Contacts of the strand formed by residues 350 - 356 (chain D) in PDB entry 7KHC


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 350 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1245C  ALA*     3.4     1.9    -      -       -      +
   1246C  ARG*     3.1    27.9    +      -       -      +
   1267C  GLY*     3.6     4.5    -      -       -      -
   1268C  GLN*     3.3    29.6    +      -       -      -
    347D  VAL*     3.3    32.7    +      -       -      -
    348D  ASP      3.6     5.2    -      -       -      -
    349D  TYR*     1.3    76.3    -      -       -      +
    351D  GLY*     1.3    59.6    +      -       -      +
    376D  LEU*     3.4     5.8    -      -       -      +
    468D  VAL      3.3    10.1    -      -       -      -
    469D  HIS*     4.0     6.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 351 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1244C  HIS      3.0    13.2    -      -       -      -
   1245C  ALA*     4.0     6.1    -      -       -      -
   1268C  GLN*     3.7     8.4    -      -       -      +
    350D  SER*     1.3    75.4    -      -       -      +
    352D  ARG*     1.3    62.6    +      -       -      +
    372D  MET*     4.6     1.8    -      -       -      -
    376D  LEU*     4.4     0.8    -      -       -      +
    467D  ALA*     3.3     7.1    -      -       -      +
    468D  VAL*     2.9    44.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 352 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1242C  LYS      3.6    13.3    +      -       -      +
   1243C  MET*     3.6     2.4    -      -       -      +
   1244C  HIS*     2.9    45.9    +      -       +      +
   1268C  GLN*     2.7    42.0    +      -       -      +
    346D  ARG*     5.1     8.7    -      -       -      +
    351D  GLY*     1.3    75.0    -      -       -      +
    353D  SER*     1.3    70.1    +      -       -      +
    372D  MET*     4.5     3.0    -      -       -      +
    447D  ILE*     4.7     1.6    -      -       -      -
    465D  GLN*     3.1    31.1    +      -       +      +
    466D  MET      3.3    20.0    -      -       -      +
    467D  ALA*     4.5     2.5    -      -       +      -
    468D  VAL*     4.2     1.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 353 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1239C  VAL*     4.4     2.4    -      -       -      +
   1242C  LYS*     4.6     7.6    -      -       -      -
   1243C  MET*     4.3     7.5    +      -       -      +
    352D  ARG*     1.3    79.7    -      -       -      +
    354D  VAL*     1.3    82.5    +      -       -      +
    355D  ILE*     4.3     0.2    -      -       -      +
    372D  MET*     4.3     8.5    -      -       -      -
    445D  LYS      3.0    25.9    +      -       -      -
    446D  ALA*     4.1     0.5    -      -       -      -
    447D  ILE*     3.8    19.4    -      -       -      +
    465D  GLN*     3.3     8.5    -      -       -      -
    466D  MET      2.9    33.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 354 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1063C  GLY*     3.6    25.8    -      -       -      +
   1075C  VAL*     5.2     3.4    -      -       +      -
   1237C  HIS*     6.5     0.9    -      -       +      -
   1239C  VAL*     3.5    33.0    -      -       +      -
   1242C  LYS*     4.6    18.8    -      -       +      +
    353D  SER*     1.3    85.2    +      -       -      +
    355D  ILE*     1.3    64.8    +      -       -      +
    446D  ALA*     3.7     2.9    -      -       +      -
    447D  ILE*     3.0    24.4    +      -       -      +
    463D  GLY*     4.5    15.3    -      -       -      +
    464D  ASP      3.9     6.1    -      -       -      +
    465D  GLN*     4.2    17.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 355 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1075C  VAL*     4.2    13.9    -      -       -      +
    353D  SER      4.3     0.7    -      -       -      +
    354D  VAL*     1.3    75.8    -      -       -      +
    356D  THR*     1.3    72.3    +      -       -      +
    447D  ILE*     3.3    16.6    -      -       +      +
    449D  LEU*     4.7     7.0    -      -       +      -
    459D  ALA*     4.1    22.4    -      -       +      -
    460D  ASP      4.0    15.9    -      -       -      +
    461D  PHE*     3.7    33.0    -      -       +      -
    463D  GLY*     5.7     0.3    +      -       -      -
    464D  ASP*     3.3    18.6    +      -       +      +
    466D  MET*     3.3    48.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 356 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    815C  SER*     6.1     0.9    -      -       -      -
   1062C  PRO*     6.0     0.4    -      -       +      -
   1063C  GLY*     4.2     2.5    -      -       -      -
   1075C  VAL*     3.4    28.3    -      -       +      -
   1076C  ILE      4.4     6.7    -      -       -      +
   1077C  SER*     4.5    16.1    +      -       -      +
    354D  VAL      5.0     0.4    -      -       -      +
    355D  ILE*     1.3    81.7    -      -       -      +
    357D  VAL*     1.3    63.2    +      -       -      +
    358D  GLY      5.2     0.2    -      -       -      -
    446D  ALA*     3.6    24.2    -      -       +      +
    447D  ILE      2.6    16.2    +      -       -      -
    448D  GLN*     3.1    18.9    +      -       -      +
    449D  LEU      2.8    25.3    +      -       -      -
    461D  PHE*     3.2    11.1    -      -       -      -
----------------------------------------------------------
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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