Contacts of the strand formed by residues 395 - 399 (chain B) 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 VAL 395 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    393B  LYS      3.6     4.9    +      -       -      +
    394B  THR*     1.3    70.6    -      -       -      +
    396B  VAL*     1.3    62.9    +      -       -      +
    397B  VAL*     4.4     0.4    -      -       +      -
    438B  PHE*     3.5    41.1    -      -       +      -
    439B  LYS      2.8    15.4    +      -       -      +
    440B  TYR*     3.1     5.4    -      -       -      +
    441B  LYS*     3.0    24.1    +      -       -      -
    473B  ASP*     3.6    26.7    -      -       +      +
    474B  ILE*     3.9    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 396 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    394B  THR*     4.1    10.8    -      -       -      +
    395B  VAL*     1.3    72.3    -      -       -      +
    397B  VAL*     1.3    60.8    +      -       -      +
    441B  LYS*     4.2     7.6    -      -       +      +
    443B  THR*     3.9    25.4    -      -       +      +
    471B  LYS      3.8    20.4    -      -       -      +
    472B  ALA*     3.7     9.3    -      -       +      +
    473B  ASP*     2.9    39.0    +      -       -      +
    474B  ILE      3.3     9.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 397 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    395B  VAL*     3.9     3.4    -      -       +      +
    396B  VAL*     1.3    71.4    -      -       -      +
    398B  THR*     1.3    66.4    +      -       -      +
    399B  THR*     4.8     0.6    -      -       -      +
    438B  PHE*     4.8     2.9    -      -       +      -
    440B  TYR*     3.5    33.9    -      -       +      -
    441B  LYS      3.3     9.3    +      -       -      +
    442B  LEU*     3.7    24.3    -      -       +      +
    443B  THR*     2.9    31.1    +      -       -      +
    474B  ILE*     3.5    22.4    -      -       +      +
    476B  ILE*     3.8    40.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 398 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    396B  VAL      3.8     1.4    +      -       -      -
    397B  VAL*     1.3    73.4    -      -       -      +
    399B  THR*     1.3    63.9    +      -       -      +
    443B  THR*     3.4    10.9    +      -       -      -
    445B  VAL*     4.0     7.8    +      -       -      +
    463B  MET*     3.7    29.7    -      -       +      +
    466B  GLU*     3.3    17.8    +      -       -      +
    467B  LEU*     4.5     1.6    -      -       +      -
    472B  ALA*     3.8    22.2    -      -       +      -
    474B  ILE      2.9    20.8    +      -       -      +
    475B  ALA*     3.5    18.4    -      -       +      +
    476B  ILE      3.2    21.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 399 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    397B  VAL*     4.8     4.9    -      -       -      +
    398B  THR*     1.3    78.2    +      -       -      +
    400B  ILE*     1.3    66.7    +      -       -      +
    406B  VAL*     3.2    29.9    -      -       +      +
    421B  TYR*     6.3     0.4    -      -       +      -
    442B  LEU*     5.0    14.1    -      -       +      -
    443B  THR      3.0    18.3    +      -       -      +
    444B  ILE*     3.3    22.2    -      -       +      +
    445B  VAL      3.1    22.0    +      -       -      -
    463B  MET*     3.6    12.6    -      -       -      -
    476B  ILE      3.1    20.8    +      -       -      -
    477B  ALA*     3.6     5.1    -      -       -      +
----------------------------------------------------------
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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