Contacts of the strand formed by residues 414 - 417 (chain L) in PDB entry 6R90


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 HIS 414 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56I    A      4.1    22.0    +      -       -      -
    107L  ALA*     5.8     4.5    -      -       +      +
    108L  ALA      3.8     5.2    +      -       -      +
    109L  PRO*     3.8    26.4    -      -       +      +
    110L  PHE*     5.8     1.1    -      -       -      -
    114L  ALA*     4.8     2.3    -      -       -      +
    390L  GLU      6.1     0.4    -      -       -      -
    410L  ALA*     3.7     3.3    -      -       -      +
    411L  MET*     2.8    57.3    +      -       +      +
    412L  GLY      3.9     7.6    -      -       -      +
    413L  TYR*     1.3    95.0    +      -       +      +
    415L  ILE*     1.3    68.3    +      -       -      +
    416L  LEU*     5.2     7.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 415 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107L  ALA*     3.6     2.4    -      -       -      -
    108L  ALA*     2.9    42.1    +      -       +      +
    110L  PHE*     4.2    18.4    -      -       +      -
    114L  ALA*     4.9     6.5    -      -       +      -
    117L  LEU*     5.3     7.4    -      -       +      -
    127L  VAL*     5.3     7.6    -      -       +      -
    129L  VAL*     3.3    47.3    -      -       +      -
    137L  MET*     4.6    11.2    -      -       +      -
    139L  TRP*     3.9    23.0    -      -       +      -
    408L  ALA*     5.4     1.8    -      -       +      -
    409L  SER      3.4    10.3    -      -       -      +
    410L  ALA*     5.1     3.1    -      -       +      -
    414L  HIS*     1.3    78.3    -      -       -      +
    416L  LEU*     1.3    69.5    +      -       -      +
    417L  ILE*     4.8     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 416 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104L  LEU*     3.6    17.3    -      -       +      -
    106L  LYS      3.5    14.8    -      -       -      +
    107L  ALA*     3.5    24.7    -      -       +      -
    390L  GLU*     5.2     0.4    -      -       -      +
    391L  SER*     3.3    26.9    -      -       -      +
    407L  LEU      3.8     0.2    -      -       -      +
    408L  ALA*     3.4     0.7    -      -       -      +
    409L  SER*     2.9    37.3    +      -       -      +
    411L  MET*     3.4    29.8    -      -       +      -
    414L  HIS*     5.2     7.0    -      -       +      -
    415L  ILE*     1.3    77.1    -      -       -      +
    417L  ILE*     1.3    73.1    +      -       -      +
    418L  TRP*     3.6    26.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 417 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104L  LEU*     3.4     3.8    -      -       -      +
    105L  GLN*     3.3    10.6    +      -       +      +
    106L  LYS*     2.9    40.1    +      -       +      +
    119L  TRP*     4.4     2.9    -      -       +      -
    127L  VAL*     5.3     2.0    -      -       +      -
    139L  TRP*     4.0    17.5    -      -       +      -
    141L  PHE*     3.3    50.5    -      -       +      -
    406L  THR*     5.1     5.2    -      -       +      -
    407L  LEU      3.4    15.9    -      -       -      +
    408L  ALA*     4.0    15.0    -      -       +      -
    415L  ILE*     4.8     3.4    -      -       +      -
    416L  LEU*     1.3    84.8    -      -       -      +
    418L  TRP*     1.3    64.0    +      -       -      +
    419L  SER*     3.6    15.7    -      -       -      +
----------------------------------------------------------
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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