Contacts of the strand formed by residues 157 - 160 (chain N) in PDB entry 3KYM


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 157 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79C  GLN*     6.2     2.0    -      -       -      +
    156N  VAL*     1.3    76.0    -      -       -      +
    158N  VAL*     1.3    62.6    +      -       -      +
    159N  SER*     3.9    15.3    -      -       -      +
    203N  ASN      3.3     4.4    -      -       -      +
    204N  VAL*     3.6     0.3    -      -       -      -
    205N  ASP*     3.0    51.5    +      -       -      +
    207N  LYS*     5.3     7.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 158 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148N  VAL*     5.5     2.5    -      -       +      -
    156N  VAL*     3.6    14.5    +      -       +      +
    157N  THR*     1.3    76.0    -      -       -      +
    159N  SER*     1.3    72.3    +      -       -      +
    160N  TRP*     4.6     3.4    -      -       -      +
    171N  THR*     3.5    37.2    +      -       +      +
    184N  LEU*     4.5    11.7    -      -       +      -
    186N  SER*     3.7    24.0    -      -       -      +
    202N  CYS*     4.5     9.2    -      -       -      -
    203N  ASN      3.2     7.2    -      -       -      +
    204N  VAL*     4.5    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 159 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157N  THR*     3.9    16.1    -      -       -      +
    158N  VAL*     1.3    77.4    +      -       -      +
    160N  TRP*     1.3    78.0    +      -       -      +
    163N  GLY*     3.6    28.5    -      -       -      -
    202N  CYS*     3.9     0.7    -      -       -      -
    203N  ASN*     3.1    41.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 160 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130N  LEU*     2.5    40.8    -      -       +      -
    144N  LEU      4.2     5.4    -      -       -      -
    146N  CYS*     4.2     3.8    -      -       -      -
    158N  VAL*     4.6     2.3    -      -       +      +
    159N  SER*     1.3    91.1    +      -       -      +
    161N  ASN*     1.3    72.9    -      -       -      +
    162N  SER      3.0     3.7    +      -       -      -
    163N  GLY*     4.8     0.2    -      -       -      -
    164N  ALA      3.4    15.6    +      -       -      +
    165N  LEU*     3.5    31.6    +      -       +      +
    169N  VAL*     3.4    27.7    -      -       +      +
    171N  THR*     5.7     1.1    -      -       -      -
    186N  SER*     3.3    37.4    +      -       -      -
    188N  VAL*     4.3    23.5    -      -       +      +
    200N  TYR*     4.5     8.5    -      +       +      -
    201N  THR      3.4    24.7    -      -       -      -
    202N  CYS*     3.8    20.0    -      -       -      -
    203N  ASN*     3.4     2.2    -      -       -      -
    217N  VAL*     4.5     9.2    -      -       +      -
----------------------------------------------------------
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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