Contacts of the strand formed by residues 63 - 67 (chain D) 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 LYS 63 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41D  VAL*     4.3    14.6    -      -       -      +
     42D  ASP*     5.3     2.0    +      -       -      +
     50D  ILE*     4.3    12.9    -      -       +      +
     51D  TYR      3.5     3.1    -      -       -      +
     52D  ASN*     3.5    25.4    +      -       -      +
     61D  TYR*     3.7     1.6    -      -       -      -
     62D  ASP*     1.3    93.3    +      -       -      +
     64D  VAL*     1.3    66.5    +      -       -      +
     95D  PHE*     4.0     9.0    -      -       +      -
     97D  SER*     3.1    29.1    +      -       -      +
     98D  LYS*     4.2    21.5    -      -       -      +
    107D  GLY      3.3     7.2    +      -       -      +
    108D  LYS*     3.6    19.5    -      -       +      -
    109D  THR*     3.2    22.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 64 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33D  VAL*     4.4     7.4    -      -       +      -
     49D  LEU      3.7     1.2    -      -       -      +
     50D  ILE*     3.3     4.4    -      -       -      +
     51D  TYR*     2.8    41.8    +      -       +      +
     53D  ILE*     4.1    29.6    -      -       +      +
     61D  TYR*     3.7    19.1    -      -       +      -
     63D  LYS*     1.3    76.7    -      -       -      +
     65D  LYS*     1.3    67.9    +      -       -      +
     66D  THR*     4.6     1.8    -      -       -      +
     84D  VAL*     5.6     0.4    -      -       +      -
    109D  THR*     3.2    32.5    -      -       +      +
    111D  MET*     4.0    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 65 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  LYS*     4.7     2.6    -      -       -      +
     44D  PHE*     4.3     6.8    -      -       +      -
     45D  PHE*     6.1     0.8    -      -       -      -
     48D  ASP*     3.7    37.6    +      -       +      +
     49D  LEU      3.4     5.2    -      -       -      +
     50D  ILE*     4.0     8.3    -      -       +      +
     64D  VAL*     1.3    74.0    -      -       -      +
     66D  THR*     1.3    62.5    +      -       -      +
     67D  GLU*     3.0    33.8    +      -       -      -
     89D  TYR*     4.8     0.2    +      -       -      -
     94D  TYR      2.8    25.2    +      -       -      +
     95D  PHE*     3.5    33.0    -      -       +      +
    109D  THR      3.2     7.6    +      -       -      +
    110D  CYS*     3.3    22.3    -      -       -      +
    111D  MET*     3.0    25.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 66 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48D  ASP*     3.2     3.5    -      -       -      +
     49D  LEU*     2.9    36.8    +      -       +      +
     51D  TYR*     4.2    11.4    -      -       +      -
     64D  VAL*     4.0     2.6    +      -       -      -
     65D  LYS*     1.3    73.3    -      -       -      +
     67D  GLU*     1.3    59.5    -      -       -      +
     68D  LEU*     3.9     4.7    +      -       +      +
     84D  VAL*     5.9     1.8    -      -       +      -
    111D  MET*     3.3    19.3    -      -       -      +
    112D  TYR      3.3     4.7    -      -       -      -
    113D  GLY      2.6    33.6    +      -       -      +
    115D  ILE*     3.8    29.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 67 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36A  MET      4.7     0.7    -      -       -      +
     37A  ALA      4.7     2.9    -      -       -      +
     39A  LYS*     2.6    43.1    +      -       -      -
     45D  PHE*     5.8     1.6    -      -       -      -
     47D  TRP*     3.2    25.4    +      -       +      +
     48D  ASP*     3.7    20.2    -      -       +      +
     65D  LYS*     3.0    32.7    +      -       +      -
     66D  THR*     1.3    73.2    -      -       -      +
     68D  LEU*     1.3    61.3    +      -       -      +
     89D  TYR*     3.6     4.9    +      -       -      -
    111D  MET      2.8    11.7    +      -       -      +
    112D  TYR*     3.2    23.7    -      -       +      -
    113D  GLY      3.0    20.6    +      -       -      -
    218D  ASN*     3.4     7.0    +      -       -      +
----------------------------------------------------------
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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