Contacts of the strand formed by residues 517 - 524 (chain A) in PDB entry 4R8A


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 ARG 517 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    481A  CYS*     4.3     8.5    +      -       -      -
    483A  PRO*     3.3    32.5    -      -       -      +
    486A  HIS*     4.5     5.1    -      -       -      -
    511A  PHE*     3.7     0.9    -      -       -      -
    512A  TRP*     2.8    35.4    +      -       +      -
    515A  GLN*     3.3    12.3    +      -       +      +
    516A  ARG*     1.3    82.6    +      -       -      +
    518A  TYR*     1.3    90.0    +      -       -      +
    519A  ARG*     3.6    35.7    -      -       -      +
    545A  GLU      6.0     0.4    +      -       -      -
    547A  PRO*     4.4    15.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 518 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    481A  CYS*     4.3     4.6    -      -       +      +
    482A  LEU*     3.8    18.6    -      -       +      -
    483A  PRO*     3.5    17.7    -      -       +      -
    486A  HIS*     2.8    24.8    +      -       -      -
    490A  TRP*     3.4    18.3    -      +       -      -
    509A  ILE*     4.5     4.5    -      -       +      -
    510A  GLN      3.4     5.4    -      -       -      +
    511A  PHE*     3.8    26.7    -      -       +      -
    512A  TRP*     4.5     0.2    -      -       -      -
    517A  ARG*     1.3   107.8    +      -       -      +
    519A  ARG*     1.3    78.9    +      -       -      +
    520A  MET*     3.5    27.8    -      -       +      -
    546A  MET*     3.7     4.8    -      -       +      +
    547A  PRO*     3.2    42.1    -      -       +      +
    548A  VAL*     5.8     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 519 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    510A  GLN*     2.9    51.3    +      -       -      +
    512A  TRP*     3.2    46.9    -      -       -      +
    515A  GLN*     3.6    23.0    -      -       -      +
    517A  ARG*     3.6    24.9    -      -       -      +
    518A  TYR*     1.3    78.5    -      -       -      +
    520A  MET*     1.3    61.5    +      -       -      +
    521A  VAL*     4.3     1.5    +      -       +      -
    547A  PRO*     3.5    21.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 520 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    390A  ILE*     4.4     7.9    -      -       +      -
    482A  LEU*     4.9     1.8    -      -       +      -
    490A  TRP*     3.7    26.2    -      -       +      -
    505A  LEU*     4.8     7.6    -      -       -      -
    506A  PRO*     3.5    28.6    -      -       +      +
    508A  LEU      3.4     3.6    -      -       -      +
    509A  ILE*     3.4    37.5    -      -       +      -
    518A  TYR*     3.5    26.0    -      -       +      -
    519A  ARG*     1.3    74.3    -      -       -      +
    521A  VAL*     1.3    64.3    +      -       -      +
    538A  LEU*     5.7     0.2    -      -       -      +
    541A  CYS*     5.2     3.6    -      -       -      -
    546A  MET*     6.4     0.2    -      -       +      -
    547A  PRO      2.9    12.5    +      -       -      +
    548A  VAL*     3.2    25.7    -      -       +      +
    549A  ALA      3.1    23.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 521 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    354A  LEU*     5.4     5.6    -      -       +      -
    371A  VAL*     5.6     0.2    -      -       +      -
    375A  LEU*     4.7    11.9    -      -       +      -
    506A  PRO*     3.6     4.7    -      -       -      +
    507A  ASP*     3.4     1.0    +      -       -      +
    508A  LEU*     2.7    54.4    +      -       +      +
    510A  GLN*     4.3    21.3    -      -       +      +
    519A  ARG*     4.3     2.0    +      -       +      +
    520A  MET*     1.3    81.4    -      -       -      +
    522A  GLU*     1.3    62.4    +      -       -      +
    523A  VAL*     4.2     5.8    -      -       +      -
    549A  ALA*     3.2    23.6    -      -       +      +
    550A  VAL      4.5     0.2    -      -       -      -
    551A  CYS*     3.5    32.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 522 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    505A  LEU      4.0     1.0    -      -       -      +
    506A  PRO*     3.3    21.1    -      -       +      +
    507A  ASP*     2.8    52.3    +      -       -      +
    521A  VAL*     1.3    74.6    -      -       -      +
    523A  VAL*     1.3    63.5    +      -       -      +
    524A  LYS*     3.1    28.9    +      -       -      -
    530A  LEU*     4.0    15.0    -      -       +      -
    534A  GLN*     3.8    18.4    +      -       +      +
    538A  LEU*     5.3     7.4    -      -       +      -
    549A  ALA      3.2     6.5    +      -       -      +
    550A  VAL*     3.4    10.3    -      -       +      +
    551A  CYS      2.9    19.4    +      -       -      -
      5B    A      2.9    15.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 523 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    367A  VAL*     4.0     8.1    -      -       +      -
    368A  GLU*     3.5    44.0    -      -       +      +
    371A  VAL*     3.7    38.6    -      -       +      -
    507A  ASP*     3.0    17.5    +      -       -      +
    508A  LEU*     3.8    21.8    -      -       +      -
    521A  VAL*     4.2     4.0    -      -       +      -
    522A  GLU*     1.3    85.8    -      -       -      +
    524A  LYS*     1.3    66.6    +      -       -      +
    551A  CYS*     3.2    18.2    -      -       +      +
    553A  VAL*     5.3     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 524 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    367A  VAL*     4.4     3.6    -      -       -      -
    368A  GLU*     5.2     1.1    -      -       -      -
    522A  GLU*     3.1    15.2    +      -       -      -
    523A  VAL*     1.3    79.9    -      -       -      +
    525A  GLY*     1.3    64.0    +      -       -      +
    528A  ASP*     2.9    45.1    +      -       -      +
    529A  ARG      3.2    25.4    +      -       -      +
    530A  LEU*     3.6    18.2    -      -       -      +
    531A  GLN*     4.4     0.6    -      -       -      +
    534A  GLN*     2.9    21.0    +      -       -      -
    550A  VAL*     4.4     9.2    -      -       +      -
    551A  CYS      2.8    11.3    +      -       -      +
    552A  TYR*     3.8    25.8    -      -       +      +
    553A  VAL*     3.0    26.0    +      -       -      +
      5B    A      3.0    12.5    +      -       -      +
----------------------------------------------------------
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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