Contacts of the strand formed by residues 587 - 593 (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 LEU 587 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149C  LEU*     6.0     0.9    -      -       +      -
    448C  LEU*     4.7    14.0    +      -       +      -
    451C  ARG      5.3     2.7    +      -       -      +
    453C  ILE*     3.2    37.2    -      -       +      -
    557C  ARG*     3.3    38.4    +      -       +      +
    558C  VAL*     3.7    30.1    -      -       +      -
    575C  LEU*     3.7    24.5    -      -       +      -
    579C  ALA*     4.8     2.5    -      -       +      -
    580C  GLN      3.3    19.3    -      -       -      +
    581C  THR*     4.7     3.6    -      -       -      +
    586C  PHE*     1.3    77.2    -      -       -      +
    588C  GLU*     1.3    60.1    +      -       -      +
    607C  SER*     3.4    15.1    -      -       -      -
    608C  ALA      4.0     1.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 588 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    557C  ARG*     4.3     3.8    -      -       -      +
    579C  ALA*     3.7     4.2    -      -       -      +
    580C  GLN*     3.2    48.8    +      -       +      +
    581C  THR      4.0     5.3    -      -       -      +
    582C  ASN*     3.1    45.4    +      -       -      +
    583C  GLU      5.1     0.2    +      -       -      -
    587C  LEU*     1.3    74.8    -      -       -      +
    589C  THR*     1.3    61.2    +      -       -      +
    605C  TYR*     3.7    30.1    -      -       +      +
    606C  LEU      3.1    22.7    -      -       -      +
    607C  SER*     3.9     4.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 589 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    555C  TYR      4.7     2.7    -      -       -      +
    556C  GLY*     3.3    27.0    +      -       -      +
    557C  ARG*     4.2     9.2    -      -       +      +
    578C  TYR*     4.9     1.7    -      -       -      +
    579C  ALA*     5.0     0.7    -      -       -      +
    588C  GLU*     1.3    75.6    -      -       -      +
    590C  PRO*     1.3    73.7    -      -       -      +
    591C  TYR*     3.3    37.8    -      -       +      +
    604C  HIS      3.7     0.3    -      -       -      +
    605C  TYR*     3.9     3.8    -      -       -      -
    606C  LEU      2.9    30.8    +      -       -      +
    611C  GLU*     4.2     5.4    -      -       -      +
    659C  GLN*     3.3    17.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 590 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22C  LEU*     3.7    21.3    -      -       +      -
    578C  TYR*     3.7    24.0    -      -       +      +
    589C  THR*     1.3    94.0    +      -       -      +
    591C  TYR*     1.3    65.9    +      -       -      +
    603C  ILE*     3.4    22.7    -      -       +      -
    604C  HIS      3.5     6.7    -      -       -      +
    605C  TYR*     3.5    27.1    -      -       +      -
    655C  VAL*     3.6    16.8    -      -       +      +
    659C  GLN*     3.5    15.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 591 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    555C  TYR*     4.4     5.7    +      -       -      -
    589C  THR*     3.3    38.1    -      -       +      +
    590C  PRO*     1.3    76.2    -      -       -      +
    592C  ARG*     1.3    64.0    +      -       -      +
    593C  LYS      3.8     0.2    +      -       -      -
    603C  ILE*     3.4     5.6    -      -       -      -
    604C  HIS*     2.9    34.4    +      -       -      +
    606C  LEU*     3.8    27.8    -      -       +      -
    611C  GLU*     3.0    28.6    +      -       -      -
    616C  ILE*     3.7    18.2    -      -       +      -
    637C  ARG*     3.1    17.9    +      -       -      -
    652C  TYR*     3.9    20.4    -      -       +      -
    653C  MET      3.5    14.6    -      -       -      +
    654C  ASP*     3.3    25.8    -      -       -      -
    655C  VAL      4.6     2.0    -      -       -      +
    659C  GLN*     3.7    10.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 592 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19C  PRO      5.2     2.0    +      -       -      -
     21C  VAL*     3.7    41.9    -      -       +      +
    591C  TYR*     1.3    75.6    -      -       -      +
    593C  LYS*     1.3    62.3    -      -       -      +
    594C  VAL*     4.0     0.7    -      -       -      +
    599C  VAL*     4.2    12.9    +      -       +      +
    600C  THR      3.8    16.9    +      -       -      +
    601C  ASP*     3.3    26.3    +      -       -      +
    602C  GLU      3.7     6.7    -      -       -      +
    603C  ILE*     4.8     5.8    -      -       +      +
    623C  LEU*     4.2    24.5    -      -       -      +
    652C  TYR*     3.1    10.1    -      -       -      -
    653C  MET*     2.8    48.3    +      -       +      +
    654C  ASP      3.8    14.8    +      -       -      -
    655C  VAL*     4.0    17.6    +      -       +      +
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Residues in contact with LYS 593 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    591C  TYR      3.8     1.2    +      -       -      -
    592C  ARG*     1.3    75.5    -      -       -      +
    594C  VAL*     1.3    79.8    +      -       -      +
    595C  THR*     4.5     8.7    -      -       +      -
    599C  VAL*     3.7     3.3    -      -       -      +
    600C  THR*     3.2    45.5    +      -       +      +
    602C  GLU*     3.1    17.1    +      -       +      +
    604C  HIS*     3.7    30.3    -      -       +      -
    614C  TYR*     6.1     1.4    -      -       -      -
    651C  ASP*     4.0     9.6    +      -       -      +
    652C  TYR*     3.7    31.6    +      -       +      -
----------------------------------------------------------
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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