Contacts of the strand formed by residues 342 - 346 (chain C) in PDB entry 1K4R


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 342 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    328C  MET*     5.4     0.4    -      -       -      -
    340C  ILE*     3.2    31.9    +      -       +      +
    341C  PRO*     1.3    71.9    -      -       -      +
    343C  ARG*     1.3    68.3    +      -       -      +
    353C  ASN*     4.5     4.9    +      -       -      -
    355C  ALA*     5.6     0.8    -      -       -      +
    357C  LEU*     4.6    17.4    -      -       +      +
    362C  PRO*     4.2    15.7    -      -       +      -
    372C  ILE*     3.9    22.2    -      -       +      -
    374C  MET*     3.6    29.4    -      -       +      -
    383C  ILE*     5.0     1.3    -      -       +      -
    384C  TYR      3.3     9.6    -      -       -      +
    385C  VAL*     4.1     9.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 343 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341C  PRO      5.3     2.4    +      -       -      +
    342C  VAL*     1.3    79.3    -      -       -      +
    344C  ALA*     1.3    65.8    +      -       -      +
    345C  VAL*     3.7    24.8    -      -       +      +
    350C  PRO      4.0     9.5    +      -       -      -
    353C  ASN*     3.7    28.7    -      -       +      +
    355C  ALA*     4.2     7.2    -      -       -      -
    374C  MET*     5.4     0.7    -      -       -      -
    383C  ILE*     3.8     4.2    -      -       -      +
    384C  TYR*     2.8    72.3    +      -       +      +
    386C  GLY      4.8     5.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 344 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343C  ARG*     1.3    79.6    -      -       -      +
    345C  VAL*     1.3    61.2    -      -       -      +
    353C  ASN*     3.2    10.7    +      -       -      +
    354C  VAL*     2.7    30.5    +      -       +      -
    355C  ALA*     3.8     8.5    -      -       +      +
    374C  MET*     4.7     1.8    -      -       -      -
    376C  LEU*     3.4    33.0    -      -       +      -
    381C  ASN*     5.2     0.9    -      -       +      -
    382C  ILE      3.2    14.1    -      -       -      +
    383C  ILE*     4.2    10.5    -      -       +      -
    384C  TYR*     5.0     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 345 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    343C  ARG*     3.7    19.5    -      -       +      +
    344C  ALA*     1.3    77.8    -      -       -      +
    346C  ALA*     1.3    67.0    +      -       -      +
    349C  SER      3.5    11.0    -      -       -      +
    350C  PRO*     3.5    33.2    -      -       +      +
    352C  VAL      3.7    14.6    -      -       -      +
    353C  ASN*     4.8     1.8    -      -       -      -
    354C  VAL*     4.0     5.8    -      -       -      -
    381C  ASN*     3.2     3.8    -      -       -      +
    382C  ILE*     2.9    41.6    +      -       +      +
    384C  TYR*     4.0    20.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 346 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    345C  VAL*     1.3    79.6    -      -       -      +
    347C  HIS*     1.3    69.4    +      -       -      +
    348C  GLY      3.1     0.7    +      -       -      -
    349C  SER*     3.0    33.7    +      -       -      +
    352C  VAL      4.5     0.2    +      -       -      -
    354C  VAL*     4.0    17.8    -      -       +      +
    377C  PRO*     5.6     3.1    -      -       +      -
    380C  ASP      3.7     7.4    -      -       -      +
    381C  ASN*     3.9     9.9    -      -       -      +
----------------------------------------------------------
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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