Contacts of the strand formed by residues 111 - 119 (chain C) in PDB entry 1KWV


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 PHE 111 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98B  LEU*     4.8     4.0    -      -       +      -
    100C  ALA*     4.2     9.6    -      -       +      -
    103C  MET*     3.3    43.7    -      -       +      -
    104C  GLY      5.3     0.7    -      -       -      -
    105C  LYS*     3.3    50.0    -      -       +      +
    109C  LYS      3.7     0.2    +      -       -      -
    110C  LYS*     1.3    76.7    -      -       -      +
    112C  PHE*     1.3    66.4    +      -       -      +
    113C  VAL*     3.2    30.3    -      -       +      -
    217C  CYS      3.9     0.5    -      -       -      +
    218C  GLU*     3.6     2.6    -      -       -      -
    219C  PHE*     3.1    70.4    +      +       +      +
    220C  PRO      5.1     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 112 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103C  MET      5.2     3.8    -      -       -      +
    110C  LYS*     3.3    37.2    -      -       +      -
    111C  PHE*     1.3    77.8    -      -       -      +
    113C  VAL*     1.3    68.3    +      -       -      +
    136C  ALA*     3.8    14.6    -      -       +      -
    137C  ILE      4.4     2.0    -      -       -      -
    143C  GLU*     4.1    11.7    -      -       +      -
    146C  ALA*     4.0    25.4    -      -       +      -
    147C  ILE*     3.8    34.8    -      -       +      -
    150C  VAL*     3.8    31.0    -      -       +      +
    216C  VAL*     4.0     9.4    -      -       +      -
    217C  CYS      3.4     2.7    -      -       -      -
    218C  GLU*     3.6    40.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 113 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98B  LEU*     4.9     1.6    -      -       +      -
    101B  PHE*     3.5    17.0    -      -       +      -
    102B  SER*     3.7    36.8    -      -       -      -
    103C  MET*     4.1     9.4    -      -       +      +
    111C  PHE*     3.2    38.6    -      -       +      -
    112C  PHE*     1.3    78.3    -      -       -      +
    114C  THR*     1.3    65.8    +      -       -      +
    150C  VAL*     4.2     4.9    -      -       -      -
    216C  VAL*     3.4     2.4    -      -       -      -
    217C  CYS      2.9    31.0    +      -       -      -
    219C  PHE*     4.1    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 114 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101B  PHE*     3.7    13.4    -      -       -      +
    102B  SER      4.1     7.6    -      -       -      +
    113C  VAL*     1.3    79.5    -      -       -      +
    115C  ASN*     1.3    61.5    +      -       -      +
    116C  HIS*     3.0    36.3    +      -       +      +
    150C  VAL*     3.6    31.8    -      -       +      +
    151C  ALA*     4.8     1.6    -      -       -      -
    214C  THR*     3.3    10.7    -      -       -      +
    215C  ALA      2.6    24.7    +      -       -      -
    216C  VAL*     4.1    10.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 115 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101B  PHE*     3.1    49.0    -      -       +      +
    104B  GLY*     3.9    10.2    -      -       -      -
    105B  LYS      2.9    26.9    +      -       -      +
    106B  LYS*     3.2    22.6    +      -       -      +
    107B  SER      4.5     0.6    -      -       -      +
    114C  THR*     1.3    73.5    +      -       -      +
    116C  HIS*     1.3    70.7    +      -       -      +
    117C  GLU*     3.0    44.6    +      -       -      +
    119C  MET*     4.8     0.2    -      -       -      +
    127C  LEU*     4.7     3.4    -      -       -      +
    215C  ALA*     4.3     4.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 116 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104B  GLY*     5.6     4.0    -      -       -      -
    106B  LYS*     4.1     9.3    -      -       -      +
    114C  THR*     3.0    37.5    +      -       +      +
    115C  ASN*     1.3    83.6    -      -       -      +
    117C  GLU*     1.3    60.9    +      -       -      +
    118C  ARG*     3.9     8.3    +      -       -      +
    150C  VAL      3.9    11.7    -      -       -      -
    151C  ALA      4.3     9.7    +      -       -      -
    152C  LYS*     4.2    21.4    -      -       +      +
    214C  THR*     4.2     9.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 117 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106B  LYS*     3.5    20.9    -      -       +      +
    107B  SER*     3.0    47.8    +      -       -      +
    114C  THR*     4.5     0.2    +      -       -      -
    115C  ASN*     3.0    27.7    +      -       -      +
    116C  HIS*     1.3    78.1    -      -       -      +
    118C  ARG*     1.3    70.8    +      -       -      +
    119C  MET*     3.3    21.1    -      -       +      +
    214C  THR*     3.3     1.3    -      -       -      -
    215C  ALA*     2.9    29.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 118 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116C  HIS      3.9     6.7    +      -       -      +
    117C  GLU*     1.3    80.8    -      -       -      +
    119C  MET*     1.3    63.7    +      -       -      +
    153C  THR*     3.4    15.8    +      -       -      +
    154C  SER*     2.7    35.4    +      -       -      -
    212C  SER*     3.4    22.1    +      -       -      -
    213C  HIS*     3.0    30.4    +      -       -      +
    214C  THR*     2.9    32.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 119 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107B  SER*     4.2     4.5    -      -       -      +
    117C  GLU*     3.3    48.0    -      -       +      +
    118C  ARG*     1.3    75.6    -      -       -      +
    120C  PRO*     1.3    77.9    -      -       +      +
    123C  LYS*     3.8    35.9    -      -       +      +
    124C  VAL*     3.4    22.9    -      -       +      -
    127C  LEU*     4.0    15.0    -      -       +      -
    156C  PHE*     3.2     6.1    -      -       -      -
    212C  SER*     3.6    10.5    -      -       -      -
    213C  HIS      2.9    26.9    +      -       -      +
    215C  ALA*     3.9    16.2    -      -       +      -
----------------------------------------------------------
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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