Contacts of the strand formed by residues 357 - 363 (chain A) in PDB entry 3KG2


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 THR 357 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246A  GLN      4.8     0.5    -      -       -      +
    247A  ILE*     3.3    21.0    -      -       -      +
    342A  SER      5.2     3.2    +      -       -      +
    343A  GLY*     5.8     5.9    -      -       -      -
    344A  ASN      5.7     2.9    -      -       -      +
    355A  ASN      5.3     0.2    +      -       -      -
    356A  TYR*     1.3    79.2    +      -       -      +
    358A  ILE*     1.3    65.0    +      -       -      +
    359A  ASN*     3.6    20.2    +      -       -      +
    373A  TYR*     3.6    32.4    -      -       +      -
    374A  TRP      3.7     3.6    -      -       -      -
    375A  SER*     5.2     2.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 358 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115A  PRO*     4.6     3.6    -      -       +      -
    116A  ASP      4.1     9.2    -      -       -      +
    117A  LEU*     4.2     2.2    -      -       +      -
    120A  ALA*     4.1    17.7    -      -       +      -
    225A  LEU*     4.0    22.9    -      -       +      -
    245A  PHE*     3.7    37.0    -      -       +      -
    246A  GLN      4.0     8.7    -      -       -      +
    247A  ILE*     4.0     9.9    -      -       +      -
    356A  TYR*     3.6    30.7    -      -       +      -
    357A  THR*     1.3    77.6    -      -       -      +
    359A  ASN*     1.3    65.6    +      -       -      +
    360A  ILE*     3.3     5.7    -      -       -      +
    374A  TRP*     2.8    41.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 359 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245A  PHE*     3.5     3.6    -      -       -      -
    246A  GLN*     2.9    50.7    +      -       +      +
    249A  ASP*     3.5    38.3    +      -       -      +
    357A  THR*     3.6    22.5    -      -       -      +
    358A  ILE*     1.3    72.7    -      -       -      +
    360A  ILE*     1.3    61.9    +      -       -      +
    361A  MET*     3.7    10.2    +      -       -      +
    370A  LYS*     4.5    13.6    -      -       +      +
    372A  GLY      3.5    10.8    -      -       -      +
    373A  TYR*     4.0     4.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 360 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    124A  LEU*     3.8    20.4    -      -       +      -
    128A  TYR*     4.9     1.3    -      -       -      +
    244A  GLY      3.7     6.7    -      -       -      +
    245A  PHE*     4.4    16.8    -      -       +      -
    358A  ILE      3.3    17.0    -      -       -      +
    359A  ASN*     1.3    70.9    -      -       -      +
    361A  MET*     1.3    66.9    +      -       -      +
    370A  LYS*     3.6     3.6    -      -       -      -
    371A  ILE*     3.0    54.4    +      -       +      -
    372A  GLY*     2.8    15.6    +      -       -      +
    373A  TYR*     3.5    21.3    -      -       -      +
    374A  TRP*     3.6    13.0    -      -       +      -
    380A  MET*     3.6    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 361 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    227A  PHE*     3.3    25.6    -      -       +      -
    228A  THR*     4.2    11.9    -      -       +      -
    243A  SER*     3.2     8.0    -      -       -      -
    244A  GLY      3.0    31.0    +      -       -      +
    246A  GLN*     3.6    33.4    -      -       +      +
    359A  ASN*     3.8     8.7    -      -       -      +
    360A  ILE*     1.3    77.1    -      -       -      +
    362A  GLU*     1.3    63.6    +      -       -      +
    368A  PRO*     3.9    14.8    -      -       +      -
    369A  ARG*     3.7    25.4    -      -       -      +
    370A  LYS*     3.7    27.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 362 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127A  TYR*     4.7     2.1    +      -       -      -
    128A  TYR*     2.7    38.9    +      -       -      +
    219A  HIS*     5.4     0.4    +      -       -      -
    227A  PHE*     4.4     4.3    -      -       -      -
    241A  GLU*     5.5     5.3    -      -       -      +
    242A  VAL      3.5     4.0    -      -       -      +
    243A  SER*     3.7     6.5    -      -       -      +
    361A  MET*     1.3    76.1    -      -       -      +
    363A  LEU*     1.3    62.9    +      -       -      +
    364A  LYS*     3.6     2.3    +      -       +      +
    368A  PRO*     3.5     1.0    -      -       -      +
    369A  ARG*     2.9    34.8    +      -       +      +
    371A  ILE*     3.3    36.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 363 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    227A  PHE*     4.1     6.9    -      -       +      -
    232A  LEU*     3.6    23.6    -      -       +      -
    235A  ILE*     3.4    35.4    -      -       +      +
    236A  GLN*     3.6    41.2    -      -       +      +
    240A  ALA      5.4     1.6    -      -       -      +
    241A  GLU*     5.3     3.3    -      -       -      +
    242A  VAL*     2.9    32.5    +      -       +      +
    362A  GLU*     1.3    71.3    -      -       -      +
    364A  LYS*     1.3    58.9    +      -       -      +
    367A  GLY      3.7     3.8    -      -       -      -
    368A  PRO*     3.6    32.3    -      -       +      -
----------------------------------------------------------
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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