Contacts of the strand formed by residues 270 - 276 (chain B) in PDB entry 2AEB


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 LEU 270 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  ARG*     5.0     2.8    -      -       -      -
     93B  ILE*     3.3    26.3    -      -       +      +
    227B  ILE*     3.7    11.0    -      -       +      +
    229B  LEU*     4.0    15.9    -      -       +      +
    264B  ILE*     4.0    29.9    +      -       +      +
    265B  TYR*     5.4     2.2    +      -       -      -
    267B  THR*     4.3     4.6    +      -       -      -
    268B  GLY      3.7     3.1    -      -       -      +
    269B  LEU*     1.3    77.2    +      -       -      +
    271B  SER*     1.3    60.7    +      -       -      +
    272B  GLY      3.4    26.5    -      -       -      +
    273B  LEU*     4.7     4.5    -      -       +      -
    303B  CYS*     3.5    44.0    -      -       +      +
    304B  PHE*     4.2    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 271 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88B  LYS*     2.8    42.9    +      -       -      +
     93B  ILE*     3.5     7.2    -      -       -      -
     94B  SER      3.4     9.9    +      -       -      -
    111B  HIS*     2.5    34.0    +      -       -      -
    115B  HIS*     4.2     4.2    +      -       -      -
    226B  PRO*     3.5    21.7    -      -       -      +
    227B  ILE      2.7    12.9    +      -       -      -
    269B  LEU      3.7     2.5    -      -       -      -
    270B  LEU*     1.3    75.6    -      -       -      +
    272B  GLY*     1.3    55.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 272 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93B  ILE*     4.1     1.3    -      -       -      +
     94B  SER*     3.4    18.4    -      -       -      -
    111B  HIS*     3.6     3.9    -      -       -      -
    227B  ILE      3.2     4.6    +      -       -      -
    228B  HIS*     3.4    17.6    -      -       -      -
    229B  LEU      3.0    24.3    +      -       -      -
    270B  LEU*     3.4    10.0    -      -       -      +
    271B  SER*     1.3    77.7    -      -       -      +
    273B  LEU*     1.3    60.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 273 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93B  ILE*     5.2     0.4    -      -       +      -
     94B  SER*     2.8    12.0    +      -       -      +
     95B  LEU*     3.9    17.9    -      -       +      -
     96B  VAL*     2.9    26.4    +      -       -      +
    228B  HIS*     4.4     1.4    -      -       -      -
    229B  LEU*     3.3    38.8    -      -       +      +
    231B  PHE*     4.8     3.6    -      -       +      -
    270B  LEU*     4.7     9.0    -      -       +      -
    272B  GLY*     1.3    74.4    -      -       -      +
    274B  ASP*     1.3    83.1    +      -       -      +
    275B  ILE*     4.3     8.7    -      -       +      -
    299B  ILE*     6.1     1.6    -      -       +      -
    300B  THR*     4.1    11.0    -      -       +      -
    303B  CYS*     4.0    16.6    -      -       +      -
    304B  PHE*     3.7    29.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 274 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96B  VAL*     3.6    10.5    -      -       -      +
    103B  LEU      6.1     0.2    -      -       -      -
    104B  ALA*     4.2     8.1    -      -       -      +
    107B  SER*     2.6    32.6    +      -       -      -
    228B  HIS*     2.7    25.4    +      -       -      -
    229B  LEU      2.9     6.3    +      -       -      -
    230B  SER*     2.8    26.3    +      -       -      +
    231B  PHE*     3.0    30.0    +      -       -      +
    273B  LEU*     1.3    81.9    -      -       -      +
    275B  ILE*     1.3    61.8    +      -       -      +
    276B  MET*     3.6    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 275 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31B  LEU*     4.1    19.5    -      -       +      +
     36B  LEU*     5.0     1.1    -      -       +      -
     95B  LEU*     3.3    32.3    -      -       +      -
     96B  VAL      2.9     8.1    +      -       -      +
     97B  LEU*     3.6    14.9    -      -       +      -
     98B  GLY*     2.9    30.0    +      -       -      +
    231B  PHE*     3.7     7.2    -      -       +      -
    233B  VAL*     4.7     5.6    -      -       +      -
    273B  LEU*     4.3    10.1    -      -       +      -
    274B  ASP*     1.3    74.2    -      -       -      +
    276B  MET*     1.3    55.6    +      -       -      +
    278B  VAL*     4.7     7.0    -      -       +      +
    296B  ALA*     4.2    22.2    -      -       +      +
    299B  ILE*     5.8     5.2    -      -       +      -
    300B  THR*     2.8    33.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 276 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96B  VAL*     4.2     7.9    -      -       +      +
     98B  GLY*     3.8    15.3    -      -       -      -
     99B  GLY      3.6    11.7    -      -       -      +
    100B  ASP      3.1    28.7    -      -       -      +
    101B  HIS*     3.7    31.9    -      -       +      +
    103B  LEU*     3.8    19.5    -      -       +      -
    104B  ALA      4.9     1.6    -      -       -      +
    231B  PHE      3.0    13.9    +      -       -      +
    232B  ASP*     4.4     1.3    -      -       -      -
    233B  VAL*     3.1    30.4    +      -       -      +
    274B  ASP*     3.6    30.7    -      -       +      -
    275B  ILE*     1.3    87.5    -      -       -      +
    277B  GLU*     1.4    68.0    +      -       +      +
    278B  VAL      3.3     4.0    +      -       -      -
----------------------------------------------------------
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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