Contacts of the strand formed by residues 548 - 555 (chain A) in PDB entry 5Y7G


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 VAL 548 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    351A  ILE*     4.0     6.4    -      -       +      +
    352A  ASP*     3.4    21.0    +      -       -      +
    506A  PRO*     5.0     1.6    -      -       +      -
    518A  TYR*     6.1     0.2    -      -       +      -
    519A  ARG*     4.3     2.7    -      -       -      +
    520A  MET*     3.1    26.5    -      -       +      +
    538A  LEU*     3.7    46.9    -      -       +      +
    541A  CYS*     3.9    26.9    -      -       +      -
    542A  ARG*     4.7    10.5    -      -       +      +
    546A  MET*     3.1    11.2    +      -       +      +
    547A  PRO*     1.3    77.5    -      -       -      +
    549A  ALA*     1.3    64.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 549 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    351A  ILE      3.9     3.6    -      -       -      -
    352A  ASP*     3.5    20.4    -      -       +      +
    354A  LEU*     5.5     5.6    -      -       +      -
    519A  ARG*     3.6    33.4    -      -       -      +
    520A  MET      2.7    10.1    +      -       -      +
    521A  VAL*     3.0    10.8    -      -       +      +
    522A  GLU*     2.8    30.9    +      -       -      +
    538A  LEU*     5.4     1.7    -      -       -      +
    548A  VAL*     1.3    77.9    -      -       -      +
    550A  VAL*     1.3    58.5    +      -       -      +
    551A  CYS      4.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 550 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    351A  ILE*     4.1    19.1    -      -       +      +
    352A  ASP      3.3     5.5    +      -       -      +
    353A  ARG*     3.8     5.8    -      -       -      +
    354A  LEU*     3.1    23.9    +      -       -      +
    521A  VAL*     5.1     0.2    -      -       -      -
    522A  GLU*     3.2    13.2    -      -       +      +
    524A  LYS*     4.4     7.2    -      -       +      -
    530A  LEU*     3.8    19.3    -      -       +      -
    538A  LEU*     3.7    29.6    -      -       +      -
    549A  ALA*     1.3    77.2    -      -       -      +
    551A  CYS*     1.3    60.6    +      -       -      +
    552A  TYR*     3.3    41.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 551 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    354A  LEU*     3.1    27.6    -      -       +      +
    356A  LEU*     3.8    25.1    -      -       -      -
    371A  VAL*     4.0    11.7    -      -       +      -
    521A  VAL*     3.9    17.3    -      -       +      -
    522A  GLU      2.7     9.6    +      -       -      +
    523A  VAL*     3.3     5.8    -      -       +      +
    524A  LYS      2.9    26.0    +      -       -      +
    549A  ALA      4.0     0.8    +      -       -      -
    550A  VAL*     1.3    70.9    -      -       -      +
    552A  TYR*     1.3    62.3    +      -       -      +
    553A  VAL*     3.8    23.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 552 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    351A  ILE*     5.0     1.9    -      -       -      +
    353A  ARG*     2.9    42.4    +      -       +      -
    354A  LEU      2.8     8.3    +      -       -      +
    355A  ASP*     3.4    37.8    -      -       -      +
    356A  LEU      3.4     2.4    +      -       -      +
    524A  LYS*     3.5    31.0    -      -       +      +
    525A  GLY      5.5     1.1    -      -       -      -
    528A  ASP      5.1     0.9    -      -       -      -
    529A  ARG*     4.6    26.9    -      -       -      -
    530A  LEU*     3.3    28.7    +      -       +      +
    550A  VAL*     3.3    27.8    -      -       +      -
    551A  CYS*     1.3    72.9    -      -       -      +
    553A  VAL*     1.3    62.5    +      -       -      +
    554A  ARG      4.2     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 553 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    356A  LEU*     3.5    16.2    -      -       +      +
    358A  LEU*     4.1    17.5    -      -       +      -
    367A  VAL*     4.0    22.0    -      -       +      -
    371A  VAL*     3.6    31.6    -      -       +      -
    523A  VAL*     4.5     2.5    -      -       +      -
    524A  LYS      3.2     7.1    +      -       -      +
    525A  GLY*     4.2     0.4    -      -       -      -
    526A  PRO*     3.3    28.0    -      -       +      +
    551A  CYS*     3.8    15.5    -      -       -      -
    552A  TYR*     1.3    72.9    -      -       -      +
    554A  ARG*     1.4    72.6    +      -       -      +
    555A  TRP*     4.4    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 554 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    356A  LEU      3.2     7.5    +      -       -      +
    357A  CYS*     3.2    35.6    -      -       -      +
    358A  LEU      3.2    22.5    +      -       -      +
    526A  PRO*     4.6     5.8    -      -       +      -
    552A  TYR      4.2     1.0    +      -       -      -
    553A  VAL*     1.4    77.9    -      -       -      +
    555A  TRP*     1.3    74.2    +      -       -      +
    556A  HIS*     3.4    40.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 555 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    358A  LEU*     3.1    48.9    -      -       +      -
    359A  ALA      3.0    24.9    -      -       -      -
    360A  PHE*     4.0    35.1    -      +       +      -
    361A  PRO*     5.3    11.9    -      -       +      -
    365A  CYS      6.2     0.4    -      -       -      -
    367A  VAL*     3.8    32.7    -      -       +      +
    370A  ALA*     5.2     6.7    -      -       +      -
    526A  PRO*     4.1    25.8    -      -       +      +
    553A  VAL*     4.4    13.7    -      -       +      -
    554A  ARG*     1.3    87.4    +      -       -      +
    556A  HIS*     1.3    67.0    +      -       -      +
----------------------------------------------------------
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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