Contacts of the strand formed by residues 789 - 799 (chain B) in PDB entry 3H44


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 SER 789 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    678B  PRO*     3.8     3.1    -      -       -      -
    788B  ASN*     1.3    74.6    -      -       -      +
    790B  GLY*     1.3    59.3    +      -       -      +
    851B  GLN*     3.3     9.5    -      -       -      +
    852B  SER      2.7    35.5    +      -       -      -
    853B  GLU*     4.9     0.4    -      -       -      +
    854B  LYS      2.7    28.0    +      -       -      -
    856B  PRO*     3.9    17.7    -      -       -      +
    859B  LEU*     4.1     6.9    -      -       -      +
    958B  VAL      3.2    14.4    -      -       -      -
    960B  ALA*     3.6    13.3    -      -       -      +
    963B  MET*     4.1     5.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 790 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    678B  PRO*     3.7    23.0    -      -       -      +
    679B  HIS      4.3     1.1    -      -       -      -
    682B  ALA*     4.5     2.7    -      -       -      -
    789B  SER*     1.3    74.8    -      -       -      +
    791B  ILE*     1.3    63.1    +      -       -      +
    850B  ILE      3.4    10.1    -      -       -      -
    851B  GLN*     4.3     1.6    -      -       -      -
    856B  PRO*     4.3     2.9    -      -       -      +
    859B  LEU*     5.7     0.2    -      -       -      -
    956B  VAL      4.4     0.2    -      -       -      -
    957B  HIS*     3.7     1.0    -      -       -      -
    958B  VAL*     2.7    43.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 791 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    679B  HIS*     5.1     1.4    -      -       -      +
    682B  ALA*     4.0     6.0    -      -       -      +
    790B  GLY*     1.3    75.0    -      -       -      +
    792B  GLU*     1.3    63.4    +      -       -      +
    793B  ILE*     3.7    23.1    -      -       +      -
    848B  PHE      3.6     1.4    -      -       -      +
    849B  ILE*     3.4     6.3    -      -       -      +
    850B  ILE*     3.0    51.4    +      -       +      +
    856B  PRO*     4.6     8.7    -      -       +      +
    859B  LEU*     4.1    19.1    -      -       +      -
    860B  GLU*     3.6    39.5    -      -       +      +
    956B  VAL      3.2    15.9    -      -       -      +
    957B  HIS*     3.7    13.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 792 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    682B  ALA*     3.7    17.8    -      -       +      +
    683B  MET*     3.1    34.7    -      -       -      +
    686B  LEU*     3.3    31.2    -      -       +      +
    791B  ILE*     1.3    75.1    -      -       -      +
    793B  ILE*     1.3    71.2    +      -       -      +
    794B  TYR      4.2     0.2    -      -       -      -
    838B  ARG*     4.3     0.4    -      -       -      -
    847B  ARG*     2.7    38.1    +      -       +      +
    848B  PHE      3.3     8.5    -      -       -      +
    849B  ILE*     3.8    14.6    -      -       +      -
    954B  VAL      4.2     0.2    -      -       -      +
    955B  SER*     3.4     3.1    -      -       -      -
    956B  VAL*     2.9    35.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 793 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    791B  ILE*     3.7    31.6    -      -       +      -
    792B  GLU*     1.3    74.4    -      -       -      +
    794B  TYR*     1.3    63.7    +      -       -      +
    795B  TYR*     3.3    36.7    -      -       +      +
    846B  LEU      3.5     1.0    -      -       -      +
    847B  ARG*     3.1     9.4    -      -       -      +
    848B  PHE*     2.8    37.6    +      -       +      +
    850B  ILE*     6.1     0.2    -      -       +      -
    860B  GLU*     4.0    20.2    -      -       -      +
    863B  VAL*     3.8    38.8    -      -       +      -
    864B  GLU*     6.5     0.2    -      -       +      -
    953B  LYS*     3.8    13.9    -      -       -      -
    954B  VAL      3.7     4.3    -      -       -      +
    955B  SER*     4.4     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 794 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    686B  LEU*     4.0    25.4    -      -       +      -
    690B  MET*     4.2    19.3    -      -       +      -
    768B  GLU*     2.8    28.7    +      -       -      -
    792B  GLU      4.2     0.2    -      -       -      -
    793B  ILE*     1.3    74.7    -      -       -      +
    795B  TYR*     1.3    65.6    +      -       -      +
    796B  GLN*     3.8    23.0    +      -       +      +
    838B  ARG*     3.7    38.6    +      -       +      -
    843B  ILE      4.6     0.2    -      -       -      -
    844B  GLN*     3.3    21.7    +      -       -      -
    845B  GLY*     3.8    16.8    -      -       -      -
    846B  LEU      3.8     7.9    -      -       -      -
    847B  ARG*     4.6     1.3    -      -       +      -
    952B  HIS      3.5     1.0    -      -       -      +
    953B  LYS*     3.2     5.4    -      -       -      +
    954B  VAL*     2.7    59.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 795 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    793B  ILE*     3.3    24.0    -      -       +      +
    794B  TYR*     1.3    71.8    -      -       -      +
    796B  GLN*     1.3    62.2    +      -       -      +
    797B  THR*     4.4     2.4    -      -       -      +
    845B  GLY*     3.2     3.5    -      -       -      -
    846B  LEU*     2.8    56.8    +      -       +      +
    848B  PHE*     4.0    20.6    -      +       -      -
    863B  VAL*     4.3     6.6    -      -       +      +
    864B  GLU*     2.5    24.6    +      -       -      +
    867B  LEU*     3.8    10.7    -      -       +      +
    943B  MET      5.6     1.6    -      -       -      +
    944B  LEU*     3.7    26.5    -      -       +      -
    951B  ARG*     3.3    39.9    -      -       +      -
    952B  HIS      3.2     6.7    -      -       -      +
    953B  LYS*     3.4    31.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 796 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    690B  MET*     5.3     1.2    -      -       -      -
    768B  GLU*     3.2    21.4    +      -       -      +
    769B  VAL      3.2    21.0    +      -       -      -
    771B  LEU*     3.2    41.3    +      -       +      +
    794B  TYR*     3.7    25.2    -      -       +      +
    795B  TYR*     1.3    72.8    -      -       -      +
    797B  THR*     1.3    62.8    +      -       -      +
    843B  ILE*     3.5     7.8    -      -       +      +
    844B  GLN      3.7     7.9    -      -       -      +
    943B  MET*     4.4     4.2    -      -       -      +
    944B  LEU*     5.9     0.2    -      -       -      +
    950B  ARG      4.7     0.2    -      -       -      +
    952B  HIS*     2.9    45.1    +      -       +      +
   1005B  PHE*     3.3    23.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 797 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    795B  TYR      3.7     0.2    +      -       -      -
    796B  GLN*     1.3    78.5    -      -       -      +
    798B  ASP*     1.3    71.0    +      -       -      +
    804B  GLU*     4.1    16.3    -      -       -      +
    808B  LEU*     4.7     7.7    -      -       +      +
    844B  GLN*     2.8    33.8    +      -       -      +
    845B  GLY*     4.0    11.5    -      -       -      -
    939B  PHE*     4.0    24.5    -      -       +      -
    943B  MET*     3.2    30.6    -      -       +      +
    944B  LEU*     4.3    19.1    -      -       +      -
    950B  ARG*     4.3     2.1    +      -       -      -
    952B  HIS*     4.2     7.4    -      -       -      -
   1005B  PHE*     5.9     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 798 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    797B  THR*     1.3    82.8    +      -       -      +
    799B  MET*     1.3    82.1    +      -       -      +
    804B  GLU*     3.7    21.1    +      -       +      +
    843B  ILE*     4.1     8.2    -      -       -      +
    844B  GLN*     3.3    25.4    +      -       -      +
    950B  ARG*     4.8    14.4    +      -       -      +
   1005B  PHE*     3.3    25.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 799 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    798B  ASP*     1.3    91.4    +      -       -      +
    800B  GLN*     1.3    77.8    +      -       -      +
    801B  SER*     3.4     5.8    +      -       -      -
    804B  GLU*     3.6    14.2    -      -       -      +
    842B  GLY      3.5     8.7    -      -       -      +
    843B  ILE*     3.7    19.8    -      -       +      +
   1005B  PHE*     4.1    11.9    -      -       +      -
   1006B  PRO*     4.0    33.2    -      -       +      +
   1007B  LEU      4.4     3.1    -      -       -      +
   1008B  VAL*     3.8    24.5    -      -       +      -
   1009B  LYS*     5.2     2.0    -      -       +      +
----------------------------------------------------------
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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