Contacts of the strand formed by residues 261 - 266 (chain D) in PDB entry 2I6A


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 ILE 261 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218D  ASP      2.9    11.7    +      -       -      +
    219D  ILE*     3.2    23.9    -      -       +      -
    220D  LEU      2.8    30.0    +      -       -      -
    259D  GLN      3.8     6.3    -      -       -      +
    260D  ARG*     1.3    85.9    -      -       -      +
    262D  VAL*     1.3    57.8    +      -       -      +
    263D  ILE*     4.3    11.9    -      -       +      -
    273D  MET*     3.9    29.6    -      -       +      -
    274D  ALA      3.5     6.7    -      -       -      +
    275D  THR*     4.5     6.7    -      -       +      -
    316D  LEU*     3.7    33.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 262 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220D  LEU*     3.5     9.2    -      -       +      +
    245D  ALA*     3.9    15.3    -      -       -      +
    248D  THR*     3.9    14.1    -      -       +      -
    249D  GLN*     3.5    36.3    -      -       +      +
    260D  ARG*     4.0     7.0    -      -       -      -
    261D  ILE*     1.3    79.3    -      -       -      +
    263D  ILE*     1.3    64.5    +      -       -      +
    264D  PHE*     3.4    41.5    -      -       +      -
    272D  ILE      3.5     1.3    -      -       -      +
    273D  MET*     3.1     5.4    -      -       -      +
    274D  ALA*     2.8    36.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 263 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219D  ILE*     5.0     2.0    -      -       +      -
    220D  LEU      2.9     9.8    +      -       -      +
    221D  PHE*     3.4    17.3    -      -       +      -
    222D  GLY      3.2    16.6    +      -       -      -
    261D  ILE*     4.4     6.7    -      -       +      -
    262D  VAL*     1.3    79.6    -      -       -      +
    264D  PHE*     1.3    75.0    +      -       -      +
    265D  THR*     4.9     1.6    -      -       +      -
    271D  THR*     3.9    14.4    -      -       +      -
    272D  ILE      3.0     2.7    -      -       -      -
    273D  MET*     3.5    30.5    -      -       +      -
    302D  PHE*     3.8    26.2    -      -       +      -
    306D  PHE*     2.9    42.6    -      -       +      -
    320D  ILE*     4.1     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 264 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197D  LEU*     3.9    20.2    -      -       +      -
    220D  LEU*     4.7     5.6    -      -       +      -
    221D  PHE      4.6     3.1    -      -       -      -
    222D  GLY*     3.0    17.3    -      -       -      +
    223D  ASN      4.9     1.6    -      -       -      -
    227D  ALA*     3.6    34.5    -      -       +      -
    230D  PHE*     5.7     1.1    -      +       -      -
    241D  ILE*     3.9    24.7    -      -       +      -
    244D  ILE*     3.9     8.5    -      -       +      -
    245D  ALA*     3.6    34.1    -      -       +      -
    248D  THR*     4.4     6.1    -      -       +      -
    262D  VAL*     3.4    29.2    -      -       +      -
    263D  ILE*     1.3    83.6    -      -       -      +
    265D  THR*     1.3    66.1    +      -       -      +
    266D  GLN*     4.2     2.1    -      -       -      +
    271D  THR*     3.4     3.4    -      -       -      -
    272D  ILE*     2.8    40.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 265 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222D  GLY      2.8    17.9    +      -       -      +
    223D  ASN*     3.2    17.0    -      -       -      +
    224D  GLU*     2.9    26.2    +      -       -      +
    263D  ILE*     4.9     2.0    -      -       +      -
    264D  PHE*     1.3    76.3    -      -       -      +
    266D  GLN*     1.3    60.6    +      -       -      +
    267D  GLY      3.8     4.5    -      -       -      -
    271D  THR*     4.4    15.7    -      -       +      +
    299D  GLY*     5.1    11.6    -      -       -      -
    302D  PHE*     4.0    40.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 266 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224D  GLU*     3.5    25.4    -      -       +      +
    241D  ILE*     2.8    51.0    -      -       +      +
    264D  PHE      4.2     2.0    -      -       -      +
    265D  THR*     1.3    75.8    -      -       -      +
    267D  GLY*     1.3    61.2    +      -       -      +
    268D  ARG      3.1     0.3    +      -       -      -
    269D  ASP*     2.9    41.2    +      -       +      +
    270D  ASP*     2.7    32.8    +      -       -      +
    271D  THR*     4.9     0.6    +      -       -      +
    272D  ILE*     3.2    11.5    -      -       -      +
----------------------------------------------------------
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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