Contacts of the strand formed by residues 174 - 179 (chain A) in PDB entry 1KLG


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 174 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  PRO      4.3    11.0    -      -       -      +
     89A  VAL*     3.6    33.0    -      -       +      +
    163A  CYS      3.4     3.8    -      -       -      +
    164A  ARG*     3.5     1.4    -      -       -      -
    165A  VAL*     2.9    36.1    +      -       +      +
    170A  LEU*     3.8    26.9    -      -       +      -
    172A  GLU      3.2     2.4    +      -       -      +
    173A  PRO*     1.3    71.9    -      -       -      +
    175A  LEU*     1.3    66.2    +      -       -      +
    176A  LYS*     4.1    22.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 175 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122A  LEU*     4.2    16.6    -      -       +      -
    162A  ASP*     4.0    26.2    -      -       +      +
    163A  CYS      3.6     2.2    -      -       -      -
    164A  ARG*     3.9    27.4    -      -       +      +
    173A  PRO*     3.9    19.7    +      -       +      +
    174A  LEU*     1.3    85.0    -      -       -      +
    176A  LYS*     1.3    68.9    +      -       -      +
    177A  HIS*     3.7     3.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 176 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89A  VAL*     3.3    50.1    +      -       +      +
     90A  THR*     4.9     3.4    -      -       -      +
     91A  VAL*     3.5    24.8    -      -       +      +
    162A  ASP*     3.0     7.4    -      -       -      -
    163A  CYS      2.9    31.7    +      -       -      +
    174A  LEU*     4.1    21.2    -      -       +      +
    175A  LEU*     1.3    78.3    -      -       -      +
    177A  HIS*     1.3    65.4    +      -       -      +
    178A  TRP*     4.0     0.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 177 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  VAL*     4.9     4.7    -      -       -      +
    160A  VAL*     3.8    34.9    -      -       +      +
    161A  TYR      3.8     3.7    +      -       -      -
    162A  ASP*     3.5    22.0    +      -       -      +
    175A  LEU      3.7     4.4    +      -       -      +
    176A  LYS*     1.3    76.3    -      -       -      +
    178A  TRP*     1.3    77.8    +      -       -      +
    179A  GLU*     4.1    14.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 178 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  VAL*     4.0    35.7    -      -       +      -
     92A  LEU*     4.9     3.2    -      -       +      +
     93A  THR*     3.5    27.7    -      -       +      +
     97A  VAL*     4.3    19.1    -      -       +      -
    105A  LEU*     3.6    18.2    -      -       +      -
    153A  PHE*     3.6    35.4    -      +       -      -
    155A  PRO*     5.7     0.7    -      -       +      -
    156A  SER      5.9     0.4    -      -       -      -
    159A  ASP      5.9     0.2    -      -       -      -
    160A  VAL*     3.9     0.2    -      -       -      -
    161A  TYR*     2.7    58.4    +      +       +      +
    176A  LYS      5.1     0.4    -      -       -      +
    177A  HIS*     1.3    78.3    +      -       -      +
    179A  GLU*     1.3    87.5    +      -       -      +
    180A  PHE*     3.9    11.4    -      +       +      -
----------------------------------------------------------
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Residues in contact with GLU 179 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157A  THR      6.0     0.7    -      -       -      +
    159A  ASP      3.9    15.9    -      -       -      +
    160A  VAL*     3.4    21.4    -      -       +      +
    177A  HIS*     4.1    13.0    -      -       -      +
    178A  TRP*     1.3   100.2    +      -       -      +
    180A  PHE*     1.3    73.3    +      -       -      +
----------------------------------------------------------
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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