Contacts of the strand formed by residues 2034 - 2043 (chain r) in PDB entry 6FF7


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 PRO2034 (chain r).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2029r  ILE*     5.9     3.8    -      -       -      +
   2032r  GLY      3.8     1.8    -      -       -      +
   2033r  GLY*     1.3    73.1    -      -       -      +
   2035r  VAL*     1.3    61.0    +      -       -      +
   2036r  VAL*     4.2     2.3    +      -       +      -
   2093r  ASP*     5.5     5.6    -      -       +      -
   2094r  PHE      3.4     9.0    -      -       -      +
   2095r  VAL*     4.9     0.4    -      -       -      -
   2096r  ALA*     5.4     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL2035 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2029r  ILE*     6.4     1.8    -      -       +      -
   2033r  GLY      3.5     1.0    +      -       -      +
   2034r  PRO*     1.3    72.8    -      -       -      +
   2036r  VAL*     1.3    60.7    +      -       -      +
   2037r  VAL      4.1     0.8    +      -       -      -
   2093r  ASP*     3.0     7.1    -      -       -      +
   2094r  PHE*     2.9    38.6    +      -       +      +
   2095r  VAL      5.3     0.2    -      -       -      -
   2096r  ALA*     4.9    15.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL2036 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2023r  VAL*     3.8     2.6    -      -       -      +
   2024r  VAL*     2.9    49.2    +      -       +      +
   2034r  PRO*     4.1     2.8    +      -       +      -
   2035r  VAL*     1.3    74.4    -      -       -      +
   2037r  VAL*     1.3    60.5    +      -       -      +
   2038r  LEU*     3.9     1.0    +      -       +      -
   2091r  LYS*     6.2     3.4    -      -       +      -
   2092r  LEU      3.8     4.5    -      -       -      +
   2093r  ASP*     4.3     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL2037 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2021r  TYR*     6.5     1.1    -      -       +      -
   2022r  GLU      3.4     9.6    -      -       -      +
   2023r  VAL*     4.6     3.8    -      -       +      +
   2035r  VAL      4.1     1.6    +      -       -      -
   2036r  VAL*     1.3    71.0    -      -       -      +
   2038r  LEU*     1.3    61.0    +      -       -      +
   2039r  VAL*     3.8     1.7    +      -       -      +
   2068r  ILE*     6.1     5.6    -      -       +      -
   2090r  VAL      4.3     0.2    -      -       -      +
   2091r  LYS*     3.7     1.7    -      -       -      -
   2092r  LEU*     2.9    41.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU2038 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2020r  SER      3.7     1.4    -      -       -      +
   2021r  TYR*     3.3     4.5    -      -       -      -
   2022r  GLU*     2.9    42.1    +      -       +      +
   2024r  VAL*     6.0     4.9    -      -       +      -
   2036r  VAL*     3.9     3.1    +      -       +      +
   2037r  VAL*     1.3    71.7    -      -       -      +
   2039r  VAL*     1.3    60.6    +      -       -      +
   2040r  GLN*     5.8     0.2    -      -       -      -
   2091r  LYS*     4.0    17.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL2039 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2019r  LEU*     5.7     4.7    -      -       +      -
   2020r  SER      3.5     4.9    -      -       -      +
   2021r  TYR*     4.4     9.4    -      -       +      +
   2037r  VAL      3.8     2.1    +      -       -      +
   2038r  LEU*     1.3    75.1    -      -       -      +
   2040r  GLN*     1.3    62.1    +      -       -      +
   2041r  LEU      4.3     0.7    -      -       -      -
   2066r  VAL*     5.7     8.3    -      -       +      -
   2089r  LYS*     3.8     1.4    -      -       -      +
   2090r  VAL*     2.8    47.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLN2040 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2018r  GLU      3.8     0.7    -      -       -      +
   2019r  LEU*     3.1     7.1    -      -       -      +
   2020r  SER*     2.9    49.8    +      -       -      +
   2039r  VAL*     1.3    75.8    -      -       -      +
   2041r  LEU*     1.3    61.3    +      -       -      +
   2042r  GLU*     5.5     0.3    -      -       -      +
   2088r  ALA      3.9     7.2    -      -       -      +
   2089r  LYS*     4.6     4.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU2041 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2017r  ILE*     6.0     4.5    -      -       +      -
   2018r  GLU      3.9     3.1    -      -       -      -
   2019r  LEU*     4.4     6.7    -      -       +      +
   2039r  VAL      4.3     0.4    -      -       -      -
   2040r  GLN*     1.3    73.0    -      -       -      +
   2042r  GLU*     1.3    64.1    +      -       -      +
   2084r  LEU*     5.3     5.6    -      -       +      -
   2087r  LYS*     3.7     2.2    -      -       -      +
   2088r  ALA*     2.9    53.7    +      -       +      +
   2089r  LYS*     4.7     0.2    -      -       -      +
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Residues in contact with GLU2042 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2017r  ILE*     3.3     6.8    -      -       -      +
   2018r  GLU*     2.9    40.4    +      -       +      +
   2041r  LEU*     1.3    77.0    -      -       -      +
   2043r  ARG*     1.3    61.7    +      -       -      +
   2044r  GLU      4.4     0.2    -      -       -      -
   2086r  GLN      4.2     7.6    -      -       -      +
   2087r  LYS*     4.6     2.5    -      -       +      +
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Residues in contact with ARG2043 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   2016r  ASN      3.4    14.8    -      -       -      +
   2017r  ILE*     4.9     3.4    -      -       +      -
   2018r  GLU      5.1     0.2    -      -       -      +
   2042r  GLU*     1.3    77.6    -      -       -      +
   2044r  GLU*     1.3    59.1    +      -       -      +
   2045r  GLU*     3.3    15.9    +      -       +      +
   2086r  GLN*     3.5    39.6    +      -       +      +
----------------------------------------------------------
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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