Contacts of the strand formed by residues 163 - 168 (chain A) in PDB entry 5CYO


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 ASN 163 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134A  HIS      3.0    22.8    +      -       -      +
    135A  CYS*     3.4     4.7    -      -       -      -
    136A  CYS*     2.8    32.1    +      -       -      +
    162A  VAL*     1.3    77.1    -      -       -      +
    164A  ILE*     1.3    58.2    +      -       -      +
    198A  TYR*     4.3    16.4    -      -       +      -
    200A  GLN*     3.2    21.4    +      -       -      +
    273A  ILE*     3.1    23.7    +      -       +      +
    276A  ILE*     3.3    10.8    -      -       -      +
    277A  THR*     3.0    22.0    +      -       -      +
    281A  HIS*     3.1    17.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 164 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  CYS*     3.5    32.1    -      -       +      +
    138A  TYR*     4.3    13.7    -      -       +      -
    155A  MET*     4.5    14.6    -      -       +      +
    158A  LEU*     3.5    26.7    -      -       +      -
    159A  SER*     3.8    21.8    -      -       -      +
    162A  VAL*     3.5    13.6    +      -       +      +
    163A  ASN*     1.3    77.1    -      -       -      +
    165A  VAL*     1.3    66.0    +      -       -      +
    166A  PRO*     4.0    15.3    -      -       +      -
    195A  ILE*     5.7     0.9    -      -       +      -
    196A  ASP      4.5    12.0    +      -       -      +
    197A  VAL*     3.4    11.4    -      -       +      +
    198A  TYR      2.8    30.7    +      -       -      +
    200A  GLN*     5.2     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  CYS*     3.6    19.7    -      -       -      -
    136A  CYS      2.9    10.0    +      -       -      -
    137A  LEU*     3.3    25.6    -      -       +      +
    138A  TYR      3.1    19.0    +      -       -      -
    164A  ILE*     1.3    78.8    -      -       -      +
    166A  PRO*     1.3    67.9    -      -       +      +
    167A  VAL*     3.8     1.3    +      -       +      +
    198A  TYR*     3.9    22.0    -      -       +      +
    220A  ILE*     4.3     7.0    -      -       +      -
    222A  PHE*     3.7    35.7    -      -       +      -
    261A  LEU*     4.4     2.9    -      -       +      -
    264A  LEU*     4.3    13.9    -      -       +      -
    265A  LEU*     6.2     0.9    -      -       +      -
    273A  ILE*     5.7     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138A  TYR*     3.4    10.1    -      -       +      +
    140A  ILE*     3.9    21.8    -      -       +      -
    155A  MET*     4.2    12.1    -      -       -      -
    164A  ILE*     3.7     4.2    -      -       +      +
    165A  VAL*     1.3    93.6    -      -       -      +
    167A  VAL*     1.3    62.0    +      -       -      +
    190A  LEU*     4.0    11.7    -      -       +      -
    197A  VAL*     3.6    31.2    -      -       +      -
    220A  ILE*     3.5    23.9    -      -       +      +
    221A  PRO*     3.3    20.8    -      -       +      +
    222A  PHE      3.4     4.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  LEU*     5.4     0.7    -      -       +      -
    137A  LEU*     5.3     4.5    -      -       +      -
    138A  TYR      2.8     8.1    +      -       -      +
    139A  PHE*     4.0    26.2    -      -       +      -
    140A  ILE*     2.8    30.0    +      -       -      +
    165A  VAL      4.7     4.3    -      -       -      +
    166A  PRO*     1.3    74.7    -      -       -      +
    168A  ILE*     1.3    67.7    +      -       -      +
    169A  ALA      3.9     2.0    -      -       -      +
    221A  PRO*     4.1     2.7    -      -       -      -
    222A  PHE*     3.4    29.2    -      -       +      +
    224A  VAL*     3.4    40.8    -      -       +      -
    261A  LEU*     4.2    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140A  ILE*     3.7     7.0    -      -       -      +
    142A  ALA*     3.9     8.3    -      -       +      -
    167A  VAL*     1.3    72.1    -      -       -      +
    169A  ALA*     1.3    73.4    +      -       -      +
    171A  ALA*     3.8     7.2    -      -       +      +
    174A  LEU*     3.9    26.2    -      -       +      -
    179A  ARG*     4.7     6.7    -      -       +      +
    182A  PHE*     3.8    20.2    -      -       +      -
    183A  LYS*     3.8    33.2    -      -       +      -
    186A  ILE*     4.1    11.7    -      -       +      -
    221A  PRO*     4.0    21.8    -      -       +      +
    222A  PHE      2.7    12.7    +      -       -      +
    223A  ALA*     4.2     5.2    -      -       +      -
    224A  VAL*     3.2    24.6    +      -       -      +
----------------------------------------------------------
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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