Contacts of the strand formed by residues 114 - 121 (chain F) in PDB entry 4BEI


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 VAL 114 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61F  GLN*     3.4     8.3    +      -       -      +
     62F  LEU*     2.7    50.4    +      -       +      +
     64F  ILE*     6.5     0.2    -      -       +      -
     76F  TYR*     3.7    25.4    -      -       +      +
    112F  LEU*     3.9    22.2    -      -       +      -
    113F  ASN*     1.3    79.5    -      -       -      +
    115F  THR*     1.3    77.8    +      -       -      +
    116F  ARG*     3.8    16.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 115 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59F  SER*     3.7    17.0    -      -       -      +
     60F  SER      3.5    12.1    -      -       -      +
     61F  GLN*     2.7    25.4    +      -       +      +
    114F  VAL*     1.3    85.0    -      -       -      +
    116F  ARG*     1.3    66.7    +      -       -      +
    117F  GLY      5.0     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 116 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60F  SER*     2.6    56.8    +      -       -      +
     62F  LEU*     4.2     9.9    -      -       +      -
     76F  TYR*     4.0    26.3    +      -       -      -
     77F  TRP*     4.5     5.5    -      -       -      +
     78F  LEU*     3.8    45.7    +      -       +      +
     90F  ALA*     5.3     3.4    -      -       -      +
     91F  LYS*     4.6    25.9    -      -       -      +
    114F  VAL*     3.8    13.4    +      -       +      +
    115F  THR*     1.3    83.3    -      -       -      +
    117F  GLY*     1.3    60.4    +      -       -      +
    118F  PHE*     4.7     1.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 117 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57F  TYR*     3.2    26.7    +      -       -      -
     58F  ILE      3.3     9.2    -      -       -      -
     59F  SER*     4.0     4.5    -      -       -      -
     78F  LEU*     6.1     0.2    -      -       -      -
     90F  ALA*     4.8     4.0    -      -       -      +
     91F  LYS*     5.9     0.7    -      -       -      -
    115F  THR*     5.0     1.6    -      -       -      +
    116F  ARG*     1.3    81.7    +      -       -      +
    118F  PHE*     1.3    65.7    +      -       -      +
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Residues in contact with PHE 118 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219E  ARG*     4.1     4.9    -      -       -      +
     46F  LEU*     4.9     0.2    -      -       +      -
     57F  TYR*     3.5     9.6    -      -       -      -
     58F  ILE*     2.9    66.5    +      -       +      +
     60F  SER*     4.6     8.5    -      -       -      -
     78F  LEU*     4.4     9.4    -      -       +      -
     80F  ILE*     3.9    19.5    -      -       +      -
     88F  PHE*     5.0     0.2    -      +       -      -
     90F  ALA*     3.6    37.5    -      -       +      +
    116F  ARG      4.7     0.4    -      -       -      -
    117F  GLY*     1.3    79.2    -      -       -      +
    119F  TRP*     1.3    63.9    +      -       -      +
    120F  VAL*     3.6    28.5    -      -       +      -
    131F  VAL*     3.6    33.0    -      -       +      -
    149F  PHE*     4.2     4.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with TRP 119 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219E  ARG*     2.4    39.9    +      -       -      +
     54F  ASN      5.9     0.9    -      -       -      -
     55F  GLY      5.1     1.1    -      -       -      -
     56F  GLY*     3.4    36.6    -      -       -      -
     57F  TYR*     3.8    33.0    -      +       +      -
    118F  PHE*     1.3    75.9    -      -       -      +
    120F  VAL*     1.3    65.3    +      -       -      +
    121F  PRO*     4.5    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 120 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219E  ARG*     4.3     0.4    -      -       -      +
     51F  LEU*     3.7    19.7    -      -       +      -
     55F  GLY*     3.2     2.4    -      -       -      -
     56F  GLY      2.9    32.5    +      -       -      +
     58F  ILE*     4.4     1.1    -      -       +      -
     88F  PHE*     4.6     8.1    -      -       +      -
    118F  PHE*     3.6    27.6    -      -       +      +
    119F  TRP*     1.3    78.0    -      -       -      +
    121F  PRO*     1.3    68.5    -      -       -      +
    124F  MET*     4.4    11.4    -      -       +      -
    129F  TYR*     4.8     7.0    -      -       +      -
    149F  PHE*     3.9    23.1    -      -       +      -
    151F  LYS*     3.9    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 121 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201E  GLU*     3.9     7.9    -      -       -      +
    219E  ARG*     3.5    18.8    -      -       -      +
    221E  LYS*     5.6     2.9    -      -       -      +
     54F  ASN      5.3     0.2    -      -       -      +
     55F  GLY*     4.2     0.4    -      -       -      -
    119F  TRP*     3.7    15.5    -      -       +      +
    120F  VAL*     1.3    91.4    -      -       -      +
    122F  GLU*     1.3    65.5    +      -       -      +
    123F  TYR*     3.2    46.2    -      -       +      +
    124F  MET*     3.1    31.2    +      -       +      +
    151F  LYS*     3.4     5.2    -      -       -      -
----------------------------------------------------------
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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