Contacts of the strand formed by residues 46 - 51 (chain N) 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 46 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98M  PHE*     5.3     0.2    -      -       -      -
     37N  VAL*     3.5     5.4    -      -       -      +
     38N  ARG*     2.5    86.5    +      -       +      +
     44N  GLY      4.3     0.4    -      -       -      -
     45N  LEU*     1.3    73.7    -      -       -      +
     47N  TRP*     1.3    72.0    +      -       -      +
     48N  VAL*     4.1     1.8    -      -       +      +
     61N  ALA*     5.7     1.1    -      -       +      -
     63N  SER*     3.8    18.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 47 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94M  TRP*     4.2     8.5    -      +       -      -
     95M  PRO*     3.8    26.9    -      -       +      -
     96M  LEU*     3.6    42.8    +      -       +      +
     98M  PHE*     4.6    11.9    -      -       +      -
     35N  PHE*     3.3    29.3    -      +       -      -
     36N  TRP      4.3     3.8    -      -       -      -
     37N  VAL*     4.2     8.3    -      -       +      -
     45N  LEU      4.0     1.8    +      -       -      -
     46N  GLU*     1.3    83.1    -      -       -      +
     48N  VAL*     1.3    63.1    +      -       -      +
     49N  SER*     3.3    35.2    +      -       -      -
     50N  TRP*     3.8    13.9    -      -       +      -
     59N  LYS*     4.0     8.1    -      -       +      -
     60N  TYR      3.3    42.6    -      -       -      -
     61N  ALA*     3.6    16.7    -      -       +      +
    106N  PHE*     4.2     6.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with VAL 48 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36N  TRP*     3.3    14.8    +      -       +      +
     37N  VAL      4.6     0.2    -      -       -      -
     38N  ARG*     3.4    48.9    -      -       +      +
     46N  GLU*     4.1     3.8    -      -       +      +
     47N  TRP*     1.3    85.9    -      -       -      +
     49N  SER*     1.3    70.4    +      -       -      +
     60N  TYR*     3.4     4.0    -      -       -      -
     61N  ALA*     2.8    32.6    +      -       +      -
     64N  VAL*     4.1    10.9    -      -       +      +
     68N  PHE*     4.0    27.4    -      -       +      -
     81N  LEU*     4.5     8.1    -      -       +      -
     94N  TYR*     4.5     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 49 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35N  PHE*     3.2     6.6    -      -       -      -
     36N  TRP*     3.0    28.8    +      -       -      -
     47N  TRP*     3.3    12.0    +      -       -      -
     48N  VAL*     1.3    82.5    +      -       -      +
     50N  TRP*     1.3    58.7    +      -       -      +
     59N  LYS      3.6     4.1    +      -       -      -
     60N  TYR*     3.5    24.6    -      -       -      -
     68N  PHE*     5.4     0.3    -      -       -      +
     70N  ILE*     3.7    22.3    -      -       -      +
     81N  LEU*     3.5    23.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 50 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7H  SER*     6.2     0.7    -      -       -      -
     33N  PRO*     3.8    10.0    -      -       +      +
     34N  MET      3.5     9.2    -      -       -      -
     35N  PHE*     3.2    34.1    -      +       +      -
     47N  TRP*     3.8    16.2    -      -       +      -
     49N  SER*     1.3    75.0    -      -       -      +
     51N  ILE*     1.3    71.0    +      -       -      +
     52N  GLY*     3.7    26.7    -      -       -      -
     53N  PRO*     5.6     0.4    -      -       +      -
     57N  ILE*     3.7    39.0    -      -       +      -
     58N  THR*     3.5     3.3    -      -       -      -
     59N  LYS*     3.0    60.4    +      -       +      +
     70N  ILE*     3.8     6.3    -      -       -      +
     99N  GLU*     2.9    24.8    +      -       -      -
    104N  TRP*     4.6    13.0    -      +       -      -
----------------------------------------------------------
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Residues in contact with ILE 51 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33N  PRO*     3.2     5.9    -      -       -      +
     34N  MET*     3.0    39.6    +      -       +      +
     50N  TRP*     1.3    85.1    -      -       -      +
     52N  GLY*     1.3    69.6    +      -       -      +
     55N  GLY*     3.8    21.3    -      -       -      -
     57N  ILE      3.8    11.0    -      -       -      +
     58N  THR*     4.0    12.8    -      -       +      -
     70N  ILE*     4.0    17.7    -      -       +      +
     71N  SER*     3.9    34.1    -      -       -      +
     72N  ARG*     3.6    17.9    -      -       +      +
     79N  LEU*     4.0     6.7    -      -       +      -
----------------------------------------------------------
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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