Contacts of the strand formed by residues 347 - 354 (chain A) in PDB entry 6OR7


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 347 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    315A  HIS*     6.0     5.8    -      -       +      -
    317A  VAL*     3.7    31.9    -      -       +      +
    342A  TYR*     3.3    16.3    -      -       -      +
    343A  GLN      4.0     2.8    +      -       -      -
    344A  GLU*     3.2    35.4    +      -       +      +
    345A  PRO      3.5     0.8    +      -       -      -
    346A  PHE*     1.3    82.5    -      -       -      +
    348A  ASN*     1.3    65.4    +      -       -      +
    349A  LEU      3.5     0.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 348 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    270A  ILE*     5.0     4.3    +      -       +      +
    272A  PRO*     5.4     4.9    -      -       -      +
    314A  VAL*     6.0     3.8    -      -       -      +
    315A  HIS      4.4     8.0    +      -       -      +
    316A  GLY*     3.4     7.3    -      -       -      -
    317A  VAL*     3.1    22.5    +      -       -      +
    340A  GLN*     3.5    37.8    -      -       -      +
    341A  ILE      3.6     5.4    -      -       -      +
    342A  TYR*     3.7    14.2    -      -       -      +
    345A  PRO      4.9     2.4    -      -       -      +
    346A  PHE*     4.0     2.7    +      -       -      -
    347A  LYS*     1.3    74.2    +      -       -      +
    349A  LEU*     1.3    62.8    +      -       -      +
    350A  LYS*     4.0    11.4    -      -       -      +
    351A  THR*     3.6    12.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 349 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  ALA*     3.3    17.7    -      -       +      +
    239A  TRP*     3.2    24.6    +      -       -      -
    316A  GLY*     4.2     0.3    -      -       -      -
    317A  VAL*     3.3    29.6    -      -       +      +
    318A  TYR      3.4    24.0    -      -       -      +
    319A  TYR*     3.8     4.3    -      -       -      +
    325A  LEU*     4.6     4.9    -      -       +      -
    341A  ILE      2.5    12.8    +      -       -      +
    342A  TYR*     3.5     4.5    -      -       -      +
    343A  GLN*     3.5    46.2    -      -       +      +
    348A  ASN*     1.3    73.3    -      -       -      +
    350A  LYS*     1.3    61.9    +      -       -      +
    383A  TRP*     3.8    28.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 350 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  HIS*     3.3    39.0    -      -       +      +
     98A  ALA*     4.3     1.1    -      -       +      -
    239A  TRP*     4.6     0.7    -      -       +      -
    269A  GLN*     3.5    15.8    +      -       -      +
    270A  ILE*     4.5     7.4    -      -       -      -
    339A  TYR*     4.7     1.4    +      -       -      -
    340A  GLN*     3.6     0.3    -      -       -      -
    341A  ILE*     2.9    35.6    +      -       +      +
    348A  ASN*     3.4     3.6    -      -       -      +
    349A  LEU*     1.3    81.2    -      -       -      +
    351A  THR*     1.3    94.1    +      -       -      +
    352A  GLY*     5.0     0.2    -      -       -      -
    378A  GLU*     2.6    29.8    +      -       -      +
    382A  ILE*     3.8    19.1    -      -       +      -
    383A  TRP*     3.9    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 351 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    268A  SER      2.7    21.3    +      -       -      -
    269A  GLN*     2.7    23.3    +      -       -      +
    270A  ILE*     3.2    23.7    +      -       +      +
    271A  TYR      3.5     2.6    +      -       -      -
    272A  PRO*     4.4    14.4    -      -       +      -
    339A  TYR*     3.2    16.4    -      -       -      -
    340A  GLN*     3.8    12.1    -      -       +      +
    348A  ASN*     3.6    25.1    -      -       +      +
    350A  LYS*     1.3   102.6    +      -       -      +
    352A  GLY*     1.3    60.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 352 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    268A  SER*     3.4    12.1    +      -       -      -
    269A  GLN*     4.9     0.2    -      -       -      -
    338A  THR*     3.3     8.8    -      -       -      +
    339A  TYR*     2.9    52.4    +      -       -      +
    350A  LYS*     5.0     0.4    -      -       -      -
    351A  THR*     1.3    78.5    +      -       -      +
    353A  LYS*     1.3    63.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 353 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    265A  ASN*     3.3    29.5    +      -       -      +
    268A  SER*     3.5    33.6    +      -       -      -
    274A  ILE*     3.1    38.8    -      -       +      +
    275A  LYS*     4.5     2.7    -      -       -      +
    276A  VAL*     3.6    17.8    -      -       -      +
    337A  TRP      3.3    10.1    -      -       -      +
    338A  THR*     4.5     4.5    -      -       +      -
    339A  TYR*     3.2    17.8    +      -       -      -
    352A  GLY*     1.3    75.0    -      -       -      +
    354A  TYR*     1.3    65.3    +      -       -      +
    355A  ALA*     5.0     7.2    -      -       +      +
    374A  LYS*     4.2     7.3    -      -       -      +
    711T    C      4.6     8.7    +      -       -      -
    712T    C      4.6     9.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 354 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    335A  GLY      5.8     0.2    -      -       -      -
    337A  TRP*     2.8    49.0    +      +       +      +
    339A  TYR*     4.9     4.3    -      -       +      -
    353A  LYS*     1.3    77.0    -      -       -      +
    355A  ALA*     1.3    62.9    +      -       -      +
    356A  ARG*     3.6    45.3    +      -       +      +
    358A  ARG*     3.6     7.4    -      -       -      +
    367A  GLN*     3.9    18.8    -      -       +      -
    370A  GLU*     2.9    40.3    +      -       +      +
    371A  ALA*     3.8    27.1    -      -       +      -
    374A  LYS*     3.5    31.2    -      -       +      -
----------------------------------------------------------
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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