Contacts of the strand formed by residues 215 - 221 (chain A) in PDB entry 1EF1


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 GLU 215 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207A  SER*     2.9    27.9    +      -       -      -
    208A  ILE      3.5    11.7    -      -       -      +
    209A  LYS*     3.7    27.3    +      -       -      +
    213A  GLY      3.5     2.4    +      -       -      +
    214A  SER*     1.3    70.8    -      -       -      +
    216A  LEU*     1.3    78.6    +      -       -      +
    217A  TRP*     5.6     2.6    -      -       -      -
    230A  GLN*     3.4    47.1    +      -       -      +
    272A  PRO*     5.9     1.2    -      -       -      +
    217B  TRP*     6.0     3.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 216 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207A  SER*     3.6     6.1    -      -       -      -
    208A  ILE*     2.8    37.8    +      -       +      +
    210A  ASN*     4.1    17.9    -      -       +      +
    214A  SER*     3.7    12.1    -      -       -      +
    215A  GLU*     1.3    95.2    -      -       -      +
    217A  TRP*     1.3    71.9    +      -       -      +
    227A  ILE*     4.2     7.6    -      -       +      -
    228A  TYR      3.6    13.5    -      -       -      +
    229A  GLU*     4.6     1.3    -      -       +      -
    230A  GLN*     4.4     8.1    -      -       -      +
    574C  PHE*     3.5    36.1    -      -       +      -
    577C  MSE      4.1    36.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 217 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205A  TYR*     4.1    21.1    -      -       +      -
    206A  PHE*     3.3    27.8    -      -       -      -
    207A  SER*     3.7    24.5    -      -       -      -
    208A  ILE*     4.3     3.8    -      -       -      -
    215A  GLU*     5.6     1.8    -      -       -      -
    216A  LEU*     1.3    80.3    -      -       -      +
    218A  LEU*     1.3    60.4    +      -       -      +
    227A  ILE*     3.4     7.8    -      -       -      +
    228A  TYR*     2.8    47.6    +      -       +      -
    229A  GLU      3.4    23.8    -      -       -      -
    230A  GLN*     2.8    34.2    +      -       +      +
    233A  ARG*     3.6    30.8    -      -       +      +
    215B  GLU*     5.3     5.2    -      -       +      -
    217B  TRP*     6.5     1.3    -      +       -      -
    230B  GLN*     3.5    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 218 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204A  ASN      3.5     1.2    -      -       -      +
    205A  TYR*     3.3     3.8    -      -       -      -
    206A  PHE*     2.8    35.4    +      -       +      +
    208A  ILE*     3.7    24.1    -      -       +      +
    217A  TRP*     1.3    73.6    -      -       -      +
    219A  GLY*     1.3    68.6    +      -       -      +
    220A  VAL*     4.1     9.6    -      -       +      -
    225A  LEU*     4.4    17.7    -      -       +      -
    226A  ASN      3.4    16.2    -      -       -      +
    227A  ILE*     3.6    16.4    -      -       +      -
    228A  TYR*     4.6     1.3    -      -       -      -
    267A  PHE*     4.9     2.0    -      -       +      -
    269A  PHE*     3.7    31.6    -      -       +      -
    280A  ILE*     3.8    30.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 219 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203A  VAL*     3.8    18.4    -      -       -      -
    204A  ASN      3.3     6.3    -      -       -      -
    205A  TYR*     4.5     0.9    -      -       -      -
    218A  LEU*     1.3    75.4    -      -       -      +
    220A  VAL*     1.3    61.1    +      -       -      -
    221A  ASP      4.2     0.2    -      -       -      -
    224A  GLY      4.1     0.3    -      -       -      +
    225A  LEU*     3.5     8.5    -      -       -      +
    226A  ASN*     2.8    35.8    +      -       -      +
    228A  TYR*     3.8    14.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 220 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204A  ASN*     2.8    47.2    +      -       +      +
    206A  PHE*     3.6    29.4    -      -       +      -
    218A  LEU*     4.1    10.5    -      -       +      -
    219A  GLY*     1.3    73.5    -      -       -      -
    221A  ASP*     1.3    64.1    +      -       -      +
    224A  GLY      3.9     2.7    -      -       -      -
    225A  LEU*     3.8    25.1    -      -       +      -
    242A  TRP*     4.3     5.4    -      -       +      -
    280A  ILE*     4.2    10.3    -      -       +      -
    283A  LEU*     4.0    26.5    -      -       +      +
    284A  CYS*     4.0    14.1    -      -       -      +
    287A  ASN*     4.2     5.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 221 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201A  TYR      5.0     1.7    -      -       -      +
    202A  GLY      3.1    26.7    -      -       -      +
    203A  VAL*     3.8    18.1    -      -       +      +
    204A  ASN*     4.6     1.1    -      -       -      +
    220A  VAL*     1.3    74.8    -      -       -      +
    222A  ALA*     1.3    67.2    +      -       -      +
    223A  LEU*     3.1    25.4    +      -       -      +
    224A  GLY      3.2    17.3    +      -       -      +
    226A  ASN*     4.0    18.6    +      -       -      -
    242A  TRP*     3.3    20.4    -      -       -      -
    287A  ASN*     3.5    11.7    -      -       -      +
    555C  LYS*     5.3     6.9    +      -       -      -
    559C  LEU*     5.9     1.6    -      -       -      +
----------------------------------------------------------
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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