Contacts of the strand formed by residues 272 - 278 (chain A) in PDB entry 2EF1


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 GLN 272 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236A  GLN*     2.9    50.2    +      -       -      +
    237A  THR*     3.5    11.6    -      -       +      +
    238A  LEU      3.0    24.7    +      -       -      -
    266A  ILE*     3.8     1.9    -      -       -      +
    267A  SER*     6.1     0.2    -      -       -      -
    271A  ILE*     1.3    78.4    -      -       -      +
    273A  PHE*     1.3    60.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 273 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    237A  THR*     4.6     1.3    -      -       -      -
    238A  LEU*     3.4    26.5    -      -       +      -
    240A  ALA*     3.9    15.9    -      -       +      -
    254A  CYS      5.8     0.2    -      -       -      -
    259A  ILE*     3.9    22.9    -      -       +      -
    262A  LEU*     3.6    31.9    -      -       +      -
    263A  GLU*     3.2    55.1    -      -       +      +
    266A  ILE*     4.0    11.2    -      -       +      -
    267A  SER*     5.4     1.5    -      -       -      +
    271A  ILE      3.7     0.4    +      -       -      -
    272A  GLN*     1.3    78.4    -      -       -      +
    274A  SER*     1.3    75.9    +      -       -      +
    275A  CYS*     3.7    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 274 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    237A  THR*     4.2    12.3    -      -       -      -
    238A  LEU      3.0     5.6    +      -       -      +
    239A  GLU*     3.2    28.8    +      -       -      +
    240A  ALA      2.8    24.8    +      -       -      -
    273A  PHE*     1.3    83.9    -      -       -      +
    275A  CYS*     1.3    64.5    +      -       -      +
    276A  LYS*     4.5     8.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 275 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240A  ALA*     3.5     9.9    -      -       -      +
    242A  VAL*     3.9    19.1    -      -       -      -
    254A  CYS*     2.0    58.2    -      -       +      +
    259A  ILE*     4.1     9.4    -      -       +      -
    273A  PHE*     3.7    17.4    -      -       +      -
    274A  SER*     1.3    78.4    +      -       -      +
    276A  LYS*     1.3    70.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 276 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    239A  GLU*     2.9    41.8    +      -       +      +
    240A  ALA      2.9    10.6    +      -       -      +
    241A  TRP*     3.4    13.6    -      -       +      +
    242A  VAL*     3.0    25.3    +      -       -      -
    254A  CYS*     3.7     5.1    -      -       -      -
    274A  SER*     4.5     7.9    -      -       -      +
    275A  CYS*     1.3    83.7    -      -       -      +
    277A  ASN*     1.3    63.2    +      -       -      +
    278A  ILE*     3.7     3.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 277 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242A  VAL*     3.9     4.8    -      -       -      +
    244A  HIS*     3.0    15.8    +      -       -      +
    252A  ASP*     2.6    30.7    +      -       -      -
    253A  LEU*     3.0    27.6    +      -       -      +
    254A  CYS*     3.7    10.8    +      -       -      -
    276A  LYS*     1.3    74.7    -      -       -      +
    278A  ILE*     1.3    61.5    +      -       -      +
    279A  TYR*     3.5    42.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 278 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241A  TRP*     3.4    38.8    -      -       +      -
    242A  VAL      2.9     9.6    +      -       -      +
    243A  ILE*     3.4    34.2    -      -       +      -
    244A  HIS*     3.1    23.6    +      -       -      -
    276A  LYS*     4.5     4.5    -      -       +      +
    277A  ASN*     1.3    74.6    -      -       -      +
    279A  TYR*     1.3    60.4    +      -       -      +
    280A  ARG      4.5     1.8    -      -       -      +
    281A  PRO*     4.0    13.2    -      -       +      +
    284A  PHE*     3.9    49.4    -      -       +      -
----------------------------------------------------------
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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