Contacts of the strand formed by residues 217 - 224 (chain A) in PDB entry 2EX4


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 HIS 217 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169A  ASN*     3.1     6.9    -      -       -      -
    170A  MET*     2.7    39.0    +      -       +      +
    172A  GLN*     4.4    22.3    +      -       +      -
    207A  ARG*     3.4    39.9    +      -       -      +
    211A  LEU*     5.2     2.7    -      -       -      -
    213A  ASP      5.8     1.8    -      -       -      -
    215A  ILE      4.6     5.8    -      -       -      -
    216A  TYR*     1.3    72.5    -      -       -      +
    218A  VAL*     1.3    57.4    +      -       -      +
    219A  TYR*     4.3    21.1    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 218 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137A  TRP*     4.3    19.1    -      -       +      -
    167A  LYS*     3.9    28.7    -      -       +      -
    168A  ASP      3.2    11.9    -      -       -      +
    169A  ASN*     4.0    14.1    -      -       -      +
    207A  ARG*     3.5     6.3    -      -       -      +
    208A  GLN*     2.8    50.4    +      -       +      +
    211A  LEU*     3.3    25.4    -      -       +      +
    215A  ILE*     5.7     1.3    -      -       +      -
    216A  TYR      3.9     6.1    -      -       -      +
    217A  HIS*     1.3    77.9    -      -       -      +
    219A  TYR*     1.3    67.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 219 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166A  ILE      3.6     1.7    -      -       -      +
    167A  LYS*     3.4     4.2    -      -       -      -
    168A  ASP      3.0    29.7    +      -       -      +
    170A  MET*     3.5    19.7    -      -       +      -
    188A  LEU*     3.4    38.9    -      -       +      +
    192A  ARG*     5.2     0.4    -      -       -      -
    205A  GLU*     4.1    22.4    -      -       +      -
    206A  GLU      3.4     5.2    -      -       -      -
    207A  ARG*     3.6    47.6    -      -       +      +
    217A  HIS*     4.3    17.6    +      -       +      -
    218A  VAL*     1.3    78.8    -      -       -      +
    220A  SER*     1.3    61.5    +      -       -      +
    221A  PHE*     3.6    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 220 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  SER*     5.8     0.9    -      -       -      -
     48A  PHE*     3.8    34.9    -      -       -      +
    134A  TRP*     5.9     0.4    -      -       -      -
    165A  VAL*     4.7     2.7    -      -       -      -
    166A  ILE      3.2     6.7    -      -       -      -
    167A  LYS*     3.2    32.7    +      -       -      +
    204A  ALA      3.8     0.3    -      -       -      +
    205A  GLU*     3.3     6.2    -      -       -      +
    206A  GLU*     2.8    41.2    +      -       -      -
    208A  GLN*     5.7     0.9    -      -       -      +
    219A  TYR*     1.3    72.4    -      -       -      +
    221A  PHE*     1.3    62.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 221 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  PHE*     4.3     3.4    -      -       -      -
    164A  ILE      3.5     1.6    -      -       -      +
    165A  VAL*     3.3     4.4    -      -       -      +
    166A  ILE*     2.8    54.8    +      -       +      +
    170A  MET*     3.8    22.9    -      -       +      -
    188A  LEU*     3.9    15.0    -      -       +      -
    191A  VAL*     4.1    13.9    -      -       +      -
    192A  ARG*     4.4    12.3    -      -       +      -
    195A  ILE*     4.2    12.8    -      -       +      -
    202A  LEU*     3.8    26.0    -      -       +      -
    204A  ALA      3.3     5.8    -      -       -      -
    205A  GLU*     3.6    30.1    -      -       +      -
    219A  TYR*     3.6    29.4    -      -       +      -
    220A  SER*     1.3    73.2    -      -       -      +
    222A  ALA*     1.3    58.9    +      -       -      +
    223A  LEU*     3.9    11.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 222 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  PHE*     3.8    14.4    -      -       +      -
     52A  PHE*     3.4    39.9    -      -       +      -
    163A  ILE*     4.2    11.9    -      -       +      -
    164A  ILE      3.4     4.3    -      -       -      -
    165A  VAL*     4.3     2.2    -      -       +      -
    202A  LEU*     3.7     0.2    -      -       -      -
    203A  LEU*     2.7    33.8    +      -       +      -
    204A  ALA      2.9    11.2    +      -       -      +
    221A  PHE*     1.3    72.2    -      -       -      +
    223A  LEU*     1.3    60.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 223 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  LEU*     4.7     0.4    -      -       +      -
    163A  ILE*     3.2     4.4    -      -       -      +
    164A  ILE*     2.8    53.5    +      -       +      +
    166A  ILE*     3.9    29.2    -      -       +      -
    195A  ILE*     3.6    33.7    -      -       +      -
    200A  LEU*     3.9    30.1    -      -       +      -
    201A  SER      3.2    13.7    -      -       -      +
    202A  LEU*     3.7    19.1    -      -       +      -
    203A  LEU*     3.7     5.1    -      -       -      +
    221A  PHE*     3.9     6.3    -      -       +      +
    222A  ALA*     1.3    84.9    -      -       -      +
    224A  ARG*     1.3    65.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 224 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52A  PHE*     4.6     6.3    -      -       -      -
     61A  THR*     4.0     4.4    +      -       -      +
    155A  LYS*     4.5    18.1    +      -       -      -
    158A  LEU*     4.0    11.2    -      -       +      -
    161A  ASN*     3.1    37.9    +      -       -      +
    162A  GLY      3.0    24.9    +      -       -      +
    163A  ILE*     3.3    14.6    -      -       -      +
    199A  GLY      4.8     0.7    -      -       -      +
    200A  LEU*     3.4    23.1    -      -       -      +
    201A  SER*     2.8    39.9    +      -       -      -
    203A  LEU*     3.8    29.9    -      -       +      +
    223A  LEU*     1.3    78.3    -      -       -      +
----------------------------------------------------------
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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