Contacts of the strand formed by residues 2171 - 2178 (chain A) in PDB entry 5W0P


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 VAL2171 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2016A  LYS*     3.6    45.5    -      -       +      +
   2017A  VAL      4.0     7.0    -      -       -      +
   2018A  SER*     3.9    10.5    -      -       -      +
   2023A  VAL*     3.9    21.5    -      -       +      +
   2025A  ILE*     4.2    14.9    -      -       +      +
   2150A  VAL      4.3     0.2    -      -       -      +
   2151A  LYS*     3.4     2.8    -      -       -      +
   2152A  ALA*     2.7    59.0    +      -       +      +
   2170A  SER*     1.3    77.8    -      -       -      +
   2172A  ARG*     1.3    65.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG2172 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    336A  TPO      3.5    32.1    +      -       -      +
    338A  SEP      4.3     0.2    +      -       -      -
   2016A  LYS*     3.0    32.8    +      -       -      +
   2025A  ILE*     5.7     1.1    -      -       -      -
   2067A  ARG*     6.3     0.2    -      -       -      -
   2149A  GLU*     3.3    31.0    +      -       -      +
   2150A  VAL      3.5     5.4    -      -       -      -
   2151A  LYS*     3.7    31.8    -      -       +      +
   2171A  VAL*     1.3    79.9    -      -       -      +
   2173A  LEU*     1.3    61.0    +      -       -      +
   2174A  LEU*     6.5     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU2173 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    338A  SEP      4.4    13.9    -      -       -      +
   2014A  PHE*     4.2    26.2    -      -       +      -
   2015A  LYS*     5.1     6.1    -      -       -      +
   2016A  LYS*     4.6    15.3    -      -       +      +
   2025A  ILE*     5.2    10.8    -      -       +      -
   2027A  LEU*     3.9    20.9    -      -       +      -
   2030A  ARG*     3.8    25.8    -      -       +      +
   2149A  GLU*     4.5     3.4    -      -       -      -
   2150A  VAL*     2.9    35.4    +      -       -      +
   2172A  ARG*     1.3    77.2    -      -       -      +
   2174A  LEU*     1.3    84.6    +      -       -      +
   2175A  ILE*     3.7    16.3    +      -       +      +
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Residues in contact with LEU2174 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    338A  SEP      5.2     3.4    +      -       -      +
   2030A  ARG*     3.6    18.9    +      -       -      +
   2067A  ARG*     4.9     6.1    -      -       -      +
   2147A  ASP*     3.7    25.6    -      -       +      +
   2148A  PHE      3.7    12.1    -      -       -      +
   2149A  GLU*     3.6    26.7    -      -       +      +
   2172A  ARG*     6.5     0.2    -      -       +      -
   2173A  LEU*     1.3    87.1    -      -       -      +
   2175A  ILE*     1.3    61.6    +      -       -      +
   2299A  LYS      5.9     1.6    -      -       -      +
   2300A  ILE*     4.6    12.5    -      -       +      +
   2301A  LYS*     5.3    12.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE2175 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2027A  LEU*     4.2     4.7    -      -       +      -
   2029A  LYS      4.6     0.2    -      -       -      +
   2030A  ARG*     3.3    19.1    -      -       -      +
   2032A  TYR*     3.8    27.8    -      -       +      -
   2042A  VAL*     3.8    11.9    -      -       +      -
   2062A  LEU*     4.1     9.2    -      -       +      -
   2123A  PHE*     4.2     5.6    -      -       +      -
   2130A  SER*     4.2     1.2    +      -       -      -
   2147A  ASP*     5.3     0.9    -      -       -      +
   2148A  PHE*     3.1    43.6    +      -       +      +
   2150A  VAL*     3.5    36.3    -      -       +      -
   2173A  LEU*     3.8    17.0    -      -       +      +
   2174A  LEU*     1.3    79.7    -      -       -      +
   2176A  ARG*     1.3    67.7    +      -       -      +
   2300A  ILE*     4.8     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG2176 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2030A  ARG      2.8    10.0    +      -       -      +
   2031A  ASP*     2.9    43.6    +      -       -      +
   2032A  TYR*     2.8    35.9    +      -       -      +
   2130A  SER*     3.4    13.5    -      -       -      +
   2148A  PHE*     4.9     1.8    -      -       -      -
   2175A  ILE*     1.3    79.4    -      -       -      +
   2177A  LYS*     1.3    56.6    -      -       -      +
   2178A  VAL*     3.9    21.5    -      -       +      +
   2297A  ASP*     4.8     8.5    -      -       -      +
   2298A  GLY*     2.8    45.0    +      -       -      +
   2299A  LYS*     4.9     0.4    -      -       -      +
   2300A  ILE*     3.5    27.8    -      -       +      +
   2303A  GLU*     3.9    17.6    +      -       -      -
   2305A  THR*     4.9     4.2    +      -       -      -
   2306A  ASN*     5.9     0.2    +      -       -      -
   2358A  HIS*     5.9     3.6    -      -       -      -
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Residues in contact with LYS2177 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2032A  TYR*     3.5     7.4    -      -       +      +
   2034A  ASP*     2.9    46.7    +      -       +      +
   2039A  VAL*     3.7    22.9    -      -       +      +
   2123A  PHE*     4.2    17.5    -      -       +      -
   2124A  PRO      5.0     1.3    +      -       -      -
   2125A  ASP      6.4     0.2    -      -       -      -
   2127A  LEU*     3.3    25.3    +      -       -      +
   2128A  PRO      3.3    16.6    +      -       -      +
   2129A  CYS*     3.3    10.3    -      -       -      +
   2130A  SER*     2.9    29.7    +      -       -      -
   2148A  PHE*     3.6    39.8    -      -       +      -
   2176A  ARG*     1.3    71.9    -      -       -      +
   2178A  VAL*     1.3    60.3    +      -       -      +
   2179A  GLN*     4.9     0.2    -      -       -      +
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Residues in contact with VAL2178 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2031A  ASP*     4.9    10.5    -      -       +      -
   2032A  TYR      3.1     9.9    +      -       -      +
   2033A  VAL*     3.5     6.9    -      -       -      +
   2034A  ASP      2.7    29.6    +      -       -      -
   2129A  CYS*     4.8     2.0    -      -       -      -
   2130A  SER*     5.4     3.8    -      -       -      +
   2176A  ARG*     3.9    37.9    -      -       +      +
   2177A  LYS*     1.3    78.3    -      -       -      +
   2179A  GLN*     1.3    71.2    +      -       -      +
   2180A  HIS*     3.9    15.8    +      -       +      +
   2297A  ASP*     5.8     6.1    -      -       +      +
   2309A  SER*     5.3     3.6    -      -       -      +
   2358A  HIS*     4.5    20.0    -      -       +      +
----------------------------------------------------------
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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