Contacts of the strand formed by residues 161 - 170 (chain A) in PDB entry 1KT8


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 ALA 161 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  GLU*     3.7     5.0    -      -       -      +
     43A  TRP*     2.9    33.9    +      -       +      +
     48A  TRP*     5.7     0.2    -      -       -      -
    109A  LEU*     4.3     5.4    -      -       +      -
    110A  PRO*     3.7    36.8    -      -       +      -
    146A  LEU*     4.4     4.9    -      -       +      -
    147A  ILE      3.3    15.0    -      -       -      +
    149A  ASN*     4.0     7.2    +      -       -      -
    158A  PRO*     5.6     0.2    -      -       +      -
    160A  ARG*     1.3    79.2    -      -       -      +
    162A  LEU*     1.3    62.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 162 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  MET*     3.3    41.5    -      -       +      -
     41A  VAL      3.6    15.9    -      -       -      +
     42A  GLU*     3.6    18.8    -      -       +      +
     48A  TRP*     5.7     0.2    -      -       -      -
     59A  LEU*     4.1    14.4    -      -       +      -
     61A  LEU*     4.9     9.2    -      -       +      -
    145A  VAL      3.9     0.9    -      -       -      +
    146A  LEU*     3.4     4.5    -      -       -      -
    147A  ILE*     2.9    53.3    +      -       +      +
    149A  ASN*     4.4    10.7    -      -       -      +
    161A  ALA*     1.3    76.4    -      -       -      +
    163A  LEU*     1.3    60.8    +      -       -      +
    164A  PHE*     4.0    19.1    +      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 163 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  PHE*     3.8    28.7    -      -       +      -
     39A  LEU*     4.7     1.6    -      -       +      -
     40A  MET*     3.3     2.8    -      -       -      -
     41A  VAL*     2.8    50.5    +      -       +      +
     48A  TRP*     4.0    14.8    -      -       +      -
    100A  MET*     4.2    15.5    -      -       +      -
    112A  PHE*     4.2    16.6    -      -       +      -
    117A  LEU*     4.2    21.5    -      -       +      -
    145A  VAL      3.3    12.1    -      -       -      +
    146A  LEU*     3.7    13.7    -      -       +      -
    162A  LEU*     1.3    74.9    -      -       -      +
    164A  PHE*     1.3    73.7    +      -       -      +
    165A  VAL*     4.5     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 164 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  MET*     4.2    21.8    -      -       +      -
     39A  LEU      3.0    16.4    -      -       -      +
     40A  MET*     4.2     7.9    -      -       -      -
     59A  LEU*     3.8    23.1    -      -       +      -
    144A  PRO*     3.4     1.7    -      -       -      +
    145A  VAL*     2.7    75.2    +      -       +      +
    147A  ILE*     4.6    11.2    -      -       +      -
    162A  LEU*     4.0    22.2    -      -       +      -
    163A  LEU*     1.3    77.6    -      -       -      +
    165A  VAL*     1.3    65.2    +      -       -      +
    166A  ILE*     4.3     9.4    -      -       +      -
    563B  PRO*     3.4    32.5    -      -       +      -
    568B  LEU*     4.7     5.4    -      -       +      -
    569B  HIS*     4.4     3.8    -      +       -      -
----------------------------------------------------------
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Residues in contact with VAL 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38A  MET*     3.2     9.5    -      -       -      +
     39A  LEU*     3.0    54.5    +      -       +      -
    117A  LEU*     4.8     0.7    -      -       +      -
    121A  ILE*     4.2    14.1    -      -       +      -
    124A  LEU*     3.6    18.5    -      -       +      +
    142A  VAL*     4.0    22.4    -      -       +      -
    143A  ARG      3.4     7.0    -      -       -      +
    144A  PRO*     3.6    18.4    -      -       +      -
    163A  LEU*     4.5     5.6    -      -       +      -
    164A  PHE*     1.3    78.9    -      -       -      +
    166A  ILE*     1.3    74.5    +      -       -      +
    167A  LEU*     4.1     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  PHE*     3.9    26.9    -      -       +      -
     37A  HIS      4.9     1.8    -      -       -      -
     38A  MET*     4.1    16.4    -      -       +      -
     56A  PHE*     3.5    26.7    -      -       +      -
    143A  ARG*     2.9    54.2    +      -       +      +
    164A  PHE*     4.3     5.6    -      -       +      -
    165A  VAL*     1.3    78.1    -      -       -      +
    167A  LEU*     1.3    67.0    +      -       -      +
    563B  PRO*     3.9    39.3    -      -       +      +
    564B  ALA*     4.1     6.1    -      -       +      -
    569B  HIS*     4.4     2.5    -      -       +      -
    653B  LEU*     4.5     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  PHE*     3.4     7.6    -      -       -      +
     35A  THR*     3.1    50.7    +      -       +      +
     37A  HIS      4.7     2.5    +      -       -      +
     56A  PHE*     5.4     1.0    -      -       -      -
    121A  ILE*     5.6     0.2    -      -       +      -
    124A  LEU*     3.7    40.2    -      -       +      +
    125A  ILE*     4.3     9.4    -      -       +      -
    128A  ASP*     4.1    17.0    -      -       +      +
    140A  LEU*     4.0    21.3    -      -       +      -
    141A  TYR      3.4     2.7    -      -       -      -
    142A  VAL*     3.9    35.0    -      -       +      -
    165A  VAL*     4.1     0.2    -      -       +      -
    166A  ILE*     1.3    83.7    -      -       -      +
    168A  CYS*     1.3    63.3    +      -       -      +
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Residues in contact with CYS 168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  GLY*     3.8    27.4    -      -       -      +
     33A  THR      3.2    12.1    -      -       -      +
     34A  PHE*     3.3    35.9    -      -       -      -
    140A  LEU*     3.6     3.5    -      -       -      -
    141A  TYR*     2.7    49.4    +      -       +      +
    143A  ARG*     6.1     0.2    -      -       -      -
    166A  ILE      5.7     0.9    -      -       -      -
    167A  LEU*     1.3    73.4    -      -       -      +
    169A  PRO*     1.3    71.1    -      -       +      +
    170A  VAL*     3.4     1.0    +      -       +      -
    653B  LEU*     3.8    13.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 169 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  PRO*     4.5     5.6    -      -       +      -
     28A  LEU*     4.1    24.3    -      -       +      +
     29A  VAL      4.9     7.1    -      -       -      +
     31A  GLY      5.5     0.7    +      -       -      -
     33A  THR*     3.2    30.0    -      -       +      +
     35A  THR*     4.2    10.3    -      -       +      -
    131A  TRP*     3.5    47.1    -      -       +      +
    133A  PRO*     4.1     6.7    -      -       +      -
    139A  SER      3.7     5.6    -      -       -      +
    140A  LEU*     4.1     5.2    -      -       +      -
    168A  CYS*     1.3    86.2    -      -       -      +
    170A  VAL*     1.3    60.6    +      -       -      +
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Residues in contact with VAL 170 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  LEU*     3.3     8.0    -      -       -      +
     30A  PHE*     3.8    39.0    -      -       +      +
     79A  LYS*     4.8    11.7    -      -       -      +
    138A  THR*     3.3     9.9    -      -       -      -
    139A  SER*     2.7    46.4    +      -       -      +
    141A  TYR*     3.4    34.5    -      -       +      +
    168A  CYS*     3.5     4.9    -      -       +      +
    169A  PRO*     1.3    77.0    -      -       -      +
    171A  GLY*     1.3    61.4    +      -       -      +
    172A  ALA*     3.9    17.5    -      -       -      +
----------------------------------------------------------
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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