Contacts of the strand formed by residues 70 - 75 (chain G) 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 GLU 70 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22G  SER*     4.1     9.4    +      -       -      -
     23G  CYS      3.7     2.5    -      -       -      +
     24G  ARG*     2.7    35.2    +      -       -      +
     66G  GLY*     3.5     4.7    -      -       -      -
     67G  SER      3.1    27.5    +      -       -      +
     68G  GLY      3.8     0.4    -      -       -      -
     69G  THR*     1.3    84.3    -      -       -      +
     71G  PHE*     1.3    74.6    +      -       -      +
     72G  THR*     4.5     6.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 71 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22G  SER*     3.7     2.6    -      -       -      -
     23G  CYS*     2.9    46.1    +      -       +      +
     25G  ALA*     4.8     3.8    -      -       +      -
     29G  VAL*     3.7    27.1    -      -       +      -
     30G  SER      3.0    28.3    -      -       -      -
     33G  LEU*     3.6    45.1    -      -       +      -
     35G  TRP*     4.3     1.8    -      -       +      -
     51G  ALA*     4.3    10.1    -      -       +      -
     65G  SER      3.5     6.7    -      -       -      +
     66G  GLY      3.8     8.1    -      -       -      -
     67G  SER*     3.6    14.8    -      -       -      -
     68G  GLY      3.7    10.3    -      -       -      -
     69G  THR*     4.0    17.0    -      -       -      -
     70G  GLU*     1.3    83.8    +      -       -      +
     72G  THR*     1.3    69.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 72 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20G  THR*     3.8    29.1    -      -       +      +
     21G  LEU      3.3     7.0    +      -       -      +
     22G  SER*     4.5     6.6    +      -       -      -
     35G  TRP*     3.8     7.0    +      -       -      -
     63G  SER      3.9     0.2    -      -       -      +
     64G  GLY*     3.2     5.2    -      -       -      -
     65G  SER*     2.9    45.3    +      -       -      +
     70G  GLU*     4.5     9.5    +      -       -      -
     71G  PHE*     1.3    81.4    +      -       -      +
     73G  LEU*     1.3    66.9    +      -       -      +
     74G  THR*     4.0     8.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 73 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19G  ALA      3.5     3.3    -      -       -      +
     21G  LEU*     2.9    46.7    +      -       +      +
     35G  TRP*     3.6    37.8    -      -       +      -
     47G  LEU*     4.2    11.7    -      -       +      -
     48G  ILE*     4.0    25.1    -      -       +      -
     62G  PHE*     4.4     9.0    -      -       +      -
     63G  SER      3.4    13.5    -      -       -      +
     64G  GLY*     4.5     0.2    -      -       -      -
     72G  THR*     1.3    74.7    -      -       -      +
     74G  THR*     1.3    66.2    +      -       -      +
     75G  ILE*     4.6     6.1    -      -       +      -
     86G  TYR*     3.4    37.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 74 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18G  ARG*     3.6    32.7    +      -       -      +
     19G  ALA      3.2     8.1    -      -       -      +
     20G  THR*     4.2     9.4    +      -       -      +
     61G  ARG      3.5     1.3    -      -       -      +
     62G  PHE*     3.6     1.9    -      -       -      -
     63G  SER*     2.8    50.0    +      -       -      +
     72G  THR*     4.0    13.4    -      -       -      +
     73G  LEU*     1.3    74.4    -      -       -      +
     75G  ILE*     1.3    78.2    +      -       -      +
     76G  SER*     3.9     5.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 75 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18G  ARG*     3.5     2.1    -      -       -      +
     19G  ALA*     2.9    41.0    +      -       +      +
     21G  LEU*     4.6     6.5    -      -       +      -
     61G  ARG*     3.2    18.6    -      -       +      +
     62G  PHE*     3.1    39.0    -      -       +      -
     73G  LEU*     4.6     8.7    -      -       +      -
     74G  THR*     1.3    74.2    -      -       -      +
     76G  SER*     1.3    65.7    +      -       -      +
     77G  SER      3.3     3.6    +      -       -      +
     78G  LEU*     3.8    23.5    +      -       +      +
     82G  ASP*     3.6    24.5    -      -       +      +
     86G  TYR*     3.6    26.5    -      -       +      +
    104G  VAL*     5.6     0.7    -      -       +      -
----------------------------------------------------------
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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