Contacts of the strand formed by residues 508 - 512 (chain B) 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 LEU 508 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    368B  GLU*     4.4     3.4    -      -       +      +
    371B  VAL*     4.3    13.0    -      -       +      +
    372B  ARG*     4.2    19.5    -      -       +      +
    375B  LEU*     5.4     2.0    -      -       +      -
    382B  VAL*     4.3    17.5    -      -       +      -
    383B  HIS      3.1    14.8    -      -       -      +
    384B  TYR*     3.5    24.2    -      -       +      -
    506B  PRO*     3.4     3.3    -      -       -      +
    507B  ASP*     1.3    91.2    -      -       +      +
    509B  ILE*     1.3    71.6    +      -       -      +
    520B  MET*     3.5     4.9    -      -       -      +
    521B  VAL*     2.8    47.8    +      -       +      +
    523B  VAL*     3.6    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 509 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    382B  VAL*     3.4     3.3    -      -       -      -
    383B  HIS*     2.9    36.3    +      -       +      +
    385B  VAL*     3.8    30.1    -      -       +      +
    389B  LEU*     3.4    30.5    -      -       +      -
    390B  ILE*     4.2    12.8    -      -       +      -
    482B  LEU*     5.8     1.6    -      -       +      -
    506B  PRO      5.7     0.4    -      -       -      +
    508B  LEU*     1.3    80.8    -      -       -      +
    510B  GLN*     1.3    64.2    +      -       -      +
    511B  PHE*     3.6    34.5    -      -       +      -
    518B  TYR*     4.9     4.5    -      -       +      -
    519B  ARG      3.7    11.2    -      -       -      +
    520B  MET*     4.4    15.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 510 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    375B  LEU*     3.4    36.1    -      -       -      +
    380B  CYS*     3.7    12.5    -      -       -      -
    381B  ALA      2.8    13.5    -      -       -      +
    382B  VAL*     3.7    10.7    -      -       +      +
    509B  ILE*     1.3    75.2    -      -       -      +
    511B  PHE*     1.3    60.6    -      -       -      +
    512B  TRP*     3.8    21.9    -      -       +      -
    518B  TYR*     3.1     8.0    -      -       -      +
    519B  ARG*     2.5    86.8    +      -       +      +
    521B  VAL*     4.4     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 511 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    380B  CYS*     3.3     4.4    -      -       -      -
    381B  ALA*     2.8    35.7    +      -       +      -
    383B  HIS*     4.2    10.8    -      +       -      -
    389B  LEU*     4.1     7.0    -      -       +      -
    474B  LEU*     3.9    21.1    -      -       +      -
    477B  GLN*     3.1    44.6    -      -       +      +
    478B  ALA*     3.9    23.1    -      -       +      -
    481B  CYS*     3.6    32.8    -      -       +      -
    482B  LEU*     4.5     7.6    -      -       +      -
    509B  ILE*     3.6    26.5    -      -       +      -
    510B  GLN*     1.3    74.5    -      -       -      +
    512B  TRP*     1.3    62.4    +      -       -      +
    513B  PRO*     3.4     6.8    -      -       +      +
    517B  ARG      3.6     1.3    -      -       -      -
    518B  TYR*     3.6    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 512 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    379B  GLY      3.5     5.4    -      -       -      +
    380B  CYS*     2.7    45.6    -      -       +      +
    510B  GLN*     3.8    16.8    -      -       +      -
    511B  PHE*     1.3    72.8    -      -       -      +
    513B  PRO*     1.3    62.6    -      -       -      +
    514B  ALA      3.3     2.7    -      -       -      -
    515B  GLN*     3.4    27.7    +      -       +      +
    516B  ARG      3.0    20.8    +      -       -      -
    517B  ARG*     2.9    68.8    +      -       +      +
    518B  TYR*     3.3    29.4    -      -       -      -
    519B  ARG*     3.5    25.8    -      -       +      -
----------------------------------------------------------
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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