Contacts of the strand formed by residues 266 - 270 (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 THR 266 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241L  HIS*     3.2    23.2    -      -       -      -
    242L  LYS*     5.4     3.1    +      -       -      +
    262L  SER*     3.5    24.0    +      -       -      -
    264L  ASP*     3.5    17.5    -      -       +      +
    265L  GLN*     1.3    86.4    -      -       +      +
    267L  VAL*     1.3    62.2    +      -       -      +
    268L  LYS*     4.5     7.4    -      -       -      -
    284L  SER*     5.8     4.0    -      -       -      -
    285L  LEU      3.4    12.6    -      -       -      +
    286L  PRO*     4.4     8.3    -      -       +      -
    287L  HIS*     4.2     3.8    -      -       -      -
    291L  VAL*     3.8     4.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 267 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241L  HIS*     5.3     0.2    -      -       -      -
    260L  THR      3.0    23.8    -      -       -      +
    261L  ALA*     3.9     3.8    -      -       +      +
    266L  THR*     1.3    74.3    -      -       -      +
    268L  LYS*     1.3    63.6    +      -       -      +
    269L  ILE*     5.1     6.3    -      -       +      -
    284L  SER*     3.8     0.5    -      -       -      -
    285L  LEU*     2.8    56.0    +      -       +      +
    287L  HIS*     3.1    28.9    -      -       +      +
    291L  VAL*     4.5     4.3    -      -       +      -
    294L  ALA*     3.6    29.8    -      -       +      -
    303L  LEU*     5.5     2.7    -      -       +      -
    305L  THR*     4.3     7.0    -      -       -      +
    315L  TYR*     4.9     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 268 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240L  MET      2.3    32.9    +      -       -      -
    241L  HIS*     3.1    38.3    +      -       +      +
    242L  LYS*     4.5     9.9    -      -       -      +
    259L  ALA*     3.5     2.8    -      -       -      -
    260L  THR*     2.8    38.9    +      -       -      +
    266L  THR*     4.5     7.0    -      -       -      +
    267L  VAL*     1.3    77.8    -      -       -      +
    269L  ILE*     1.3    64.8    +      -       -      +
    270L  TRP*     3.3    37.4    -      -       +      +
    279L  ALA*     6.3     0.2    -      -       -      +
    281L  PHE*     5.1    15.3    -      -       +      -
    283L  TYR      3.6    10.5    -      -       -      +
    284L  SER*     4.4    11.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 269 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257L  PHE*     4.6    15.5    -      -       +      -
    258L  LEU      3.4    12.8    -      -       -      +
    259L  ALA*     4.1     8.1    -      -       +      -
    267L  VAL*     5.1     3.1    -      -       +      -
    268L  LYS*     1.3    81.9    -      -       -      +
    270L  TRP*     1.3    64.2    +      -       -      +
    281L  PHE*     4.7     0.7    -      -       -      +
    282L  LEU*     3.4    12.5    +      -       +      +
    283L  TYR*     2.9    44.7    +      -       +      +
    285L  LEU*     3.5    25.1    -      -       +      -
    296L  PHE*     5.2     4.0    -      -       +      -
    303L  LEU*     3.5    32.1    -      -       +      -
    320L  TRP*     4.8    28.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 270 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236L  TRP*     6.3     0.2    -      -       +      -
    239L  ARG      5.2     0.7    -      -       -      -
    240L  MET*     3.4    57.2    -      -       +      -
    257L  PHE*     3.1    10.6    -      -       -      +
    258L  LEU*     2.8    45.3    +      -       +      +
    260L  THR*     2.7    41.2    +      -       +      +
    268L  LYS*     3.3    41.7    -      -       +      +
    269L  ILE*     1.3    75.5    -      -       -      +
    271L  ASP*     1.3    63.1    +      -       -      +
    272L  LEU*     4.7     1.6    -      -       -      +
    275L  VAL*     3.9    20.9    -      -       +      -
    279L  ALA*     4.8    14.8    -      -       +      -
    280L  SER      5.3     0.2    -      -       -      -
    281L  PHE*     3.6    33.4    -      +       +      -
    282L  LEU*     4.4     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