Contacts of the strand formed by residues 129 - 135 (chain F) in PDB entry 1KD1


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 ASP 129 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2338A    G      3.0    63.0    +      -       -      +
   2347A    C      5.4     2.2    -      -       -      +
     22F  VAL      4.2     0.7    -      -       -      +
     23F  VAL*     3.2     3.5    -      -       -      +
     24F  HIS*     3.1    50.2    +      -       +      +
     26F  GLY      4.6     2.6    +      -       -      -
    105F  SER*     4.5     3.4    -      -       -      +
    106F  PHE      3.9     2.9    -      -       -      -
    107F  GLY      4.1     3.1    -      -       -      +
    128F  LEU*     1.3    79.3    +      -       -      +
    130F  VAL*     1.3    71.2    +      -       -      +
    131F  THR*     4.9     5.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 130 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21F  VAL*     3.6    17.9    -      -       +      -
     22F  VAL      3.5     4.5    -      -       -      -
     23F  VAL*     3.9     4.0    -      -       +      -
     83F  PHE*     3.5    39.7    -      -       +      -
     84F  LEU*     4.4     1.6    -      -       +      -
     87F  ALA*     5.1     0.9    -      -       +      -
    105F  SER*     3.6     1.7    +      -       -      -
    106F  PHE*     3.1    67.9    +      -       +      +
    107F  GLY*     5.9     0.2    -      -       -      -
    128F  LEU*     3.7    19.1    -      -       +      -
    129F  ASP*     1.3    81.7    -      -       -      +
    131F  THR*     1.3    60.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 131 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2337A    G      3.6    19.9    +      -       +      +
   2347A    C      4.3     6.6    +      -       -      -
   2348A    C      4.1    26.8    +      -       -      +
     20F  LYS      4.1     0.2    -      -       -      +
     21F  VAL*     3.0    10.4    -      -       -      +
     22F  VAL*     2.9    42.0    +      -       -      +
    103F  ASN*     5.9     2.5    -      -       +      -
    104F  PHE      3.7     5.2    -      -       -      +
    105F  SER*     3.2    31.6    +      -       -      +
    129F  ASP*     4.9     3.6    -      -       -      +
    130F  VAL*     1.3    77.5    +      -       -      +
    132F  VAL*     1.3    65.4    +      -       -      +
    133F  ASN      4.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 132 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2348A    C      5.8     0.9    -      -       -      -
     18F  ILE*     4.2    21.1    -      -       +      -
     20F  LYS      4.0     2.2    -      -       -      -
     21F  VAL*     4.1     5.4    -      -       +      +
     84F  LEU*     3.9    26.2    -      -       +      -
    103F  ASN*     3.6     9.1    -      -       -      +
    104F  PHE*     3.1    63.1    +      -       +      +
    106F  PHE*     4.3     5.8    -      -       +      -
    131F  THR*     1.3    79.7    -      -       -      +
    133F  ASN*     1.3    63.9    +      -       -      +
    134F  LEU*     3.6    27.2    +      -       +      +
    166F  ILE*     5.0     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 133 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2348A    C      4.3     5.4    -      -       -      +
   2349A    G      3.4    22.7    +      -       -      +
     18F  ILE*     4.0     0.3    -      -       -      -
     19F  GLU*     2.9    55.1    +      -       -      +
     20F  LYS*     3.2    36.5    +      -       +      +
     22F  VAL*     6.4     0.2    -      -       +      -
    101F  THR*     6.0     1.0    -      -       -      +
    103F  ASN*     2.9    31.4    +      -       -      +
    131F  THR      4.1     1.2    -      -       -      -
    132F  VAL*     1.3    72.7    -      -       -      +
    134F  LEU*     1.3    69.0    +      -       -      +
    135F  VAL*     5.7     1.5    -      -       -      +
    139F  TYR*     4.7     6.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 134 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16F  PRO*     5.6     0.4    -      -       +      -
     17F  ARG      3.7    11.0    -      -       -      +
     18F  ILE*     3.5    32.3    -      -       +      -
    101F  THR*     4.0     7.6    -      -       -      +
    102F  GLY      3.1    24.7    -      -       -      +
    103F  ASN*     3.1    15.6    +      -       -      +
    104F  PHE*     4.4     3.8    -      -       +      -
    132F  VAL*     3.6    17.9    -      -       +      +
    133F  ASN*     1.3    80.0    +      -       -      +
    135F  VAL*     1.3    67.4    +      -       -      +
    157F  LEU*     3.5    16.4    -      -       +      +
    162F  ALA*     4.1    12.6    -      -       +      +
    165F  PHE*     4.5     8.5    -      -       +      -
    166F  ILE*     3.2    36.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 135 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16F  PRO*     3.7     3.8    -      -       -      +
     17F  ARG*     3.2    44.7    +      -       -      +
     19F  GLU*     4.4    16.6    -      -       +      +
    101F  THR*     6.2     3.1    -      -       +      -
    133F  ASN*     5.7     2.0    -      -       -      +
    134F  LEU*     1.3    79.0    -      -       -      +
    136F  ARG*     1.3    78.1    +      -       +      +
    139F  TYR*     3.5    51.6    -      -       +      -
    151F  ILE*     5.8     4.0    -      -       +      -
    155F  HIS*     5.3     2.7    -      -       +      +
    156F  ARG*     5.9     3.6    -      -       -      -
    157F  LEU*     3.8    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