Contacts of the strand formed by residues 216 - 223 (chain A) in PDB entry 5CVE


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 216 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168A  ASN*     3.4     3.1    -      -       -      -
    169A  MET*     2.8    36.1    +      -       +      +
    171A  GLN*     4.4    17.9    +      -       -      -
    206A  ARG*     3.1    52.3    +      -       -      +
    210A  LEU*     6.0     0.7    -      -       -      -
    214A  ILE      4.2     7.4    -      -       -      -
    215A  TYR*     1.3    78.6    -      -       -      +
    217A  VAL*     1.3    59.0    -      -       -      +
    218A  TYR*     4.0    18.9    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 217 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  TRP*     3.9    19.5    -      -       +      +
    166A  LYS*     4.0    28.3    -      -       +      -
    167A  ASP      3.4    10.8    -      -       -      +
    168A  ASN*     3.6    22.0    -      -       -      +
    206A  ARG*     3.5     7.0    -      -       -      +
    207A  GLN*     2.8    42.9    +      -       +      +
    210A  LEU*     3.6    29.8    -      -       +      +
    214A  ILE*     4.9     2.9    -      -       +      -
    215A  TYR      3.8     4.9    -      -       -      +
    216A  HIS*     1.3    79.3    -      -       -      +
    218A  TYR*     1.3    61.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 218 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165A  ILE      3.5     2.1    -      -       -      +
    166A  LYS*     3.2     5.7    -      -       -      +
    167A  ASP      3.0    31.0    +      -       -      +
    169A  MET*     3.6    22.9    -      -       +      -
    187A  LEU*     3.8    36.8    -      -       +      +
    204A  GLU*     4.0    20.2    -      -       +      -
    205A  GLU*     3.4     6.3    -      -       -      -
    206A  ARG*     3.6    47.5    -      -       +      +
    207A  GLN      5.4     0.2    -      -       -      -
    216A  HIS*     4.0    16.7    +      -       +      -
    217A  VAL*     1.3    79.5    -      -       -      +
    219A  SER*     1.3    61.4    +      -       -      +
    220A  PHE*     3.8    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 219 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  SER*     5.9     0.5    -      -       -      -
     48A  PHE*     3.8    35.1    -      -       -      +
    133A  TRP*     5.6     0.5    -      -       -      -
    164A  VAL*     4.7     2.6    -      -       -      +
    165A  ILE      3.2     6.3    -      -       -      -
    166A  LYS*     3.3    34.7    +      -       -      +
    203A  ALA      3.8     0.5    -      -       -      +
    204A  GLU*     3.3     6.8    -      -       -      +
    205A  GLU*     2.9    36.9    +      -       -      -
    207A  GLN*     5.8     0.7    -      -       -      +
    218A  TYR*     1.3    73.1    -      -       -      +
    220A  PHE*     1.3    62.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 220 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  PHE*     4.2     2.7    -      -       -      -
    163A  ILE      3.5     1.6    -      -       -      +
    164A  VAL*     3.2     6.2    -      -       -      -
    165A  ILE*     2.7    50.7    +      -       +      +
    169A  MET*     3.6    26.0    -      -       +      -
    187A  LEU*     3.8    24.9    -      -       +      -
    190A  VAL*     4.1    16.2    -      -       +      -
    191A  ARG*     4.0    14.6    -      -       -      -
    194A  ILE*     4.1    13.7    -      -       +      -
    201A  LEU*     3.8    18.6    -      -       +      -
    203A  ALA      3.4     4.5    -      -       -      -
    204A  GLU*     3.5    29.4    -      -       +      -
    218A  TYR*     3.8    14.1    -      -       +      -
    219A  SER*     1.3    75.4    -      -       -      +
    221A  ALA*     1.3    60.5    +      -       -      +
    222A  LEU*     4.0    17.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 221 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48A  PHE*     3.8    14.6    -      -       +      -
     52A  PHE*     3.4    39.0    -      -       +      -
    162A  ILE*     4.6     3.8    -      -       +      -
    163A  ILE      3.5     5.2    -      -       -      +
    164A  VAL*     4.4     5.8    -      -       +      -
    201A  LEU*     3.7     0.9    -      -       -      +
    202A  LEU*     2.7    34.2    +      -       +      -
    203A  ALA      2.9    14.0    +      -       -      +
    220A  PHE*     1.3    71.5    -      -       -      +
    222A  LEU*     1.3    61.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 222 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150A  LEU*     5.0     0.2    -      -       +      -
    162A  ILE*     3.3     4.2    -      -       -      +
    163A  ILE*     2.8    49.0    +      -       +      +
    165A  ILE*     3.8    34.3    -      -       +      -
    194A  ILE*     3.7    33.7    -      -       +      -
    199A  LEU*     4.0    27.4    -      -       +      -
    200A  SER      3.2    10.1    -      -       -      +
    201A  LEU*     3.7    20.2    -      -       +      -
    202A  LEU*     4.0     5.5    -      -       -      +
    220A  PHE*     4.0     7.2    -      -       +      +
    221A  ALA*     1.3    83.7    -      -       -      +
    223A  ARG*     1.3    65.4    +      -       -      +
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Residues in contact with ARG 223 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52A  PHE*     4.8     5.5    -      -       -      -
     58A  ASN      4.9     4.9    +      -       -      -
     60A  THR*     3.9     4.4    +      -       -      -
    154A  LYS*     3.6    26.3    -      -       -      +
    157A  LEU*     4.2    10.8    -      -       +      +
    160A  ASN*     3.0    36.5    +      -       -      +
    161A  GLY      2.9    24.8    +      -       -      +
    162A  ILE*     3.3    14.1    -      -       -      +
    198A  GLY      4.6     0.9    -      -       -      +
    199A  LEU*     3.5    18.0    -      -       -      +
    200A  SER*     2.8    41.1    +      -       -      -
    202A  LEU*     3.5    33.8    -      -       +      +
    222A  LEU*     1.3    76.9    -      -       -      +
    109B  LYS*     3.9    36.5    -      -       -      +
----------------------------------------------------------
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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