Contacts of the strand formed by residues 302 - 306 (chain F) in PDB entry 1K9V


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 ARG 302 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301F  MET*     1.3    94.3    -      -       +      +
    303F  ILE*     1.3    62.1    +      -       -      +
    331F  SER*     3.7    15.9    +      -       -      -
    333F  GLU*     3.3    32.6    +      -       +      -
    340F  ASN*     4.8     1.0    -      -       -      +
    341F  ASP*     2.7    49.4    +      -       -      +
    342F  LEU      3.3    14.3    +      -       -      -
    343F  TYR*     3.2    30.4    -      -       +      +
    344F  ASP*     2.7    29.9    +      -       -      -
    345F  LEU      3.3     2.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 303 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301F  MET      5.1     2.0    -      -       -      +
    302F  ARG*     1.3    74.6    -      -       -      +
    304F  GLY*     1.3    64.1    +      -       -      +
    305F  ILE*     4.5     1.1    -      -       +      -
    320F  VAL*     4.1    20.0    -      -       +      -
    324F  SER*     4.5     1.6    -      -       -      -
    330F  VAL*     3.6    28.0    -      -       +      -
    331F  SER      2.6    16.4    +      -       -      +
    332F  ILE*     3.3    11.1    -      -       +      -
    333F  GLU*     2.9    24.6    +      -       -      +
    343F  TYR*     3.6     4.9    -      -       -      -
    345F  LEU*     3.3    33.0    -      -       +      +
    347F  PHE*     3.8    26.2    -      -       +      -
    494F  ILE*     4.1    19.3    -      -       +      -
    497F  SER*     5.8     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 304 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303F  ILE*     1.3    74.1    -      -       -      +
    305F  ILE*     1.3    66.2    +      -       -      +
    333F  GLU      3.4     5.4    -      -       -      -
    335F  VAL*     4.0     4.5    -      -       -      -
    343F  TYR*     3.5    22.8    -      -       -      -
    345F  LEU      2.7    13.8    +      -       -      +
    346F  LEU*     3.4     8.0    -      -       -      -
    347F  PHE*     2.7    28.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 305 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303F  ILE*     4.5     2.0    -      -       +      -
    304F  GLY*     1.3    78.2    -      -       -      +
    306F  ILE*     1.3    71.9    +      -       -      +
    307F  SER*     3.1     2.3    +      -       -      -
    313F  ILE*     4.8    13.9    -      -       +      +
    316F  LEU*     3.8    31.6    -      -       +      -
    317F  TYR*     3.8    34.8    -      -       +      -
    320F  VAL*     4.1    14.1    -      -       +      -
    332F  ILE*     4.1     8.7    -      -       +      -
    333F  GLU      2.9    14.8    +      -       -      +
    334F  LEU*     3.3     9.2    -      -       +      -
    335F  VAL*     2.8    24.2    +      -       -      +
    347F  PHE*     3.8    15.5    -      -       +      -
    349F  PRO*     4.2     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 306 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    305F  ILE*     1.3    71.2    -      -       -      +
    307F  SER*     1.3    62.9    +      -       -      +
    308F  VAL*     3.9    14.4    -      -       +      +
    309F  GLY*     4.5     4.2    +      -       -      +
    313F  ILE*     4.0     2.3    -      -       -      +
    335F  VAL*     3.4    15.9    -      -       +      +
    346F  LEU*     4.0    17.0    -      -       +      -
    347F  PHE      3.0    15.1    +      -       -      +
    348F  ILE*     4.0    18.2    -      -       +      -
    349F  PRO*     3.2    29.6    -      -       +      +
    361F  LEU*     4.0    17.5    -      -       +      -
    366F  LEU*     3.8    27.6    -      -       +      -
    369F  PHE*     5.7     0.9    -      -       +      -
    370F  VAL*     3.8    29.2    -      -       +      -
----------------------------------------------------------
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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