Contacts of the strand formed by residues 505 - 512 (chain V) in PDB entry 5IY8


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 505 (chain V).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    494V  MET*     4.1    19.3    -      -       +      -
    503V  ALA*     4.0     6.4    +      -       +      -
    504V  LYS*     1.3    73.3    -      -       -      +
    506V  GLN*     1.3    74.3    +      -       -      +
    507V  CYS*     3.2    20.9    +      -       -      -
    640V  LEU*     4.0    18.2    -      -       +      -
    644V  LEU*     4.2    16.2    -      -       +      -
    654V  GLU      5.4     0.2    -      -       -      -
    655V  TYR*     4.3     1.6    -      -       -      -
    657V  ALA*     3.5    19.5    -      -       +      +
    659V  PHE*     3.9    20.0    -      -       +      +
    685V  TYR*     4.2    15.8    -      -       +      -
    686V  SER*     3.8    12.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 506 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    505V  VAL*     1.3    69.5    -      -       -      +
    507V  CYS*     1.3    84.7    +      -       -      +
    508V  ALA*     5.1     3.0    -      -       +      +
    655V  TYR*     3.7    42.6    -      -       +      +
    657V  ALA      3.1     7.5    +      -       -      +
    658V  PHE*     3.6    24.0    -      -       +      -
    659V  PHE      3.1    23.4    +      -       -      +
    660V  TYR*     5.9     0.4    -      -       +      -
    686V  SER*     3.6    23.1    +      -       -      -
    687V  PHE      4.2     0.6    -      -       -      +
    688V  LYS*     3.1    42.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 507 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    505V  VAL*     3.8    15.3    -      -       -      -
    506V  GLN*     1.3    90.2    +      -       -      +
    508V  ALA*     1.3    60.5    +      -       -      +
    640V  LEU*     4.0    17.5    -      -       -      -
    659V  PHE*     3.7    11.4    -      -       +      -
    680V  LEU*     4.3     4.3    -      -       -      -
    685V  TYR*     3.7    33.7    -      -       -      -
    686V  SER      3.0    17.1    +      -       -      +
    687V  PHE*     3.3    22.8    -      -       +      -
    688V  LYS*     3.0    14.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 508 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    506V  GLN*     5.1     4.0    -      -       +      +
    507V  CYS*     1.3    76.4    -      -       -      +
    509V  GLU*     1.3    60.0    +      -       -      +
    659V  PHE*     2.9    16.9    +      -       -      +
    660V  TYR*     3.4    15.9    -      -       +      -
    661V  SER*     3.0    24.6    +      -       -      -
    687V  PHE*     4.3     6.7    -      -       -      -
    688V  LYS*     3.3    15.0    -      -       +      +
    690V  ILE*     3.7    31.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 509 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    508V  ALA*     1.3    74.0    -      -       -      +
    510V  VAL*     1.3    63.9    +      -       -      +
    511V  TRP*     3.3    19.9    +      -       +      -
    661V  SER*     3.4     8.3    -      -       -      +
    663V  VAL*     3.5    22.1    -      -       +      +
    673V  SER*     2.5    36.2    +      -       -      -
    676V  ARG*     2.7    35.4    +      -       -      +
    687V  PHE*     3.9    19.3    -      -       +      -
    688V  LYS      2.9     8.3    +      -       -      +
    689V  VAL*     3.4    11.9    -      -       +      +
    690V  ILE*     2.8    28.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 510 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    508V  ALA      4.9     0.4    -      -       -      +
    509V  GLU*     1.3    77.8    -      -       -      +
    511V  TRP*     1.3    71.4    +      -       -      +
    512V  CYS*     3.6    14.5    +      -       -      -
    543V  ALA*     5.0     4.5    -      -       +      -
    547V  LEU*     4.5     7.9    -      -       +      -
    660V  TYR*     4.4    15.3    -      -       +      -
    661V  SER      2.8    15.6    +      -       -      +
    662V  LEU*     4.1    20.4    -      -       +      -
    663V  VAL*     2.9    31.1    +      -       -      +
    690V  ILE*     3.3    34.5    -      -       +      +
    691V  THR      6.1     0.2    -      -       -      -
    692V  LYS      6.4     0.4    -      -       -      -
    693V  LEU*     4.9    16.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 511 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    3912  ILE*     5.2    10.1    -      -       +      -
    3952  GLU*     3.0    50.5    -      -       +      -
    3982  ARG*     6.5     1.1    -      -       -      -
    509V  GLU*     3.3    25.9    +      -       +      -
    510V  VAL*     1.3    78.1    -      -       -      +
    512V  CYS*     1.3    61.6    +      -       -      +
    513V  PRO*     4.5     1.0    -      -       -      +
    663V  VAL*     3.6    17.2    -      -       +      +
    665V  GLN*     3.9    26.6    -      -       +      +
    670V  MET*     4.0    16.0    -      -       +      +
    673V  SER*     4.7     6.6    +      -       -      -
    689V  VAL*     3.7    27.3    -      -       +      +
    690V  ILE      2.9    15.6    +      -       -      +
    691V  THR*     3.5    41.5    -      -       +      +
    692V  LYS*     5.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 512 (chain V). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    510V  VAL*     3.7    25.8    -      -       -      -
    511V  TRP*     1.3    77.2    -      -       -      +
    513V  PRO*     1.3    71.6    -      -       +      +
    537V  ASN*     4.5     0.7    -      -       -      +
    539V  ASN      4.7     1.8    -      -       -      +
    540V  LYS*     3.9    43.5    -      -       +      +
    543V  ALA*     4.2    11.9    -      -       -      -
    662V  LEU*     4.8     3.4    -      -       -      -
    663V  VAL      2.9    14.3    +      -       -      +
    664V  SER*     3.6     1.2    -      -       -      -
    665V  GLN*     2.8    34.0    +      -       -      +
----------------------------------------------------------
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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