Contacts of the strand formed by residues 298 - 302 (chain B) in PDB entry 4KPF


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 ILE 298 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    254B  ILE      3.4     2.9    -      -       -      +
    255B  VAL*     3.3     4.8    -      -       -      -
    256B  ILE*     2.8    59.6    +      -       +      +
    259B  ILE*     4.7    13.5    -      -       +      -
    265B  LYS*     4.2    16.6    -      -       +      -
    268B  LEU*     4.9     9.4    -      -       +      -
    269B  VAL*     3.7    35.4    -      -       +      -
    272B  ILE*     5.3     2.7    -      -       +      -
    287B  VAL*     4.5    11.2    -      -       +      -
    288B  ARG      3.5    11.4    -      -       -      +
    289B  ASP*     4.5     7.0    -      -       -      +
    296B  LEU*     4.4     6.3    -      -       +      -
    297B  ARG*     1.3    80.2    -      -       -      +
    299B  ALA*     1.3    60.5    +      -       -      +
    300B  ILE*     3.7     9.5    +      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 299 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    253B  GLN*     4.6    15.9    -      -       -      +
    254B  ILE      3.6     3.4    -      -       -      -
    255B  VAL*     4.6     5.6    -      -       -      +
    286B  GLU      3.8     1.6    -      -       -      +
    287B  VAL*     3.7     3.1    -      -       -      +
    288B  ARG*     3.0    44.2    +      -       -      +
    290B  GLU*     5.0     8.6    -      -       -      +
    297B  ARG*     4.1     5.1    +      -       -      +
    298B  ILE*     1.3    71.0    -      -       -      +
    300B  ILE*     1.3    62.0    +      -       -      +
    301B  GLU      3.6     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 300 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    253B  GLN*     4.3     0.4    -      -       -      +
    254B  ILE*     2.7    45.2    +      -       +      +
    256B  ILE*     4.0    16.4    -      -       +      -
    272B  ILE*     3.9    26.5    -      -       +      -
    284B  ILE*     4.1    35.9    -      -       +      -
    286B  GLU      3.8     2.9    -      -       -      -
    287B  VAL*     4.4     9.6    -      -       +      +
    298B  ILE*     4.4    11.7    -      -       +      +
    299B  ALA*     1.3    74.8    -      -       -      +
    301B  GLU*     1.3    62.9    +      -       -      +
    302B  LEU*     3.5     8.4    +      -       +      +
    311B  VAL*     5.0     3.8    -      -       +      -
    315B  LEU*     3.6    26.5    -      -       +      -
    321B  LEU*     5.0     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 301 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    247B  LEU*     3.6    20.7    -      -       +      +
    251B  LYS*     6.0     1.1    -      -       -      -
    252B  GLU      3.9     1.6    -      -       -      -
    253B  GLN*     3.7    18.9    -      -       +      +
    284B  ILE*     4.1     2.3    -      -       -      +
    285B  ALA*     3.0    32.7    +      -       +      +
    286B  GLU*     3.1    27.1    +      -       +      +
    288B  ARG*     3.0    30.7    +      -       -      +
    299B  ALA      3.6     1.8    -      -       -      -
    300B  ILE*     1.3    74.7    -      -       -      +
    302B  LEU*     1.3    62.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 302 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    251B  LYS*     4.0    12.1    -      -       -      +
    252B  GLU*     3.0    51.6    +      -       +      +
    253B  GLN*     3.8     3.4    -      -       -      +
    254B  ILE*     4.1    17.3    -      -       +      +
    283B  GLY      3.1    13.5    -      -       -      +
    284B  ILE*     4.5     2.5    -      -       +      -
    285B  ALA*     3.6     8.0    -      -       -      +
    300B  ILE*     3.5    15.0    -      -       +      +
    301B  GLU*     1.3    77.4    -      -       -      +
    303B  LYS*     1.3    70.6    +      -       -      +
    306B  ALA*     4.4     6.3    -      -       +      -
    308B  THR*     4.3    16.6    -      -       +      -
    311B  VAL*     3.5    44.0    -      -       +      -
----------------------------------------------------------
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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