Contacts of the strand formed by residues 817 - 824 (chain B) in PDB entry 1KT8


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 VAL 817 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    674B  PHE*     4.0     5.4    -      -       -      -
    774B  LEU*     4.5     5.4    -      -       +      -
    809B  PHE*     3.4    35.2    -      -       +      -
    810B  GLY      3.5     2.0    -      -       -      -
    815B  CYS*     4.2     2.0    -      -       -      -
    816B  GLN*     1.3    90.0    -      -       +      +
    818B  CYS*     1.3    59.2    +      -       -      +
    819B  PRO*     3.6     5.6    -      -       -      +
    842B  ILE*     3.8    24.9    -      -       +      +
    845B  PHE*     4.0    19.3    -      -       +      -
    846B  GLN*     3.1    44.9    +      -       +      +
    849B  LEU*     4.2    11.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 818 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    673B  TYR*     4.3     7.6    -      -       -      -
    674B  PHE*     4.4     5.4    -      -       -      -
    682B  VAL*     4.0    33.0    -      -       -      -
    741B  MET*     3.7    20.4    -      -       +      +
    809B  PHE*     3.2     6.3    -      -       -      -
    810B  GLY      2.7    35.3    +      -       -      +
    815B  CYS*     3.2    28.3    -      -       -      -
    817B  VAL*     1.3    71.9    -      -       -      +
    819B  PRO*     1.3    71.9    -      -       -      +
    820B  VAL*     3.8     3.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 819 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    674B  PHE*     4.0     9.0    -      -       +      -
    679B  VAL*     3.3    31.6    -      -       +      -
    680B  THR      4.1     6.5    -      -       -      +
    681B  PRO*     3.1     9.3    -      -       +      +
    682B  VAL*     2.9    26.3    +      -       -      +
    808B  VAL      3.9     6.3    -      -       -      +
    809B  PHE*     4.1     0.4    -      -       -      -
    817B  VAL      3.6     7.6    -      -       -      +
    818B  CYS*     1.3    87.1    -      -       +      +
    820B  VAL*     1.3    59.7    +      -       -      +
    834B  THR*     4.2     2.0    -      -       +      -
    835B  MET*     3.8    26.9    -      -       -      -
    839B  PRO*     4.7     0.4    -      -       +      -
    842B  ILE*     3.9    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 820 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    681B  PRO*     4.2     0.9    -      -       -      -
    682B  VAL*     3.5    20.4    -      -       +      +
    684B  LEU*     3.8    28.9    -      -       +      -
    738B  VAL*     5.5     3.1    -      -       +      -
    741B  MET*     6.2     0.7    -      -       +      -
    743B  ILE*     6.1     0.7    -      -       +      -
    808B  VAL*     3.1    29.6    +      -       +      +
    809B  PHE*     4.0     9.9    -      -       -      -
    810B  GLY*     4.5     2.0    -      -       -      +
    818B  CYS      3.8     9.4    -      -       -      +
    819B  PRO*     1.3    80.0    -      -       -      +
    821B  HIS*     1.3    64.1    +      -       -      +
    822B  ARG      3.8    16.6    -      -       -      +
    823B  ILE*     4.1     9.4    -      -       +      -
    832B  ILE*     3.6     7.7    -      -       +      +
    834B  THR*     2.7    28.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 821 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    681B  PRO*     3.3    39.0    -      -       +      +
    682B  VAL*     3.1    28.1    +      -       -      -
    683B  SER*     3.7    10.1    -      -       -      -
    723B  GLU*     4.3     4.3    -      -       -      -
    820B  VAL*     1.3    74.2    -      -       -      +
    822B  ARG*     1.3    77.3    +      -       +      +
    831B  HIS*     3.6    17.3    +      +       +      -
    832B  ILE*     2.6    41.6    +      -       -      +
    835B  MET*     4.8     7.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 822 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    682B  VAL      3.7     0.4    +      -       -      -
    683B  SER*     3.3    24.4    +      -       -      -
    684B  LEU      2.9    23.0    +      -       -      -
    720B  ARG      5.3     0.6    +      -       -      -
    721B  GLY*     2.8    28.9    +      -       -      -
    722B  CYS*     4.2    15.0    -      -       -      -
    820B  VAL*     3.7     4.1    -      -       -      +
    821B  HIS*     1.3   103.4    +      -       +      +
    823B  ILE*     1.3    71.9    +      -       -      +
    824B  LEU*     4.4     5.3    -      -       -      +
    829B  ASN*     2.7    47.6    +      -       -      +
    830B  LEU      3.3    13.2    -      -       -      +
    831B  HIS*     5.2     1.8    -      -       -      +
    832B  ILE*     3.9     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 823 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    684B  LEU*     3.3    15.5    -      -       +      +
    686B  ALA*     3.8    26.7    -      -       +      -
    726B  LEU*     4.3    16.6    -      -       +      -
    735B  LEU*     5.4     1.3    -      -       +      -
    743B  ILE*     6.0     0.7    -      -       +      -
    793B  MET*     4.7     2.9    -      -       +      -
    796B  LEU*     4.0    24.5    -      -       +      -
    808B  VAL*     5.1     8.3    -      -       +      -
    820B  VAL*     4.1    13.0    -      -       +      -
    822B  ARG*     1.3    83.5    -      -       -      +
    824B  LEU*     1.3    60.9    +      -       -      +
    825B  TYR*     4.5     1.6    -      -       +      +
    830B  LEU*     2.7    58.3    +      -       +      +
    832B  ILE*     4.0    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 824 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    684B  LEU      2.9     8.5    +      -       -      -
    685B  LEU*     3.7    12.9    -      -       +      +
    686B  ALA      2.9    28.0    +      -       -      +
    720B  ARG*     3.7    49.4    -      -       +      +
    722B  CYS*     3.8    21.5    -      -       -      -
    822B  ARG*     4.3     2.6    -      -       -      +
    823B  ILE*     1.3    70.5    -      -       -      +
    825B  TYR*     1.3    58.2    +      -       -      +
    826B  LYS      4.5     0.2    +      -       -      -
    827B  ASP*     3.1    32.5    -      -       -      +
    828B  ARG      3.0    18.2    -      -       -      +
    829B  ASN*     3.7    22.7    -      -       -      +
----------------------------------------------------------
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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