Contacts of the strand formed by residues 236 - 245 (chain F) in PDB entry 6GL7


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 236 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    332C  GLU*     2.9    37.0    +      -       -      +
    234F  ARG*     3.5    23.0    -      -       -      +
    235F  GLU*     1.3    86.6    -      -       +      +
    237F  TYR*     1.3    69.2    +      -       -      +
    238F  GLU*     6.5     0.7    -      -       +      -
    260F  VAL      3.9     7.4    -      -       -      +
    261F  THR*     5.7     0.7    -      -       -      -
    262F  VAL*     3.6    10.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 237 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212F  LEU*     4.0    16.2    -      -       +      -
    213F  PRO*     3.7    24.7    -      -       +      +
    214F  PHE*     3.7    23.8    -      +       +      -
    229F  LEU*     2.9    38.9    -      -       +      +
    233F  GLN*     3.7    15.1    +      -       -      +
    234F  ARG*     3.6    32.7    -      -       +      +
    236F  LYS*     1.3    80.5    -      -       -      +
    238F  GLU*     1.3    60.7    +      -       -      +
    239F  LEU*     3.9    18.2    -      -       +      -
    258F  PHE      4.4     0.2    -      -       -      -
    259F  PRO*     3.4     4.2    -      -       -      +
    260F  VAL*     2.9    41.6    +      -       +      +
    262F  VAL*     3.5    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 238 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208F  GLU*     5.7     1.2    -      -       -      +
    236F  LYS*     6.4     1.1    -      -       +      -
    237F  TYR*     1.3    75.1    -      -       -      +
    239F  LEU*     1.3    69.5    +      -       -      +
    240F  VAL*     5.5     0.9    -      -       -      +
    257F  PRO*     4.1    15.5    -      -       +      +
    258F  PHE      3.6     7.0    -      -       -      +
    259F  PRO*     4.1    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 239 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206F  LEU*     4.1    16.6    -      -       +      -
    207F  LEU      4.3     3.1    -      -       -      +
    208F  GLU*     4.2     9.0    -      -       -      +
    209F  GLY*     3.6    25.6    -      -       -      +
    212F  LEU*     3.9    24.9    -      -       +      -
    214F  PHE*     3.9    30.3    -      -       +      -
    237F  TYR*     3.9    24.7    -      -       +      -
    238F  GLU*     1.3    81.8    -      -       -      +
    240F  VAL*     1.3    66.6    +      -       -      +
    257F  PRO*     3.6     4.0    -      -       -      +
    258F  PHE*     2.7    49.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 240 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206F  LEU*     3.5     5.3    -      -       -      +
    207F  LEU*     2.8    56.2    +      -       +      +
    208F  GLU*     4.2    22.4    -      -       -      +
    238F  GLU      5.5     0.7    -      -       -      +
    239F  LEU*     1.3    77.5    -      -       -      +
    241F  ALA*     1.3    61.5    +      -       -      +
    255F  MET*     3.7    39.5    -      -       +      -
    256F  VAL      3.8     7.4    -      -       -      +
    257F  PRO*     5.8     1.6    -      -       +      -
    258F  PHE*     4.5     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 241 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167F  PHE*     3.5    23.1    -      -       +      -
    188F  PHE*     3.9    23.8    -      -       +      -
    205F  ARG      3.7     4.7    -      -       -      -
    206F  LEU*     4.3     2.5    -      -       +      -
    239F  LEU      4.1     1.2    +      -       -      -
    240F  VAL*     1.3    72.8    -      -       -      +
    242F  VAL*     1.3    58.5    +      -       -      +
    255F  MET*     3.0     4.6    -      -       -      +
    256F  VAL*     2.8    45.3    +      -       +      +
    258F  PHE*     3.9    15.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 242 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167F  PHE*     3.8     3.6    -      -       -      -
    204F  TYR*     3.4     3.8    -      -       -      +
    205F  ARG*     2.8    76.4    +      -       +      +
    207F  LEU*     3.7    27.1    -      -       +      -
    241F  ALA*     1.3    74.6    -      -       -      +
    243F  CYS*     1.3    65.2    +      -       -      +
    253F  VAL*     3.5    25.6    -      -       +      -
    254F  VAL      3.5    12.6    -      -       -      +
    255F  MET*     3.9    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 243 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162F  PRO*     5.0     0.7    -      -       -      -
    166F  CYS*     2.0    53.2    -      -       -      -
    167F  PHE*     3.7     2.2    -      -       +      -
    202F  VAL*     4.2     0.7    -      -       +      -
    203F  ALA      3.1    16.4    -      -       -      +
    204F  TYR*     3.6    16.6    -      -       +      -
    205F  ARG*     5.6     1.8    -      -       -      +
    242F  VAL*     1.3    75.8    -      -       -      +
    244F  THR*     1.3    62.5    +      -       -      +
    253F  VAL*     3.4     8.5    -      -       -      +
    254F  VAL*     3.0    50.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 244 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201F  SER      3.8     0.7    -      -       -      +
    202F  VAL*     3.4     6.6    -      -       -      +
    203F  ALA*     3.1    30.0    +      -       -      +
    205F  ARG*     4.4    14.1    +      -       -      +
    219F  ASP*     5.9     2.7    -      -       -      -
    243F  CYS*     1.3    78.3    +      -       -      +
    245F  VAL*     1.3    71.4    +      -       -      +
    246F  HIS      4.3     6.5    -      -       -      +
    251F  GLU*     4.2    17.9    -      -       +      -
    252F  GLU      3.4     9.9    -      -       -      +
    253F  VAL*     3.6    17.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 245 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162F  PRO*     3.7    21.3    -      -       +      -
    165F  LEU*     3.9    11.9    -      -       +      -
    166F  CYS*     5.0     2.4    -      -       -      -
    200F  ILE*     3.2    35.9    -      -       +      -
    201F  SER      3.3     5.6    -      -       -      +
    202F  VAL*     3.9     7.9    -      -       +      -
    244F  THR*     1.3    73.5    -      -       -      +
    246F  HIS*     1.3    87.3    +      -       +      +
    251F  GLU*     3.3     1.9    -      -       -      -
    252F  GLU*     3.1    48.9    +      -       +      +
----------------------------------------------------------
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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