Contacts of the strand formed by residues 846 - 853 (chain A) in PDB entry 3I89


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 GLY 846 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    771A  PHE*     4.4     5.3    -      -       -      -
    811A  GLU*     5.4     0.7    -      -       -      -
    833A  THR*     3.9     2.0    -      -       -      -
    834A  ALA*     3.8    15.3    -      -       -      -
    835A  MET*     4.2     5.8    -      -       -      -
    845A  GLN*     1.3    75.1    -      -       -      +
    847A  ARG*     1.3    58.3    +      -       -      +
    865A  GLU*     3.6     3.6    -      -       -      +
    866A  VAL*     2.6    42.7    +      -       -      +
    868A  GLY      3.3     8.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 847 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    766A  SER*     3.2    27.3    +      -       -      -
    768A  SER*     4.1     6.3    +      -       -      -
    770A  LEU*     5.0     3.4    -      -       -      -
    771A  PHE*     4.2    17.6    -      -       +      -
    807A  PHE*     4.4     3.6    -      -       -      -
    808A  LEU*     3.2    26.4    -      -       -      +
    811A  GLU*     2.7    33.9    +      -       -      +
    831A  VAL      3.2     4.7    -      -       -      +
    833A  THR*     2.6    54.5    +      -       -      +
    846A  GLY*     1.3    74.0    -      -       -      +
    848A  ILE*     1.3    67.5    +      -       -      +
    849A  VAL*     3.5    29.9    +      -       +      +
    860A  THR*     6.2     1.0    -      -       -      +
    863A  GLU*     3.5    26.7    +      -       -      +
    864A  LYS      3.5    19.3    -      -       -      +
    865A  GLU*     4.0     3.4    -      -       -      +
    866A  VAL*     3.8     3.0    -      -       -      +
    870A  VAL*     4.5     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 848 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    830A  ILE*     3.5    25.1    -      -       +      -
    831A  VAL      3.6     4.7    -      -       -      +
    832A  GLY*     4.4     0.2    -      -       -      -
    847A  ARG*     1.3    77.5    -      -       -      +
    849A  VAL*     1.3    63.7    +      -       -      +
    850A  VAL*     5.5     1.1    -      -       +      -
    863A  GLU*     3.4     2.8    -      -       -      -
    864A  LYS*     3.1    41.4    +      -       +      +
    866A  VAL*     3.9    10.1    -      -       +      -
    870A  VAL*     4.1    17.5    -      -       +      -
    873A  MET*     4.1    12.6    -      -       +      -
    880A  LEU*     4.0    14.6    -      -       +      -
    882A  ALA*     4.9     5.2    -      -       +      -
    884A  ILE*     5.4     0.9    -      -       +      -
    891A  TYR*     3.2    46.7    -      -       +      +
    899A  VAL*     5.3     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 849 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    766A  SER*     6.1     0.2    -      -       -      +
    807A  PHE*     4.8     3.8    -      -       +      -
    829A  PHE      3.7     1.7    -      -       -      +
    830A  ILE*     3.3     6.6    -      -       -      +
    831A  VAL      3.0    35.5    +      -       -      +
    833A  THR*     4.6     6.3    -      -       +      -
    847A  ARG*     3.5    35.9    -      -       +      +
    848A  ILE*     1.3    80.8    -      -       -      +
    850A  VAL*     1.3    70.6    +      -       -      +
    851A  PHE*     3.4    35.7    -      -       +      -
    860A  THR*     4.3    14.4    -      -       +      -
    862A  ALA      3.5     9.9    -      -       -      +
    863A  GLU*     4.5     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 850 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    821A  LEU*     5.2     3.1    -      -       +      -
    828A  TYR*     2.9    46.2    -      -       +      -
    829A  PHE      4.2     2.0    -      -       -      -
    830A  ILE*     4.0    23.6    -      -       +      -
    848A  ILE*     5.5     0.7    -      -       +      -
    849A  VAL*     1.3    79.8    -      -       -      +
    851A  PHE*     1.3    56.2    +      -       -      +
    860A  THR*     3.6     2.8    -      -       -      -
    861A  VAL*     2.8    34.8    +      -       +      -
    862A  ALA*     2.6    25.5    +      -       +      +
    893A  TRP*     4.0    23.1    -      -       +      -
    899A  VAL*     4.8    11.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 851 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    766A  SER*     5.4     1.6    -      -       -      -
    791A  LEU*     4.1    13.7    -      -       +      -
    805A  HIS*     4.0    27.6    -      +       -      -
    807A  PHE*     4.3    14.8    -      +       -      -
    828A  TYR*     3.3    10.7    -      -       -      +
    829A  PHE*     2.9    54.4    +      -       +      +
    831A  VAL*     4.4     8.3    -      -       +      -
    849A  VAL*     3.4    37.7    -      -       +      -
    850A  VAL*     1.3    74.2    -      -       -      +
    852A  GLN*     1.3    60.1    +      -       -      +
    858A  LEU*     3.6    32.8    -      -       +      -
    859A  GLN      3.3    14.1    -      -       -      -
    860A  THR*     3.9    23.3    -      -       +      -
    861A  VAL*     3.9     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 852 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    727A  GLN*     5.6     0.2    -      -       -      +
    826A  ASN*     3.1    45.8    +      -       -      +
    827A  THR      4.2    15.7    +      -       -      +
    828A  TYR*     4.5     3.1    -      -       +      -
    829A  PHE*     5.1     1.1    -      -       -      +
    851A  PHE*     1.3    75.4    -      -       -      +
    853A  TYR*     1.3    73.6    +      -       -      +
    854A  SER*     4.7     7.6    +      -       -      +
    857A  LYS      3.2     0.3    -      -       -      +
    858A  LEU*     3.2    11.8    -      -       -      +
    859A  GLN*     2.8    55.5    +      -       +      +
    861A  VAL*     3.9    14.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 853 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    727A  GLN*     3.8    21.3    +      -       -      +
    730A  SER*     4.2    19.4    +      -       -      -
    732A  CYS*     4.1    14.6    -      -       -      -
    793A  ILE*     3.7    29.8    -      -       +      -
    802A  LEU*     3.4    34.4    -      -       +      +
    803A  HIS*     4.2    14.2    +      -       +      +
    829A  PHE*     4.6     5.7    -      -       +      -
    852A  GLN*     1.3    82.3    +      -       -      +
    854A  SER*     1.3    65.8    +      -       -      +
    855A  ASP      4.8     5.9    +      -       -      -
    856A  GLY*     3.7    34.9    +      -       -      -
    857A  LYS      3.0    15.5    -      -       -      -
    858A  LEU*     4.0    14.6    -      -       +      -
----------------------------------------------------------
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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