Contacts of the strand formed by residues 130 - 135 (chain G) 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 GLU 130 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84G  MET      3.5     8.5    -      -       -      +
     85G  GLU*     4.3    13.8    -      -       +      +
    125G  GLU      4.3     0.3    -      -       -      +
    126G  ILE*     3.7     3.7    -      -       -      +
    127G  ASP*     2.9    38.2    +      -       +      +
    128G  GLY      3.2     1.2    -      -       -      -
    129G  GLU*     1.3    84.7    -      -       -      +
    131G  LEU*     1.3    64.3    +      -       -      +
    170G  ARG*     5.3     7.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 131 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83G  GLY*     3.4     4.2    -      -       -      -
     84G  MET*     2.7    54.7    +      -       +      +
     86G  VAL*     5.5     5.6    -      -       +      +
     95G  VAL*     4.2    22.4    -      -       +      -
     97G  VAL*     5.3     1.1    -      -       +      -
    102G  VAL*     6.1     0.2    -      -       +      -
    124G  VAL*     3.7    26.5    -      -       +      -
    125G  GLU      3.7     3.1    -      -       -      +
    126G  ILE*     3.3    38.4    -      -       +      -
    130G  GLU*     1.3    77.5    -      -       -      +
    132G  THR*     1.3    61.2    +      -       -      +
    133G  VAL      4.2     0.4    -      -       -      -
    148G  ILE*     4.5     6.3    -      -       +      -
    166G  VAL*     3.7    29.8    -      -       +      -
    170G  ARG*     5.4     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 132 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81G  GLU*     3.9    25.8    +      -       -      +
     82G  TYR      3.3     8.4    +      -       -      -
    123G  ASP      3.2     5.2    -      -       -      +
    124G  VAL*     3.6     0.6    -      -       -      -
    125G  GLU*     3.0    52.7    +      -       +      +
    131G  LEU*     1.3    77.0    -      -       -      +
    133G  VAL*     1.3    62.8    +      -       -      +
    134G  SER*     3.8     3.0    +      -       -      +
    170G  ARG*     4.7     9.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 133 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81G  GLU*     3.0     4.3    -      -       -      +
     82G  TYR*     2.7    46.5    +      -       +      +
     84G  MET*     3.2    36.1    -      -       +      -
    122G  THR*     3.4    28.7    -      -       +      -
    123G  ASP      3.5     4.0    -      -       -      +
    124G  VAL*     4.3     7.0    -      -       +      -
    132G  THR*     1.3    74.1    -      -       -      +
    134G  SER*     1.3    61.4    +      -       -      +
    141G  VAL*     3.8    23.2    -      -       +      +
    144G  THR*     4.0    10.5    -      -       +      -
    145G  ALA*     4.1     8.7    -      -       +      +
    148G  ILE*     4.5     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 134 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80G  TRP      2.8    14.4    -      -       -      -
     81G  GLU*     3.3    26.0    +      -       -      -
    122G  THR*     3.4     3.8    -      -       -      -
    123G  ASP*     2.8    54.5    +      -       -      +
    125G  GLU*     5.6     2.6    -      -       -      +
    132G  THR*     4.5     4.0    +      -       -      +
    133G  VAL*     1.3    77.8    -      -       -      +
    135G  GLY*     1.3    60.3    +      -       -      +
    141G  VAL*     3.9     7.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 135 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26G  ASN*     4.3     6.3    -      -       -      -
     79G  GLY      3.8     0.3    -      -       -      -
     80G  TRP*     2.9    37.2    +      -       -      +
    121G  ASP      4.1     6.1    -      -       -      -
    123G  ASP*     4.6     3.8    -      -       -      -
    134G  SER*     1.3    76.1    -      -       -      +
    136G  PRO*     1.3    70.1    -      -       -      +
    137G  ASP      3.5     2.2    -      -       -      -
    141G  VAL*     3.6    11.4    -      -       -      +
----------------------------------------------------------
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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