Contacts of the strand formed by residues 456 - 460 (chain A) in PDB entry 3K72


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 456 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    445A  SER*     3.5     1.0    -      -       -      -
    446A  VAL*     3.1    54.5    +      -       +      +
    448A  VAL*     4.3    12.3    -      -       +      -
    454A  THR*     3.5     3.6    -      -       -      +
    455A  ASP*     1.3    79.5    -      -       -      +
    457A  VAL*     1.3    77.1    +      -       -      +
    458A  LEU*     4.3     9.0    -      -       +      -
    475A  VAL*     3.9    20.0    -      -       +      -
    476A  CYS      4.2     0.2    -      -       -      -
    477A  PRO*     3.5    24.2    -      -       +      -
    478A  LEU*     4.2     1.8    -      -       -      +
    542A  GLY      3.8    11.4    -      -       -      +
    543A  PRO*     3.9     3.1    -      -       +      -
    544A  SER      3.7    33.0    -      -       -      +
    545A  ILE*     4.9     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 457 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    391A  GLU*     6.4     1.1    -      -       +      -
    393A  ALA*     5.3     2.5    -      -       +      -
    402A  VAL*     5.3    11.4    -      -       +      -
    416A  ILE*     5.8     1.6    -      -       +      -
    443A  LEU*     4.3    17.7    -      -       +      -
    444A  CYS      3.6     9.2    -      -       -      +
    445A  SER*     3.9    17.7    -      -       -      +
    456A  LEU*     1.3    84.0    -      -       -      +
    458A  LEU*     1.3    79.2    +      -       -      +
    459A  ILE*     4.7     4.7    -      -       +      -
    474A  SER      3.6     0.2    -      -       -      +
    476A  CYS*     2.8    45.1    +      -       +      +
    478A  LEU*     3.5    26.9    -      -       +      -
    485A  TRP*     5.1     7.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 458 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    443A  LEU*     3.2    19.5    -      -       -      -
    444A  CYS*     2.9    38.1    +      -       +      +
    446A  VAL*     4.9     2.9    -      -       +      -
    456A  LEU*     4.3     9.6    -      -       +      -
    457A  VAL*     1.3    77.7    -      -       -      +
    459A  ILE*     1.3    68.7    +      -       -      +
    473A  VAL*     4.2    16.4    -      -       +      -
    474A  SER      3.3     2.9    -      -       -      +
    475A  VAL*     4.0    31.9    -      -       +      +
    506A  LEU*     4.4    15.9    -      -       +      -
    520A  VAL*     4.4    33.2    -      -       +      -
    522A  ILE*     5.0     4.3    -      -       +      -
    545A  ILE*     4.9    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 459 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    414A  ALA*     3.9    14.4    -      -       +      -
    439A  PHE*     3.2    53.8    -      -       +      -
    440A  GLY*     3.8    13.7    -      -       -      +
    442A  SER*     3.1    11.0    -      -       -      +
    443A  LEU*     4.0    12.8    -      -       +      -
    457A  VAL*     4.6     3.4    -      -       +      +
    458A  LEU*     1.3    81.4    -      -       -      +
    460A  GLY*     1.3    68.0    +      -       -      +
    473A  VAL*     3.0    13.8    -      -       -      +
    474A  SER*     2.9    32.4    +      -       -      +
    476A  CYS*     3.8     3.4    -      -       +      -
    485A  TRP*     4.7     4.5    -      -       +      -
    487A  CYS*     3.3    22.9    -      -       -      -
    506A  LEU*     5.1     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 460 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    438A  TYR      3.1     1.7    -      -       -      +
    439A  PHE*     3.6     0.9    -      -       -      -
    440A  GLY      3.0    25.8    +      -       -      -
    441A  ALA*     3.4     3.7    +      -       -      -
    442A  SER*     2.8    23.9    +      -       -      -
    459A  ILE*     1.3    77.0    -      -       -      +
    461A  ALA*     1.3    63.7    +      -       -      +
    462A  PRO*     3.7     4.5    -      -       -      -
    472A  GLN      3.6     3.1    -      -       -      -
    473A  VAL*     4.7     0.9    -      -       -      -
    503A  GLY*     3.9    15.7    -      -       -      -
    506A  LEU*     5.4     0.2    -      -       -      -
----------------------------------------------------------
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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