Contacts of the strand formed by residues 830 - 843 (chain C) in PDB entry 7KHI


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 THR 830 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    690C  VAL*     3.5    21.3    -      -       +      +
    691C  PRO      3.4    24.1    +      -       -      +
    692C  THR*     4.8     3.2    -      -       -      +
    693C  LEU      5.0     0.2    -      -       -      +
    763C  THR*     5.2     1.6    -      -       +      -
    828C  PHE      3.9     1.1    +      -       -      -
    829C  THR*     1.3    73.8    -      -       -      +
    831C  ILE*     1.3    68.2    +      -       -      +
    832C  HIS*     3.1    34.3    -      -       +      +
   1056C  VAL      3.7     0.5    -      -       -      +
   1057C  LYS*     3.6     3.2    -      -       -      -
   1058C  ARG*     2.9    35.0    +      -       -      +
   1234C  LYS*     3.1    25.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 831 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  TYR*     3.6    34.5    -      -       +      +
     79A  LEU*     3.9    27.4    -      -       +      -
    691C  PRO      5.1     0.4    +      -       -      -
    692C  THR      5.8     0.4    -      -       -      -
    693C  LEU*     4.8    15.7    -      -       +      +
    756C  TYR*     4.4     9.9    -      -       +      -
    763C  THR*     3.8     0.2    -      -       -      -
    764C  CYS*     3.2    49.0    +      -       +      +
    766C  ASN*     5.9     0.4    -      -       -      +
    829C  THR      4.9     1.1    -      -       -      +
    830C  THR*     1.3    78.9    -      -       -      +
    832C  HIS*     1.3    70.9    +      -       -      +
   1055C  ALA*     4.6     7.4    -      -       +      -
   1056C  VAL      3.6     7.2    -      -       -      +
   1057C  LYS*     4.1    14.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 832 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    690C  VAL*     4.4     6.5    -      -       -      +
    761C  GLN      5.9     0.4    -      -       -      -
    762C  ASN*     3.1    15.9    -      -       +      +
    763C  THR*     4.5    10.7    -      -       +      +
    830C  THR*     3.1    28.8    -      -       +      +
    831C  ILE*     1.3    85.2    -      -       -      +
    833C  ILE*     1.3    63.7    +      -       -      +
    834C  GLN*     3.7     5.5    +      -       +      +
   1054C  LEU      3.5     1.6    -      -       -      +
   1055C  ALA*     3.5     1.1    -      -       -      -
   1056C  VAL*     2.9    49.5    +      -       +      +
   1058C  ARG*     3.0    34.1    +      -       +      +
   1236C  ASN*     5.6     4.3    +      -       -      -
   1238C  LEU*     3.5    33.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 833 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    756C  TYR*     3.7    26.9    -      -       +      +
    757C  THR*     3.8    19.1    -      -       -      +
    758C  ARG*     3.5    33.8    +      -       +      +
    762C  ASN*     2.6    24.7    +      -       -      +
    764C  CYS*     3.3    31.4    -      -       +      -
    832C  HIS*     1.3    71.7    -      -       -      +
    834C  GLN*     1.3    62.4    +      -       -      +
    929C  ILE*     4.5    12.6    -      -       +      -
   1053C  TYR*     4.1    24.7    -      -       +      -
   1054C  LEU      3.2     8.5    -      -       -      +
   1055C  ALA*     4.4    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 834 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    758C  ARG*     4.7     0.7    -      -       -      -
    762C  ASN*     4.6    21.4    -      -       +      +
    832C  HIS*     3.7     8.0    +      -       +      +
    833C  ILE*     1.3    78.8    -      -       -      +
    835C  GLU*     1.3    63.3    +      -       -      +
    836C  LEU*     4.5    15.5    -      -       +      +
    921C  PRO*     5.5     3.5    -      -       -      +
    924C  VAL*     4.0    25.6    -      -       -      +
   1053C  TYR*     3.3     6.3    -      -       -      +
   1054C  LEU*     2.9    37.7    +      -       +      +
   1056C  VAL*     4.2    12.7    -      -       -      +
   1058C  ARG*     3.1    32.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 835 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    758C  ARG*     3.8    39.6    +      -       -      +
    762C  ASN*     5.5     0.2    +      -       -      -
    833C  ILE      4.2     0.4    +      -       -      -
    834C  GLN*     1.3    73.3    -      -       -      +
    836C  LEU*     1.3    78.2    +      -       -      +
    837C  ALA*     4.9     4.7    -      -       -      +
   1051C  LYS*     3.4    30.5    +      -       +      +
   1052C  VAL      3.8     2.0    -      -       -      -
   1053C  TYR*     3.5    27.4    +      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 836 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    834C  GLN*     4.5    14.4    -      -       +      +
    835C  GLU*     1.3    87.2    -      -       -      +
    837C  ALA*     1.3    61.5    +      -       -      +
    883C  LEU*     3.8    24.5    -      -       +      -
    918C  LEU*     4.0    25.1    -      -       +      -
    919C  ARG      4.6     0.4    -      -       -      +
    920C  VAL*     4.6     1.8    -      -       -      -
    921C  PRO*     3.8    31.6    -      -       +      -
    924C  VAL*     6.5     0.2    -      -       +      -
   1050C  VAL      3.9     0.3    -      -       -      +
   1051C  LYS*     3.3     6.1    -      -       -      +
   1052C  VAL*     2.9    41.5    +      -       +      +
   1054C  LEU*     3.9    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 837 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    835C  GLU*     4.9     4.0    -      -       -      +
    836C  LEU*     1.3    76.4    -      -       -      +
    838C  CYS*     1.3    60.5    +      -       -      +
    839C  VAL*     4.1     3.9    +      -       +      +
    918C  LEU*     3.7    15.0    -      -       -      +
   1049C  ILE*     4.9     7.2    -      -       +      -
   1050C  VAL      3.5     5.4    -      -       -      +
   1051C  LYS*     4.2    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 838 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    837C  ALA*     1.3    72.0    -      -       -      +
    839C  VAL*     1.3    60.6    +      -       -      +
    840C  SER      4.3     0.3    +      -       -      -
    850C  ILE*     4.6     3.9    -      -       -      +
    884C  VAL*     4.1    23.8    -      -       +      -
    886C  LYS*     3.6    36.6    -      -       -      -
    918C  LEU*     3.8    28.4    -      -       +      +
   1048C  LYS      4.3     0.3    -      -       -      +
   1049C  ILE*     3.5     3.4    -      -       -      -
   1050C  VAL*     2.9    47.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 839 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    837C  ALA*     5.6     3.1    -      -       +      +
    838C  CYS*     1.3    74.0    -      -       -      +
    840C  SER*     1.3    62.8    +      -       -      +
    841C  ARG*     3.8    34.9    +      -       +      +
    848C  GLU*     4.5     0.2    -      -       -      +
    886C  LYS*     3.7    16.9    +      -       -      +
   1046C  VAL*     3.5    37.2    -      -       +      -
   1048C  LYS      3.7     2.9    -      -       -      +
   1049C  ILE*     3.8    23.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 840 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    838C  CYS*     4.2     0.6    -      -       -      -
    839C  VAL*     1.3    71.4    -      -       -      +
    841C  ARG*     1.3    62.2    -      -       -      +
    848C  GLU*     3.9    21.3    +      -       -      -
    850C  ILE*     3.8    25.7    -      -       -      +
    886C  LYS*     3.9     7.9    -      -       -      -
   1047C  LEU*     2.9    29.2    +      -       -      +
   1048C  LYS*     2.9    38.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 841 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    839C  VAL*     3.8    30.1    +      -       +      +
    840C  SER*     1.3    78.6    -      -       -      +
    842C  ASP*     1.3    64.4    +      -       -      +
    843C  THR*     4.0     3.6    -      -       +      -
    847C  PRO*     4.4     0.2    -      -       -      +
    848C  GLU*     3.4    37.8    +      -       -      +
   1045C  GLY      3.5    17.3    -      -       -      +
   1046C  VAL*     3.9    22.1    -      -       +      +
   1047C  LEU*     4.7     2.9    -      -       -      +
    256D  ASP*     3.7    36.5    +      -       -      +
    257D  GLY*     4.1    26.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 842 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    841C  ARG*     1.3    76.2    -      -       -      +
    843C  THR*     1.3    64.8    +      -       -      +
    847C  PRO*     3.7    31.0    -      -       +      -
    936C  ARG*     5.3     2.1    +      -       -      -
   1045C  GLY*     2.9    22.8    -      -       -      +
   1047C  LEU*     4.2    17.1    -      -       +      +
    499F  LYS*     4.2    17.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 843 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    841C  ARG*     4.0     4.5    +      -       +      -
    842C  ASP*     1.3    79.6    -      -       -      +
    844C  LYS*     1.3    68.4    +      -       -      +
    845C  LEU*     4.0    14.6    +      -       -      +
    846C  GLY*     3.0    33.4    +      -       -      -
    847C  PRO*     5.0     0.3    -      -       -      +
    848C  GLU*     4.5    12.9    +      -       -      +
    888C  THR*     4.3    18.1    -      -       +      +
----------------------------------------------------------
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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