Contacts of the strand formed by residues 45 - 50 (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 PHE 45 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  PHE*     3.5    12.9    -      -       +      -
     39A  LEU*     3.9    13.2    -      -       +      -
     41A  GLU      3.6    24.2    -      -       -      -
     42A  VAL      3.1    10.5    +      -       -      +
     43A  TRP      4.7     2.1    -      -       -      +
     44A  PHE*     1.3    90.3    -      -       +      +
     46A  GLY*     1.3    59.0    +      -       -      +
     61A  LEU*     6.0     0.7    -      -       -      +
     80A  PHE*     3.3    41.3    -      +       +      -
     81A  ARG*     3.5    15.5    -      -       -      +
     82A  ALA*     3.6    17.3    -      -       +      -
     83A  LYS*     4.5     6.3    -      -       -      +
     84A  PHE*     5.7     1.6    -      -       -      -
     98A  THR*     4.2    16.6    -      -       +      -
    101A  LEU*     4.0    31.2    -      -       +      -
    102A  PHE*     4.0    18.8    -      +       -      -
    105A  GLN*     5.3     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 46 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  PHE*     4.0     7.6    -      -       -      -
     45A  PHE*     1.3    76.9    -      -       -      +
     47A  LEU*     1.3    63.9    +      -       -      -
     58A  TRP*     3.6    17.6    -      -       -      -
     61A  LEU*     6.3     1.3    -      -       -      -
     80A  PHE*     3.5     8.9    -      -       -      -
     81A  ARG      2.9    32.1    +      -       -      -
     83A  LYS*     5.0     3.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 47 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  VAL*     3.5    31.6    -      -       +      -
     29A  LEU*     3.8    31.4    -      -       +      +
     30A  PHE*     4.0    26.3    -      -       +      -
     33A  VAL*     4.5     2.9    -      -       +      -
     46A  GLY*     1.3    75.2    -      -       -      -
     48A  GLN*     1.3    60.1    +      -       -      +
     58A  TRP*     3.5     6.1    -      -       -      +
     59A  LEU*     2.9    56.7    +      -       +      +
     61A  LEU*     5.5     2.7    -      -       +      +
     78A  PHE*     4.1    15.0    -      -       +      -
     79A  LYS      3.5     0.4    -      -       -      -
     80A  PHE*     3.8    24.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 48 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  LEU*     1.3    75.2    -      -       -      +
     49A  TYR*     1.3    62.8    +      -       -      +
     56A  SER*     3.8    19.8    +      -       -      +
     57A  THR      3.2    22.0    -      -       -      +
     58A  TRP*     3.6    27.1    -      -       +      +
     78A  PHE*     3.3     6.4    -      -       -      -
     79A  LYS*     2.7    47.4    +      -       +      +
     81A  ARG*     4.0    23.2    -      -       -      +
    279A  ARG*     3.4    25.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 49 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  GLN*     1.3    78.2    -      -       -      +
     50A  GLN*     1.3    74.9    +      -       -      +
     51A  ASP*     3.7    23.3    -      -       +      +
     55A  PHE      3.2     1.4    -      -       -      +
     56A  SER*     3.5     2.3    -      -       -      -
     57A  THR*     2.8    74.6    +      -       -      +
     58A  TRP      4.0     0.7    -      -       -      -
     59A  LEU*     3.6    36.6    -      -       +      -
     68A  GLN*     3.8    20.1    +      -       +      +
     69A  ASP*     3.8    14.5    +      -       -      +
     70A  VAL*     3.7    24.0    -      -       +      -
     77A  LEU      3.8    11.4    -      -       -      +
     78A  PHE*     3.6    19.7    -      +       +      -
----------------------------------------------------------
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Residues in contact with GLN 50 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  GLN*     5.8     0.3    -      -       -      +
     49A  TYR*     1.3    84.0    -      -       -      +
     51A  ASP*     1.3    64.9    +      -       -      +
     54A  GLY*     2.9    31.0    +      -       -      -
     55A  PHE      3.4     2.3    -      -       -      -
     56A  SER*     2.8    28.0    +      -       -      +
     71A  ARG*     3.4    32.3    +      -       +      +
     77A  LEU      4.7     3.0    +      -       -      -
     79A  LYS*     5.7     2.6    +      -       -      -
----------------------------------------------------------
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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