Contacts of the strand formed by residues 48 - 51 (chain H) 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 VAL 48 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36H  THR*     4.0     7.9    -      -       +      -
     40H  ILE*     3.9    36.6    -      -       +      -
     45H  ALA*     4.0     9.9    -      -       +      -
     47H  LEU*     1.3    75.4    -      -       -      +
     49H  PHE*     1.3    60.7    +      -       -      +
     50H  VAL*     5.3     0.4    -      -       +      -
     63H  ILE*     4.4    10.3    -      -       +      -
     67H  ALA*     4.7     1.3    -      -       +      -
     72H  VAL*     4.1     4.3    -      -       +      -
     73H  PRO      3.0    12.8    +      -       -      +
     74H  PHE*     3.1    24.9    -      -       +      +
     75H  ILE*     2.8    32.2    +      -       -      +
     96H  ALA      3.3     6.1    -      -       -      +
     97H  ALA*     3.6    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 49 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16H  ALA*     3.6    42.8    -      -       +      -
     17H  LEU*     4.2     3.1    -      -       +      -
     19H  ALA*     5.5     1.6    -      -       +      -
     20H  LEU*     4.1    19.5    -      -       +      -
     47H  LEU*     3.5    31.9    -      -       +      -
     48H  VAL*     1.3    76.9    -      -       -      +
     50H  VAL*     1.3    63.8    +      -       -      +
     75H  ILE*     3.4    14.6    -      -       +      +
     77H  VAL*     3.9    16.6    -      -       +      -
     83H  LEU*     3.4    30.5    -      -       +      -
     95H  ALA*     2.9     9.4    -      -       -      +
     96H  ALA*     2.7    39.5    +      -       +      +
     98H  VAL*     3.4    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 50 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3H  TYR*     3.8     1.6    -      -       +      -
     48H  VAL*     5.0     4.5    -      -       +      +
     49H  PHE*     1.3    82.1    -      -       -      +
     51H  ALA*     1.3    73.8    +      -       -      +
     60H  VAL*     3.2    27.6    -      -       +      -
     63H  ILE*     3.3    40.4    -      -       +      -
     74H  PHE*     5.4     2.2    -      -       +      -
     75H  ILE      3.0     8.7    +      -       -      +
     76H  PHE*     3.3    33.5    -      -       +      -
     77H  VAL      2.9    23.6    +      -       -      +
     83H  LEU*     4.3     2.5    -      -       -      -
     94H  ALA      3.6     3.8    -      -       -      +
     95H  ALA*     4.3     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 51 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3H  TYR*     2.8    18.1    +      -       -      -
     50H  VAL*     1.3    84.4    -      -       -      +
     52H  GLU*     1.3    61.0    +      -       -      +
     53H  ASP*     3.3    19.1    -      -       -      +
     54H  VAL*     3.7    11.1    -      -       +      +
     77H  VAL*     3.3    10.8    -      -       -      +
     79H  GLN      4.4     1.8    -      -       -      +
     80H  GLN*     3.9    19.1    -      -       +      +
     83H  LEU*     4.0     4.2    -      -       +      +
     93H  SER      4.1     6.5    -      -       -      +
     94H  ALA*     2.8    19.0    +      -       -      +
----------------------------------------------------------
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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