Contacts of the strand formed by residues 376 - 381 (chain A) in PDB entry 4PKO


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 376 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169A  VAL*     4.3     1.3    -      -       -      -
    174A  VAL*     3.5    28.7    -      -       +      -
    176A  THR*     5.4     4.5    -      -       +      +
    189A  VAL*     3.9     3.1    -      -       -      +
    190A  VAL*     3.0    39.8    +      -       +      +
    192A  GLY      5.1     4.0    +      -       -      +
    194A  GLN*     4.6    28.5    -      -       +      +
    370A  ALA*     5.2     1.1    -      -       +      +
    371A  LYS*     4.9    23.8    -      -       +      +
    375A  GLY*     1.3    75.8    -      -       -      -
    377A  ALA*     1.3    72.3    +      -       -      +
    378A  VAL*     4.6    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 377 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165A  ALA*     4.4    13.2    -      -       +      -
    169A  VAL*     3.8    19.7    -      -       +      -
    174A  VAL      2.9    13.4    +      -       -      +
    175A  ILE*     3.2    19.7    -      -       +      -
    176A  THR*     3.1    21.3    +      -       -      -
    187A  LEU*     4.9     4.0    -      -       +      -
    188A  ASP      3.6     9.2    -      -       -      +
    189A  VAL*     4.6     3.4    -      -       +      +
    375A  GLY      4.0     0.2    +      -       -      -
    376A  VAL*     1.3    78.8    -      -       -      +
    378A  VAL*     1.3    66.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 378 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176A  THR*     3.0    23.3    -      -       -      +
    178A  GLU*     3.9    23.3    -      -       -      +
    187A  LEU*     4.0     0.7    -      -       -      +
    188A  ASP*     2.9    60.8    +      -       +      +
    190A  VAL*     5.3    10.3    -      -       +      -
    194A  GLN*     5.9     3.4    -      -       -      +
    376A  VAL*     4.6    11.4    -      -       +      +
    377A  ALA*     1.3    77.2    -      -       -      +
    379A  ILE*     1.3    64.1    +      -       -      +
    380A  LYS*     4.0     3.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 379 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161A  LEU*     4.4    17.0    -      -       +      +
    162A  ILE*     4.2    32.8    -      -       +      +
    165A  ALA*     4.9     1.1    -      -       +      -
    175A  ILE*     3.6    27.6    -      -       +      -
    176A  THR      2.8    13.0    +      -       -      +
    177A  VAL*     3.4     9.5    -      -       +      +
    178A  GLU*     3.1    24.3    +      -       -      +
    185A  ASP*     5.7     1.6    -      -       +      -
    186A  GLU      3.7     9.4    -      -       -      +
    187A  LEU*     4.1    17.5    -      -       +      -
    378A  VAL*     1.3    75.5    -      -       -      +
    380A  LYS*     1.3    69.9    +      -       -      +
    381A  VAL*     3.7     4.0    +      -       +      +
    396A  VAL*     4.5    22.0    -      -       +      -
    400A  LEU*     5.1     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 380 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178A  GLU*     3.3    44.0    -      -       +      +
    179A  ASP      4.9     2.7    -      -       -      +
    181A  THR*     3.1    40.6    +      -       +      +
    184A  GLN      4.0     2.4    -      -       -      +
    185A  ASP*     3.5     2.4    -      -       -      +
    186A  GLU*     3.0    45.2    +      -       +      +
    188A  ASP*     3.5    26.3    +      -       -      +
    378A  VAL*     4.0     4.4    +      -       -      +
    379A  ILE*     1.3    73.9    -      -       -      +
    381A  VAL*     1.3    62.2    +      -       -      +
    382A  GLY      3.7     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 381 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177A  VAL*     5.7     1.3    -      -       +      -
    178A  GLU      3.1    16.4    +      -       -      +
    179A  ASP*     4.4     1.3    -      -       -      -
    180A  GLY*     2.6    32.5    +      -       -      -
    181A  THR      4.9     0.4    -      -       -      -
    185A  ASP*     3.6    14.4    -      -       -      +
    379A  ILE*     3.7     6.3    +      -       +      +
    380A  LYS*     1.3    71.6    -      -       -      +
    382A  GLY*     1.3    57.8    +      -       -      +
    389A  MET*     3.5    10.3    -      -       -      +
    392A  LYS*     3.3    35.0    -      -       +      -
    393A  LYS*     4.0    28.9    -      -       +      -
    396A  VAL*     3.7    27.4    -      -       +      -
----------------------------------------------------------
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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