4    +      -       -      -
    539A  LEU*     1.3    71.2    -      -       -      +
    541A  ILE*     1.3    60.5    +      -       -      +
    542A  SER*     4.1    10.3    +      -       -      -
    544A  GLU      3.5     6.9    -      -       -      +
    545A  LEU*     3.6     2.1    -      -       -      -
    546A  LYS*     2.9    38.6    +      -       +      +
    548A  ILE*     3.7    25.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 541 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    444A  TYR*     4.1    26.9    -      -       +      -
    445A  ARG      2.8    12.2    +      -       -      +
    446A  PHE*     4.0    12.8    -      -       +      -
    447A  ASP*     2.7    31.2    +      -       -      -
    448A  PHE*     3.2     3.0    +      -       +      +
    496A  THR*     5.0     7.0    -      -       +      -
    499A  ARG*     5.6     3.6    -      -       +      -
    500A  MET*     3.8    43.3    -      -       +      -
    503A  ILE*     5.8     4.3    -      -       +      -
    504A  TRP*     5.1     4.3    -      -       +      -
    526A  TRP*     5.6     0.9    -      -       +      -
    539A  LEU*     3.8    24.7    -      -       +      +
    540A  ASN*     1.3    74.5    -      -       -      +
    542A  SER*     1.3    62.0    +      -       -      +
    545A  LEU*     3.9    20.6    -      -       +      -
----------------------------------------------------------
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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