Contacts of the strand formed by residues 99 - 106 (chain F) in PDB entry 6AHU


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 TYR 99 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8F  ARG*     3.5    43.2    +      -       -      +
     98F  ARG*     1.3    88.5    -      -       +      +
    100F  ARG*     1.3    64.7    +      -       -      +
    101F  SER      4.3     0.4    -      -       -      -
    131F  ASN*     5.6    13.7    -      -       +      +
    132F  VAL      4.3     4.7    -      -       -      -
     86G  LEU*     2.6    54.5    +      -       +      -
     87G  GLN*     4.2     4.0    -      -       +      -
     89G  GLN*     4.4     3.9    -      -       +      +
     90G  ALA*     3.4    28.9    +      -       +      +
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Residues in contact with ARG 100 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6F  LYS      4.9    10.8    -      -       -      +
      7F  VAL*     6.3     0.4    -      -       -      -
      8F  ARG*     5.0     3.6    -      -       -      +
     37F  HIS*     5.8     3.6    -      -       -      -
     68F  SER*     4.1    15.7    -      -       -      -
     69F  GLY*     3.0    38.5    +      -       -      +
     70F  CYS*     3.6    22.6    -      -       +      +
     98F  ARG*     4.1     9.3    +      -       +      +
     99F  TYR*     1.3    81.3    -      -       -      +
    101F  SER*     1.3    62.9    +      -       -      +
    102F  VAL*     5.4     1.6    -      -       +      -
    131F  ASN*     3.8     3.0    -      -       -      -
    132F  VAL*     3.2    47.5    +      -       +      +
    134F  GLY*     3.9     7.6    -      -       -      -
    135F  LEU      3.5    22.8    +      -       -      +
    136F  ALA*     4.2     8.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 101 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4F  PHE      3.7     1.4    +      -       -      +
      5F  ARG*     3.4    22.5    -      -       -      +
      6F  LYS*     3.5    32.9    +      -       -      +
      8F  ARG*     3.5    34.0    +      -       -      +
     99F  TYR      4.3     0.6    -      -       -      -
    100F  ARG*     1.3    70.5    -      -       -      +
    102F  VAL*     1.3    62.0    +      -       -      +
    103F  ARG      4.2     0.4    -      -       -      -
    129F  LEU*     4.2    13.9    -      -       -      -
    130F  LYS      3.5     5.2    -      -       -      -
    131F  ASN*     4.0     7.4    -      -       -      -
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Residues in contact with VAL 102 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3F  ASN*     4.4    12.3    -      -       +      -
      4F  PHE      3.8     2.0    -      -       -      -
      5F  ARG*     3.5    44.0    -      -       +      +
     70F  CYS*     5.2     2.9    -      -       -      -
    100F  ARG*     4.2     2.2    -      -       +      +
    101F  SER*     1.3    75.5    -      -       -      +
    103F  ARG*     1.3    60.4    +      -       -      +
    104F  GLU*     3.9    14.8    +      -       +      +
    128F  VAL      4.0     0.2    -      -       -      +
    129F  LEU*     4.1     2.0    -      -       -      +
    130F  LYS*     2.7    56.7    +      -       +      +
    132F  VAL*     3.7    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 103 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3F  ASN*     4.2     0.7    -      -       -      -
      4F  PHE*     2.7    66.6    +      -       +      +
    101F  SER      4.2     0.2    -      -       -      -
    102F  VAL*     1.3    71.8    -      -       -      +
    104F  GLU*     1.3    58.7    +      -       -      +
    105F  VAL*     5.4     3.1    -      -       +      +
    127F  SER*     3.2    32.8    +      -       -      -
    128F  VAL*     3.5    15.0    -      -       -      +
    129F  LEU*     4.0    32.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 104 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A    C      5.4     5.2    +      -       -      -
      1F  MET*     4.5    21.6    -      -       -      +
      2F  GLU      3.4     9.6    -      -       -      +
      3F  ASN*     4.0    11.2    -      -       +      +
    102F  VAL*     3.8     8.6    -      -       +      +
    103F  ARG*     1.3    74.8    -      -       -      +
    105F  VAL*     1.3    63.9    +      -       -      +
    106F  TRP*     4.3    14.4    +      -       +      -
    126F  LEU      4.1     0.5    -      -       -      +
    127F  SER*     3.9     0.5    -      -       -      -
    128F  VAL*     3.4    41.5    +      -       +      +
    130F  LYS*     3.4    35.8    +      -       +      +
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Residues in contact with VAL 105 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1F  MET*     2.8    23.1    +      -       -      -
      2F  GLU*     3.0    25.2    +      -       +      +
      4F  PHE*     4.5    17.3    -      -       +      -
    103F  ARG*     4.9     4.0    -      -       +      +
    104F  GLU*     1.3    79.5    -      -       -      +
    106F  TRP*     1.3    63.3    -      -       -      +
    107F  GLN*     5.7     2.0    -      -       +      +
    125F  SER*     4.0    24.9    -      -       -      -
    126F  LEU      3.4    13.0    -      -       -      +
    127F  SER*     4.0    19.7    -      -       -      -
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Residues in contact with TRP 106 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1F  MET*     4.1    26.7    -      -       +      +
    104F  GLU*     4.7    16.2    -      -       +      -
    105F  VAL*     1.3    76.7    -      -       -      +
    107F  GLN*     1.3    86.1    +      -       -      +
    108F  SER*     3.6    25.6    -      -       -      -
    126F  LEU*     3.1    58.0    +      -       +      +
    128F  VAL*     4.4    21.3    -      -       +      +
----------------------------------------------------------
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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