Contacts of the strand formed by residues 96 - 102 (chain F) in PDB entry 6XAV


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 THR 96 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52F  ASP*     5.1     5.2    -      -       +      +
     53F  GLY*     3.4    25.4    -      -       -      +
     54F  VAL*     3.8    17.3    -      -       +      +
     94F  GLY      3.1     7.8    +      -       -      -
     95F  ASP*     1.3    67.7    -      -       -      +
     97F  ILE*     1.3    62.6    +      -       -      +
     98F  SER*     5.7     2.2    -      -       -      -
    118F  GLU      3.8     1.6    -      -       -      +
    119F  VAL*     3.6     4.0    -      -       -      -
    120F  ASN*     2.5    48.6    +      -       -      -
    121F  PHE*     4.3    25.9    -      -       +      +
    249F  LYS*     4.3    12.1    -      -       -      +
    253F  LEU*     6.1     1.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 97 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52F  ASP*     3.3    14.0    -      -       -      -
     53F  GLY      3.2     7.0    +      -       -      -
     55F  LEU*     4.9     2.5    -      -       +      -
     65F  LEU*     3.3    35.6    -      -       +      +
     81F  VAL*     6.0     0.7    -      -       +      -
     91F  LEU*     3.7    39.5    -      -       +      -
     95F  ASP*     3.1    16.5    +      -       +      +
     96F  THR*     1.3    78.6    -      -       -      +
     98F  SER*     1.3    64.6    +      -       -      +
    113F  LEU*     3.7    30.5    -      -       +      -
    116F  VAL*     3.7    15.7    -      -       +      -
    118F  GLU      4.0     0.9    -      -       -      -
    119F  VAL*     3.8    24.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 98 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51F  GLY      3.2    13.9    -      -       -      -
     52F  ASP*     3.7    13.5    -      -       -      -
     96F  THR*     5.5     2.9    -      -       -      -
     97F  ILE*     1.3    77.9    -      -       -      +
     99F  GLY*     1.3    57.8    +      -       -      +
    116F  VAL*     3.9     0.5    -      -       -      +
    117F  ASN*     2.9    21.4    +      -       -      +
    118F  GLU*     3.0    40.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 99 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50F  PHE*     3.5     6.3    -      -       -      +
     51F  GLY      3.2    27.6    +      -       -      -
     65F  LEU*     6.1     0.6    -      -       -      +
     97F  ILE      4.3     0.6    -      -       -      -
     98F  SER*     1.3    74.3    -      -       -      +
    100F  LYS*     1.3    65.9    +      -       -      -
    101F  ILE*     3.3     4.9    +      -       -      +
    113F  LEU*     4.0    12.0    -      -       -      +
    115F  LYS      3.3    11.0    -      -       -      -
    116F  VAL*     4.1     0.7    -      -       -      -
    117F  ASN*     3.3    15.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 100 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48F  ASP*     3.5    42.1    +      -       +      +
     49F  ILE      3.4    13.0    -      -       -      +
     50F  PHE*     3.8    17.7    -      -       +      -
     99F  GLY*     1.3    70.6    -      -       -      -
    101F  ILE*     1.3    65.4    +      -       -      +
    113F  LEU*     3.6     3.8    -      -       -      +
    114F  LEU*     3.2    41.7    +      -       +      +
    115F  LYS*     3.0    19.5    +      -       +      +
    117F  ASN*     3.4     6.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 101 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3F  LEU*     4.9     9.4    -      -       +      -
     39F  LEU*     5.7     1.1    -      -       +      -
     49F  ILE*     2.7    54.6    +      -       +      +
     50F  PHE      3.8     7.4    -      -       -      +
     51F  GLY*     3.7    21.3    -      -       -      +
     79F  ILE*     3.7    44.0    -      -       +      -
     99F  GLY      3.6     9.6    -      -       -      +
    100F  LYS*     1.3    81.4    -      -       -      +
    102F  ARG*     1.3    62.1    +      -       -      +
    111F  PHE*     4.3    22.9    -      -       +      -
    112F  ALA      3.3    10.8    -      -       -      +
    113F  LEU*     4.2     7.4    -      -       +      -
    114F  LEU*     4.0     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 102 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101F  ILE*     1.3    75.9    -      -       -      +
    103F  PRO*     1.3    84.1    +      -       +      +
    104F  PRO*     4.7     0.2    -      -       -      +
    105F  LYS*     3.4    46.9    -      -       -      +
    108F  GLU*     4.1    19.6    +      -       -      -
    111F  PHE*     3.2    25.3    -      -       -      -
    112F  ALA*     3.2    30.9    +      -       +      +
    114F  LEU*     3.7    32.5    -      -       +      +
    185G  SER*     5.3    11.7    -      -       -      -
    187G  ARG*     5.8     2.6    -      -       -      +
----------------------------------------------------------
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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