Contacts of the strand formed by residues 180 - 185 (chain A) in PDB entry 4BY7


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 LYS 180 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  PHE*     4.7     2.5    -      -       -      -
    176A  LYS*     3.6     5.3    -      -       -      +
    177A  ASP*     2.8    44.6    +      -       +      +
    178A  GLY      3.4     0.2    -      -       -      -
    179A  LEU*     1.4    84.4    -      -       +      +
    181A  LEU*     1.4    63.2    +      -       -      +
    182A  VAL*     4.9     3.8    -      -       +      -
    201A  VAL*     4.1    30.4    -      -       +      +
    290A  GLU*     4.2    10.1    +      -       -      +
    294A  SER*     3.8    32.7    +      -       -      -
    297A  GLN*     6.2     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 181 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  PHE*     4.0    15.3    -      -       +      -
     96A  ILE*     4.6    10.5    -      -       +      +
     99A  ILE*     3.9    28.3    -      -       +      -
    100A  LYS*     3.8    46.0    -      -       +      +
    103A  CYS*     4.9     2.7    -      -       -      -
    174A  ILE*     3.8    15.5    -      -       +      -
    175A  ARG      3.6     0.7    -      -       -      -
    176A  LYS*     4.2    16.4    -      -       +      -
    180A  LYS*     1.4    76.6    -      -       -      +
    182A  VAL*     1.4    55.7    +      -       -      +
    183A  GLY      4.3     0.2    -      -       -      -
    201A  VAL*     3.8     2.9    -      -       -      +
    202A  LEU*     2.8    37.9    +      -       +      +
    207A  ILE*     4.0    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 182 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173A  THR      3.4     2.9    -      -       -      +
    174A  ILE*     3.4     3.6    -      -       -      +
    175A  ARG*     2.9    52.2    +      -       +      +
    177A  ASP*     4.4    21.8    -      -       +      -
    180A  LYS*     4.8     2.2    -      -       +      +
    181A  LEU*     1.4    77.3    -      -       -      +
    183A  GLY*     1.3    61.0    +      -       -      +
    199A  LEU*     3.8    27.6    -      -       +      -
    200A  ARG      3.6    17.7    -      -       -      +
    201A  VAL*     3.7    24.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 183 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172A  PRO*     3.7    17.5    -      -       -      -
    173A  THR      3.5     7.0    -      -       -      -
    174A  ILE*     4.3     1.6    -      -       -      -
    182A  VAL*     1.3    74.7    -      -       -      +
    184A  SER*     1.4    61.2    +      -       -      -
    185A  TRP*     3.4    22.5    -      -       -      -
    199A  LEU*     3.6     6.9    -      -       -      +
    200A  ARG      3.2    22.9    +      -       -      -
    202A  LEU*     4.3     7.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 184 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171A  GLN      5.0     0.3    -      -       -      +
    172A  PRO*     3.9     1.0    -      -       -      +
    173A  THR*     3.2    44.8    +      -       -      +
    175A  ARG*     6.6     0.2    -      -       -      -
    183A  GLY*     1.4    72.9    -      -       -      -
    185A  TRP*     1.3    61.3    +      -       -      +
    197A  PRO*     3.4    25.3    -      -       -      +
    198A  GLU      3.4     4.5    -      -       -      -
    199A  LEU*     3.7    23.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 185 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  MET*     5.7     2.8    -      -       +      +
    170A  THR*     3.2    32.4    +      -       +      -
    171A  GLN*     3.9     5.1    -      -       -      +
    172A  PRO*     3.4    44.1    -      -       +      +
    183A  GLY*     3.4    23.6    -      -       -      -
    184A  SER*     1.3    71.5    -      -       -      +
    186A  LYS*     1.4    62.1    +      -       -      +
    197A  PRO*     3.2    24.9    -      -       -      +
    198A  GLU*     3.3    43.8    +      -       +      +
    200A  ARG*     3.7    44.4    -      -       +      -
    202A  LEU*     3.7    25.6    -      -       +      -
----------------------------------------------------------
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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