Contacts of the strand formed by residues 68 - 73 (chain H) in PDB entry 3KYM


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 PHE 68 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38H  ARG*     4.4     1.1    -      -       -      -
     48H  VAL*     3.8    14.8    -      -       +      -
     60H  TYR*     3.0    23.6    -      -       +      -
     64H  VAL*     3.3    41.0    +      -       +      +
     66H  GLY      4.9     3.1    +      -       -      -
     67H  ARG*     1.3    94.9    +      -       +      +
     69H  THR*     1.3    62.6    +      -       -      +
     81H  LEU*     3.8    30.3    -      -       +      -
     82H  GLN      3.4     2.9    -      -       -      -
     83H  MET*     3.6    42.6    -      -       +      -
     84H  ASN      4.4     3.6    -      -       -      -
     86H  LEU*     5.2     3.1    -      -       +      -
     90H  ASP*     4.0    25.6    -      -       +      -
     94H  TYR*     3.9    17.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with THR 69 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58H  THR*     6.0     0.2    -      -       -      +
     60H  TYR*     3.0     9.3    +      -       -      -
     67H  ARG      4.0     1.5    +      -       -      -
     68H  PHE*     1.3    74.2    +      -       -      +
     70H  ILE*     1.3    62.6    +      -       -      +
     71H  SER*     4.0     7.9    +      -       -      +
     81H  LEU*     3.8     3.2    -      -       -      +
     82H  GLN*     2.8    61.0    +      -       +      +
     84H  ASN*     5.5     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 70 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34H  MET      4.6     2.0    -      -       -      +
     36H  TRP*     3.5    26.2    -      -       +      +
     49H  SER*     3.1    33.2    -      -       -      +
     50H  TRP*     3.9     8.1    -      -       -      +
     51H  ILE*     3.9    26.2    -      -       +      +
     58H  THR*     3.3    36.3    -      -       +      +
     60H  TYR*     2.4    28.5    +      -       +      +
     69H  THR*     1.3    70.6    +      -       -      +
     71H  SER*     1.3    66.6    +      -       -      +
     79H  LEU*     4.0    15.0    -      -       +      -
     80H  TYR      3.4    14.8    -      -       -      +
     81H  LEU*     4.4     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 71 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19H  ARG*     5.2     2.9    +      -       -      -
     51H  ILE*     3.8     9.0    -      -       -      -
     69H  THR*     4.5     9.2    +      -       -      +
     70H  ILE*     1.3    80.8    -      -       -      +
     72H  ARG*     1.3    61.6    +      -       -      +
     79H  LEU*     3.7     3.1    -      -       -      +
     80H  TYR*     2.9    50.4    +      -       -      +
     82H  GLN*     5.7     2.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 72 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29H  PHE*     2.8    50.8    +      -       +      -
     30H  SER*     4.2     0.2    -      -       -      +
     32H  TYR      2.8    23.0    +      -       -      -
     34H  MET*     3.9     5.0    -      -       -      +
     51H  ILE*     3.7    24.1    -      -       +      +
     52H  GLY      3.8     0.6    -      -       -      -
     53H  PRO*     2.9    34.4    +      -       -      +
     54H  SER      4.2     1.8    -      -       -      +
     55H  GLY*     3.8    24.0    -      -       -      -
     71H  SER*     1.3    76.7    -      -       -      +
     73H  ASP*     1.3    64.6    +      -       -      +
     74H  ASN*     2.4    31.8    +      -       -      +
     78H  THR      3.5    11.9    -      -       -      +
     79H  LEU*     4.0     9.6    -      -       +      -
     80H  TYR*     4.4     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 73 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72H  ARG*     1.3    75.1    -      -       -      +
     74H  ASN*     1.3    65.9    +      -       -      +
     75H  SER*     3.3     7.0    +      -       -      -
     76H  LYS*     2.9    24.9    +      -       +      +
     77H  ASN      3.4     6.9    +      -       -      -
     78H  THR      3.0    13.0    +      -       -      +
     80H  TYR*     3.5    26.0    +      -       +      +
     31M  SER*     5.2     2.1    +      -       -      -
     32M  TYR*     2.6    27.7    +      -       -      +
----------------------------------------------------------
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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