Contacts of the strand formed by residues 116 - 119 (chain A) in PDB entry 1LVK


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 TYR 116 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  LEU*     5.0     3.4    -      -       +      -
    109A  ARG*     2.7    33.6    +      -       -      -
    114A  LEU      3.4     0.2    -      -       -      -
    115A  ILE*     1.3    90.1    -      -       +      +
    117A  THR*     1.4    59.9    +      -       -      +
    123A  LEU*     3.9    11.9    -      -       +      -
    124A  VAL      3.3     2.7    -      -       -      -
    125A  ALA*     3.5    26.9    -      -       +      -
    134A  ILE*     3.8    18.4    -      -       +      -
    135A  TYR*     2.7    28.3    +      +       -      -
    153A  PRO*     3.4    27.2    -      -       +      +
    154A  HIS*     3.7    17.7    -      +       -      -
    155A  ILE*     3.4    31.5    -      -       +      +
    188A  ASN*     2.7    30.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88A  VAL      3.8    22.4    -      -       -      +
     89A  GLU      3.8     7.0    -      -       -      +
     90A  ASP      4.5     0.2    -      -       -      +
     91A  MET*     3.8    22.2    -      -       +      -
    105A  ASN*     3.9     4.5    -      -       -      +
    106A  LEU*     3.7    21.3    -      -       -      +
    109A  ARG*     3.0    24.8    +      -       -      +
    114A  LEU      4.6     1.9    +      -       -      -
    115A  ILE      4.8     1.2    +      -       -      -
    116A  TYR*     1.4    74.7    +      -       -      +
    118A  TYR*     1.3    69.5    +      -       -      +
    123A  LEU*     4.0     4.2    -      -       -      +
    124A  VAL*     2.6    44.3    +      -       -      +
    153A  PRO*     4.1     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 118 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89A  GLU*     3.0    26.3    +      -       +      +
     90A  ASP*     3.3     9.7    -      -       +      +
     91A  MET*     2.8    34.0    +      -       -      +
    117A  THR*     1.3    75.4    -      -       -      +
    119A  SER*     1.3    54.6    +      -       -      +
    122A  PHE      3.1    12.3    -      -       -      +
    123A  LEU*     3.7    25.8    -      -       +      -
    124A  VAL*     5.0     0.2    -      -       -      -
    148A  ARG*     3.5    75.5    +      -       +      +
    152A  ALA      4.4     0.5    +      -       -      -
    153A  PRO*     3.7    30.1    -      -       +      +
    157A  ALA*     3.7    24.9    -      -       -      +
    158A  ILE*     4.1    13.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 119 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  ASP*     3.7     2.0    -      -       -      -
     91A  MET*     3.6    17.0    -      -       -      +
     92A  SER*     3.6     0.2    -      -       -      -
    117A  THR      3.9     0.2    +      -       -      -
    118A  TYR*     1.3    75.5    -      -       -      +
    120A  GLY*     1.3    64.7    +      -       -      +
    121A  LEU      3.0     1.0    +      -       -      -
    122A  PHE*     2.7    33.8    +      -       -      +
    124A  VAL*     4.3    18.2    -      -       -      -
    681A  VAL*     4.2    11.0    +      -       -      +
    685A  ILE*     3.5    30.8    -      -       -      +
----------------------------------------------------------
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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