Contacts of the strand formed by residues 209 - 216 (chain F) in PDB entry 6H25


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 ALA 209 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186F  SER*     3.5     3.1    +      -       -      -
    187F  LEU*     2.9    37.9    +      -       +      +
    195F  TRP*     4.2    11.5    -      -       +      -
    207F  ALA*     5.0     2.5    -      -       -      -
    208F  ALA*     1.3    80.8    -      -       +      +
    210F  GLY*     1.3    58.7    +      -       -      +
    228F  SER      3.7     9.0    -      -       -      +
    229F  GLY*     3.7     3.6    -      -       -      -
    230F  GLU*     3.4    26.0    -      -       +      +
    231F  GLY      4.6    10.8    -      -       -      +
    237F  TRP*     5.0     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 210 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185F  LEU      3.5    12.3    -      -       -      -
    186F  SER*     4.1     4.3    -      -       -      -
    195F  TRP*     5.3     1.1    -      -       -      -
    209F  ALA*     1.3    74.1    -      -       -      +
    211F  LEU*     1.3    59.7    +      -       -      -
    227F  GLY*     3.2     1.9    -      -       -      -
    228F  SER*     2.9    35.0    +      -       -      +
    237F  TRP*     5.4     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 211 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    239E  MET*     4.7     3.4    -      -       +      -
    184F  GLY*     3.3     0.2    -      -       -      -
    185F  LEU*     2.5    64.1    +      -       +      +
    195F  TRP*     4.8     8.0    -      -       +      -
    210F  GLY*     1.3    74.4    -      -       -      +
    212F  THR*     1.3    76.6    +      -       -      +
    213F  VAL*     3.7    26.2    -      -       +      -
    225F  LEU*     5.8     4.0    -      -       +      -
    226F  LEU      4.0     0.7    -      -       -      -
    227F  GLY*     3.7    11.7    -      -       -      +
    237F  TRP*     3.5    35.0    -      -       +      +
    240F  ALA*     4.4    23.3    -      -       +      +
    241F  VAL*     4.4    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 212 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156F  SER*     5.8     0.7    -      -       -      -
    158F  LEU*     3.8    35.0    +      -       +      +
    159F  ALA*     4.1    20.6    -      -       +      +
    162F  LEU*     5.2     1.6    -      -       +      -
    183F  CYS      3.6    11.7    -      -       -      +
    184F  GLY*     3.7     5.8    -      -       -      -
    211F  LEU*     1.3    81.5    +      -       -      +
    213F  VAL*     1.3    68.9    +      -       -      +
    224F  GLY      4.0     0.7    -      -       -      +
    225F  LEU*     3.4     4.3    -      -       -      +
    226F  LEU      3.1    38.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 213 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162F  LEU*     5.5     0.2    -      -       -      -
    182F  GLY*     3.2     2.8    -      -       -      -
    183F  CYS      2.9    35.5    +      -       -      +
    185F  LEU*     4.7     3.6    -      -       +      -
    211F  LEU*     3.7    17.9    -      -       +      -
    212F  THR*     1.3    84.4    -      -       -      +
    214F  ALA*     1.3    63.2    +      -       -      +
    215F  LEU*     5.4     0.9    -      -       +      -
    222F  VAL*     5.3     4.0    -      -       +      -
    224F  GLY      3.7     4.9    -      -       -      +
    225F  LEU*     3.8    22.0    -      -       +      -
    241F  VAL*     4.6    16.8    -      -       +      -
    244F  GLY*     3.9    35.0    -      -       -      +
    245F  LEU*     4.4    11.0    -      -       +      +
    248F  CYS*     4.7     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 214 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129F  ALA*     5.2     1.8    -      -       +      -
    162F  LEU*     3.7    28.3    -      -       +      -
    180F  VAL*     4.0    14.1    -      -       +      -
    181F  VAL      3.3     7.9    -      -       -      +
    182F  GLY*     3.7     7.6    -      -       -      -
    213F  VAL*     1.3    79.0    -      -       -      +
    215F  LEU*     1.3    61.0    +      -       -      +
    222F  VAL*     3.8     3.3    -      -       -      +
    223F  ALA*     2.8    26.2    +      -       +      +
    224F  GLY      3.2    16.6    +      -       -      +
    248F  CYS*     4.9     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 215 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180F  VAL*     5.0     0.9    -      -       -      -
    181F  VAL*     3.0    25.2    +      -       -      +
    213F  VAL*     5.4     1.1    -      -       +      -
    214F  ALA*     1.3    76.1    -      -       -      +
    216F  MET*     1.3    70.9    +      -       -      +
    217F  PRO*     3.4    17.1    -      -       +      +
    220F  ASN*     4.0    20.6    -      -       -      +
    221F  GLN      3.3    17.0    -      -       -      +
    222F  VAL*     3.9     9.6    -      -       +      -
    223F  ALA*     4.0     2.5    -      -       -      +
    244F  GLY      4.6     0.2    -      -       -      +
    245F  LEU*     3.7    45.5    -      -       +      +
    248F  CYS*     3.6    30.5    -      -       +      +
    249F  GLN*     5.1     5.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 216 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246E  SER*     4.0    18.2    -      -       -      +
    132F  PRO*     3.8    41.1    -      -       +      +
    133F  ALA*     4.1    14.6    -      -       -      -
    177F  TYR*     5.1     1.1    -      -       -      -
    178F  ASP*     3.2    28.7    -      -       +      +
    179F  LEU      3.3    16.2    -      -       -      +
    180F  VAL*     4.3     9.9    -      -       +      -
    215F  LEU*     1.3    72.5    -      -       -      +
    217F  PRO*     1.3    61.6    -      -       -      +
    219F  LEU*     4.9    18.4    -      -       +      -
    220F  ASN*     2.9    28.2    +      -       -      -
    221F  GLN*     3.2    19.7    +      -       +      +
    223F  ALA*     4.7     9.2    -      -       +      -
----------------------------------------------------------
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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