Contacts of the strand formed by residues 261 - 266 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218A  ASP      2.8    13.9    +      -       -      +
    219A  ILE*     3.1    23.8    -      -       +      +
    220A  LEU      2.7    32.2    +      -       -      -
    259A  GLN      4.1     6.3    -      -       -      +
    260A  ARG*     1.3    81.9    -      -       -      +
    262A  VAL*     1.3    59.8    +      -       -      +
    263A  ILE*     4.0    10.1    -      -       +      -
    273A  MET*     3.8    26.0    -      -       +      -
    274A  ALA      3.5    11.0    -      -       -      +
    275A  THR*     4.4     6.3    -      -       +      -
    316A  LEU*     3.1    37.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 262 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220A  LEU*     3.6     9.0    -      -       +      +
    245A  ALA*     3.6    12.1    -      -       +      +
    248A  THR*     3.7    14.6    -      -       +      -
    249A  GLN*     3.4    39.7    -      -       +      +
    260A  ARG*     4.1     7.0    -      -       -      -
    261A  ILE*     1.3    76.1    -      -       -      +
    263A  ILE*     1.3    71.8    +      -       -      +
    264A  PHE*     3.2    44.9    -      -       +      -
    272A  ILE      3.5     1.1    -      -       -      +
    273A  MET*     3.2     2.8    -      -       -      +
    274A  ALA*     3.0    33.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 263 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219A  ILE*     4.5     3.6    -      -       +      -
    220A  LEU      2.8    14.9    +      -       -      +
    221A  PHE*     3.3    25.8    -      -       +      +
    222A  GLY      3.2    11.8    +      -       -      +
    261A  ILE*     4.0     7.4    -      -       +      -
    262A  VAL*     1.3    82.7    -      -       -      +
    264A  PHE*     1.3    63.4    +      -       -      +
    265A  THR*     5.0     1.4    -      -       +      +
    271A  THR*     4.0    14.4    -      -       +      -
    272A  ILE      3.4     2.5    -      -       -      +
    273A  MET*     3.5    26.7    -      -       +      -
    302A  PHE*     3.8    26.9    -      -       +      -
    306A  PHE*     3.1    40.4    -      -       +      -
    320A  ILE*     4.1     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 264 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197A  LEU*     4.0    25.6    -      -       +      -
    220A  LEU*     4.6     2.2    -      -       +      -
    221A  PHE      4.5     2.9    -      -       -      -
    222A  GLY      3.1    17.3    -      -       -      +
    223A  ASN      4.7     1.6    -      -       -      -
    227A  ALA*     3.5    19.3    -      -       +      -
    230A  PHE*     5.9     0.9    -      +       -      -
    241A  ILE*     3.3    36.3    -      -       +      -
    244A  ILE*     3.7    19.7    -      -       +      -
    245A  ALA*     3.7    18.6    -      -       +      -
    248A  THR*     4.5     9.6    -      -       +      -
    262A  VAL*     3.2    29.2    -      -       +      -
    263A  ILE*     1.3    79.3    -      -       -      +
    265A  THR*     1.3    66.0    +      -       -      +
    266A  GLN*     3.9     0.8    +      -       +      +
    270A  ASP      4.1     1.4    -      -       -      +
    271A  THR*     3.3     3.3    -      -       -      -
    272A  ILE*     2.8    42.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 265 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222A  GLY      3.1     7.9    +      -       -      +
    223A  ASN*     3.1    21.3    -      -       -      +
    224A  GLU*     3.0    25.5    +      -       -      +
    263A  ILE*     5.0     1.8    -      -       +      +
    264A  PHE*     1.3    74.8    -      -       -      +
    266A  GLN*     1.3    59.5    +      -       -      +
    267A  GLY      3.7     5.0    +      -       -      -
    271A  THR*     4.2    16.2    -      -       +      +
    299A  GLY*     5.0    11.8    -      -       -      +
    302A  PHE*     3.7    43.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 266 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224A  GLU*     3.4    36.8    -      -       +      +
    241A  ILE*     3.5    28.3    -      -       +      +
    264A  PHE      4.4     1.1    -      -       -      +
    265A  THR*     1.3    73.9    -      -       -      +
    267A  GLY*     1.3    64.5    +      -       -      +
    268A  ARG      3.2     0.7    +      -       -      -
    269A  ASP*     3.2    33.7    +      -       +      +
    270A  ASP*     2.6    38.9    +      -       -      +
    271A  THR*     4.9     0.8    +      -       -      -
    272A  ILE*     3.1    22.1    -      -       +      +
----------------------------------------------------------
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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