Contacts of the strand formed by residues 91 - 99 (chain C) in PDB entry 5LK5


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 LEU 91 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22C  TYR*     5.1     0.2    -      -       +      -
     84C  PHE*     3.6    33.7    -      -       +      -
     86C  ASN*     3.9    19.7    -      -       +      +
     89C  GLN      3.7     0.6    +      -       -      -
     90C  THR*     1.3    73.8    -      -       -      +
     92C  VAL*     1.3    64.9    +      -       -      +
     93C  VAL*     4.3     9.2    -      -       +      -
    112C  LEU*     4.1     9.9    -      -       +      -
    130C  ILE*     3.9    27.8    -      -       +      -
    174C  LEU*     3.7     1.6    -      -       +      +
    175C  ILE*     3.5     2.3    -      -       -      -
    176C  VAL*     2.8    50.9    +      -       +      +
    311C  PHE*     3.9    18.6    -      -       +      -
    332C  ILE*     3.8    17.3    -      -       +      -
    333C  THR      3.8     3.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 92 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90C  THR*     4.0    17.3    -      -       +      -
     91C  LEU*     1.3    78.9    -      -       -      +
     93C  VAL*     1.3    66.9    +      -       -      +
     94C  GLN*     4.7     2.5    -      -       +      -
    173C  THR*     3.8    17.5    -      -       +      -
    174C  LEU      3.3     9.9    -      -       -      +
    175C  ILE*     4.0    15.7    -      -       +      -
    331C  LEU      3.7     1.1    -      -       -      +
    332C  ILE*     3.3     9.2    -      -       -      +
    333C  THR*     2.8    49.8    +      -       +      +
    335C  ASP      4.1     4.7    -      -       -      +
    336C  GLU*     4.0    17.7    -      -       -      +
    339C  ALA*     3.7    23.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 93 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91C  LEU*     4.3    13.5    -      -       +      -
     92C  VAL*     1.3    75.2    -      -       -      +
     94C  GLN*     1.3    63.6    +      -       -      +
     95C  PHE*     4.7     4.5    -      -       +      -
    110C  VAL*     4.0    27.6    -      -       +      -
    112C  LEU*     3.4    35.0    -      -       +      -
    130C  ILE*     5.8     1.8    -      -       +      -
    132C  PHE*     3.9    11.2    -      -       +      -
    172C  TYR      3.8     0.7    -      -       -      +
    173C  THR*     3.4     2.4    -      -       -      +
    174C  LEU*     2.8    56.3    +      -       +      +
    314C  LEU*     5.0     2.7    -      -       +      -
    331C  LEU      3.6     4.7    -      -       -      +
    332C  ILE*     4.8     7.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 94 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92C  VAL*     4.7     4.9    -      -       +      -
     93C  VAL*     1.3    78.3    -      -       -      +
     95C  PHE*     1.3    70.4    +      -       -      +
    171C  LEU*     3.7    20.9    -      -       +      +
    172C  TYR      3.2    13.5    -      -       -      +
    173C  THR*     2.8    29.5    +      -       +      +
    188C  ASN*     4.5     2.3    -      -       -      +
    329C  ASN      4.2     1.9    +      -       -      +
    330C  PHE*     3.4     1.2    -      -       -      +
    331C  LEU*     2.8    45.6    +      -       +      +
    339C  ALA*     2.9    37.0    +      -       -      +
    342C  PHE*     4.1    15.4    -      -       -      -
    343C  GLY*     3.6    18.8    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 95 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93C  VAL*     4.7     1.6    -      -       +      -
     94C  GLN*     1.3    83.8    -      -       -      +
     96C  THR*     1.3    66.3    +      -       -      +
     97C  VAL*     3.2    31.6    -      -       +      -
    108C  GLY      3.4    14.1    -      -       -      -
    110C  VAL*     3.8    28.3    -      -       +      -
    132C  PHE*     3.6    41.5    -      +       -      -
    133C  GLY*     4.2     7.6    -      -       -      -
    134C  PRO*     4.5     0.9    -      -       +      -
    171C  LEU*     3.7     4.1    -      -       -      +
    172C  TYR*     2.9    37.4    +      -       +      +
    327C  PHE*     4.5     9.6    -      +       -      -
    328C  ASP      3.8     4.7    -      -       -      +
    329C  ASN      3.5     9.9    -      -       -      -
    330C  PHE*     3.7    26.7    -      +       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 96 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95C  PHE*     1.3    76.0    -      -       -      +
     97C  VAL*     1.3    65.9    +      -       -      +
    169C  THR*     3.6    21.8    -      -       +      +
    170C  HIS      3.3     5.8    -      -       -      +
    171C  LEU*     3.8    23.3    -      -       +      -
    326C  ILE      4.4     1.3    +      -       -      -
    327C  PHE*     3.4     6.8    -      -       -      -
    328C  ASP*     2.9    55.5    +      -       -      +
    329C  ASN*     3.6    18.9    +      -       +      +
    347C  TRP*     4.0    20.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 97 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95C  PHE*     3.2    35.7    -      -       +      -
     96C  THR*     1.3    75.7    -      -       -      +
     98C  LYS*     1.3    62.3    +      -       -      +
     99C  HIS*     3.8    34.9    -      -       +      +
    108C  GLY      3.6     9.4    -      -       -      +
    134C  PRO*     4.2     7.2    -      -       +      -
    168C  PHE      3.7     2.3    -      -       -      +
    169C  THR*     3.6     1.3    -      -       -      -
    170C  HIS*     2.8    37.6    +      -       -      +
    172C  TYR*     4.1    19.0    -      -       +      -
    325C  THR*     3.9    10.5    -      -       +      -
    326C  ILE      3.6     3.8    -      -       -      -
    327C  PHE*     4.1     8.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 98 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53C  SER      3.5    14.1    +      -       -      -
     56C  PHE*     2.7    47.2    +      -       -      -
     57C  TYR*     4.4     3.2    -      -       -      +
     63C  ASP*     5.6     4.4    +      -       -      +
     97C  VAL*     1.3    76.7    -      -       -      +
     99C  HIS*     1.3    60.9    +      -       -      +
    100C  GLU*     3.1    27.4    +      -       +      +
    167C  GLU      3.5    14.4    -      -       -      +
    168C  PHE      3.7     5.6    -      -       -      +
    169C  THR*     3.3    27.1    -      -       +      +
    324C  GLY      4.0     0.5    -      -       -      +
    325C  THR*     3.3     1.6    -      -       -      -
    326C  ILE*     2.9    50.4    +      -       +      +
    354C  GLU*     3.5    13.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 99 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97C  VAL*     3.8    18.4    -      -       +      +
     98C  LYS*     1.3    69.5    -      -       -      +
    100C  GLU*     1.3    63.3    +      -       -      +
    101C  GLN*     3.1    13.9    +      -       -      +
    102C  ASN*     3.1     9.0    +      -       -      -
    103C  ILE*     3.7    39.0    -      -       +      +
    106C  GLY      4.9     1.1    -      -       -      -
    107C  GLY      4.3    12.8    -      -       -      -
    108C  GLY*     4.4     4.2    +      -       -      -
    134C  PRO*     4.7    10.2    -      -       +      +
    136C  ILE*     4.2    19.7    -      -       +      +
    164C  LYS      4.6     8.5    -      -       -      -
    165C  ASP*     5.3     1.8    -      -       -      +
    166C  ASP      3.6    13.4    +      -       -      +
    167C  GLU*     3.4    15.9    -      -       -      -
    168C  PHE      4.3     4.4    +      -       -      -
    325C  THR*     2.7    37.6    +      -       +      +
----------------------------------------------------------
 Back to top of page


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