Contacts of the strand formed by residues 785 - 795 (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 GLU 785 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    255A  GLN      5.6     1.6    -      -       -      +
    276A  MET*     4.8    12.5    -      -       -      +
    740A  ILE*     3.8    28.8    -      -       +      +
    741A  GLU      3.5     4.5    -      -       -      +
    742A  VAL*     4.2    13.0    -      -       +      +
    752A  LEU*     4.7     5.5    -      -       -      +
    783A  GLY      3.2    13.2    +      -       -      +
    784A  GLU*     1.3    74.8    -      -       -      +
    786A  VAL*     1.3    64.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 786 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    740A  ILE*     3.2     6.9    -      -       -      +
    741A  GLU*     3.0    32.5    +      -       +      -
    749A  THR*     4.0    30.7    -      -       +      +
    784A  GLU      4.1     0.2    +      -       -      -
    785A  GLU*     1.3    76.5    -      -       -      +
    787A  GLU*     1.3    81.7    +      -       +      +
    788A  VAL*     4.5     6.7    -      -       +      -
    809A  GLN*     6.1     5.4    -      -       +      -
    810A  ASN*     3.3    29.6    -      -       -      +
    812A  TYR*     5.8     4.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 787 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    382A  PHE*     5.7     4.0    -      -       -      -
    722A  ARG*     3.1    25.3    +      -       -      -
    738A  SER*     3.1    12.9    +      -       -      +
    739A  ARG      3.2     5.4    -      -       -      +
    740A  ILE*     4.7    11.7    -      -       +      -
    786A  VAL*     1.3    89.4    -      -       -      +
    788A  VAL*     1.3    68.1    +      -       -      +
    789A  HIS*     2.6    39.3    +      -       +      +
    810A  ASN*     5.3     7.1    +      -       -      -
    811A  GLU      5.3     1.4    -      -       -      +
    812A  TYR*     3.1    36.3    +      -       +      +
     19B  SER*     5.8     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 788 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    738A  SER*     3.2     1.7    -      -       -      -
    739A  ARG*     2.5    74.6    +      -       +      +
    741A  GLU*     3.6    34.5    -      -       +      +
    749A  THR*     4.8     2.9    -      -       -      +
    786A  VAL*     4.5     6.3    -      -       +      -
    787A  GLU*     1.3    79.3    -      -       -      +
    789A  HIS*     1.3    65.2    +      -       -      +
    790A  ASN*     4.2     0.7    +      -       -      -
    806A  GLN*     3.5    31.2    -      -       +      +
    807A  PHE      5.4     1.1    -      -       -      +
    808A  LEU      6.1     1.3    -      -       -      +
    811A  GLU      5.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 789 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    722A  ARG*     3.2    29.5    -      -       +      +
    737A  SER      3.2    12.1    +      -       -      +
    738A  SER*     3.8     6.3    +      -       -      -
    787A  GLU*     2.6    33.8    +      -       +      -
    788A  VAL*     1.3    80.4    -      -       -      +
    790A  ASN*     1.3    66.5    +      -       -      +
    806A  GLN*     3.7     1.4    -      -       -      +
    807A  PHE*     3.0    41.1    +      -       +      +
    808A  LEU      5.9     1.0    +      -       -      -
    811A  GLU      3.4    27.0    +      -       -      +
    812A  TYR*     3.3    25.8    -      +       +      -
    813A  ALA*     3.5    23.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 790 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    735A  VAL      3.4     1.2    -      -       -      +
    736A  LEU*     3.5     2.8    -      -       -      +
    737A  SER*     2.7    48.6    +      -       -      +
    739A  ARG*     3.0    29.0    +      -       -      +
    757A  SER*     3.2    21.4    +      -       -      +
    788A  VAL      4.2     4.6    +      -       -      -
    789A  HIS*     1.3    78.4    -      -       -      +
    791A  LEU*     1.3    72.0    +      -       -      +
    792A  LEU*     3.7     7.4    -      -       +      -
    804A  ALA*     4.5     5.0    -      -       -      +
    805A  HIS      3.2     5.6    -      -       -      +
    806A  GLN*     3.1    31.4    +      -       -      +
    807A  PHE*     3.7     7.0    -      -       -      -
    813A  ALA*     5.6     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 791 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    734A  GLY*     4.1     6.1    -      -       -      -
    735A  VAL      3.5    17.7    -      -       -      +
    736A  LEU*     4.1     4.5    -      -       +      -
    790A  ASN*     1.3    73.7    -      -       -      +
    792A  LEU*     1.3    89.7    +      -       -      +
    793A  ILE*     4.5     8.5    -      -       +      -
    805A  HIS*     3.1    33.3    +      -       +      +
    807A  PHE*     3.3    18.5    -      -       +      -
    816A  LEU*     4.1    17.7    -      -       +      -
    829A  PHE*     4.4    20.0    -      -       +      -
    831A  VAL*     4.4     7.0    -      -       +      -
    851A  PHE*     4.1    31.2    -      -       +      -
    858A  LEU*     4.4    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 792 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    717A  LEU*     4.6     9.2    -      -       +      -
    719A  GLU*     4.4     1.1    -      -       -      +
    734A  GLY*     3.3     6.8    -      -       -      -
    735A  VAL*     2.9    43.8    +      -       +      +
    737A  SER*     3.6    24.5    -      -       -      +
    756A  ALA*     4.3    23.6    -      -       +      +
    757A  SER*     3.9     9.2    -      -       -      -
    790A  ASN*     3.7    14.4    -      -       +      -
    791A  LEU*     1.3    88.8    -      -       -      +
    793A  ILE*     1.3    64.6    +      -       -      +
    794A  ILE*     3.7    15.9    -      -       +      -
    801A  VAL*     4.2    10.8    -      -       +      -
    803A  HIS      3.6     3.6    -      -       -      +
    804A  ALA*     3.8    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 793 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    732A  CYS*     4.0    17.7    -      -       +      -
    733A  PHE      3.5     2.5    -      -       -      +
    791A  LEU*     4.5     8.1    -      -       +      -
    792A  LEU*     1.3    83.6    -      -       -      +
    794A  ILE*     1.3    60.5    +      -       -      +
    800A  GLU      3.2     0.5    -      -       -      +
    801A  VAL*     3.5     1.6    -      -       -      +
    802A  LEU*     2.7    36.0    +      -       +      +
    803A  HIS*     3.0    34.5    +      -       +      +
    805A  HIS      6.3     0.2    -      -       -      +
    829A  PHE*     3.3    35.4    -      -       +      -
    853A  TYR*     3.7    35.9    -      -       +      +
    858A  LEU*     4.3    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 794 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    387A  LEU*     5.0    10.5    -      -       +      -
    715A  VAL*     6.0     3.1    -      -       +      -
    717A  LEU*     5.5     7.0    -      -       +      -
    732A  CYS*     3.0     6.5    -      -       -      +
    733A  PHE*     2.7    48.0    +      -       +      +
    735A  VAL*     4.3    16.8    -      -       +      -
    792A  LEU*     3.7    30.7    -      -       +      +
    793A  ILE*     1.3    78.5    -      -       -      +
    795A  ASP*     1.3    80.4    +      -       -      +
    796A  GLN      3.1     0.2    +      -       -      -
    799A  PHE*     3.3    38.1    -      -       +      +
    800A  GLU      3.2    14.4    -      -       -      +
    801A  VAL*     4.3     7.6    -      -       +      +
    802A  LEU*     4.5     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 795 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    731A  GLN      4.3     7.8    -      -       -      +
    794A  ILE*     1.3    73.3    -      -       -      +
    796A  GLN*     1.3    62.7    +      -       -      +
    797A  HIS*     2.9    18.5    +      -       -      +
    798A  THR*     2.7    50.9    +      -       -      +
    799A  PHE*     2.9    28.6    +      -       -      -
    800A  GLU      3.0     9.9    +      -       -      +
    802A  LEU*     3.8    34.3    -      -       +      +
----------------------------------------------------------
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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