Contacts of the strand formed by residues 173 - 178 (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 ARG 173 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171F  GLY      3.8     2.6    +      -       -      +
    172F  GLN*     1.3    80.9    -      -       -      +
    174F  GLY*     1.3    57.8    +      -       -      +
    301F  PHE*     3.4    53.4    -      -       +      +
    302F  GLY*     4.2     9.9    +      -       -      -
    304F  ALA*     3.2    29.0    +      -       +      +
    305F  ARG*     5.4     0.4    -      -       -      +
    315F  ILE      3.6     4.0    -      -       -      -
    338F  THR*     3.2    29.5    +      -       -      +
    339F  GLY*     3.4    10.1    -      -       -      +
    340F  ASN*     2.9    51.4    +      -       -      +
    341F  MET      3.7     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 174 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172F  GLN*     3.9     1.4    -      -       -      +
    173F  ARG*     1.3    75.3    -      -       -      +
    175F  LEU*     1.3    63.7    +      -       -      -
    176F  ILE*     5.7     0.7    -      -       -      -
    301F  PHE*     3.2    17.9    -      -       -      -
    315F  ILE      3.5     6.3    +      -       -      -
    316F  ILE*     4.0    11.8    -      -       -      +
    317F  ALA      3.3    17.5    +      -       -      -
    341F  MET*     3.3    27.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 175 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    174F  GLY*     1.3    75.2    -      -       -      +
    176F  ILE*     1.3    64.1    +      -       -      +
    177F  VAL*     3.2    14.3    +      -       +      +
    267F  ILE*     3.7    18.4    -      -       +      -
    301F  PHE*     3.5    28.3    -      -       +      -
    317F  ALA*     3.3    16.8    -      -       +      +
    319F  ALA*     4.8     8.7    -      -       +      -
    332F  TYR*     5.4     5.6    -      -       +      +
    335F  PHE*     3.5    35.4    -      -       +      +
    336F  LYS*     4.0    10.1    -      -       +      +
    339F  GLY*     5.3     3.1    -      -       -      +
    341F  MET*     2.7    13.8    +      -       -      +
    342F  GLU*     3.4    13.4    -      -       +      +
    343F  LEU      3.0    24.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 176 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162F  LEU*     4.5    10.8    -      -       +      -
    168F  ILE*     5.5     3.1    -      -       +      -
    174F  GLY*     5.7     0.4    -      -       -      -
    175F  LEU*     1.3    71.0    -      -       -      +
    177F  VAL*     1.3    59.4    +      -       -      +
    178F  ALA*     3.6     4.0    +      -       +      +
    184F  LYS*     5.8     4.1    -      -       +      +
    187F  LEU*     3.7    31.9    -      -       +      -
    191F  ILE*     4.9     2.9    -      -       +      -
    316F  ILE*     4.1    20.4    -      -       +      -
    317F  ALA      2.6    21.7    +      -       -      +
    318F  THR*     3.3    20.4    -      -       +      +
    319F  ALA      2.7    27.3    +      -       -      +
    341F  MET*     6.2     3.8    -      -       +      -
    343F  LEU*     3.8    37.9    -      -       +      +
    345F  LEU*     4.9     7.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 177 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175F  LEU*     3.7    18.2    -      -       +      +
    176F  ILE*     1.3    68.3    -      -       -      +
    178F  ALA*     1.3    66.8    +      -       -      +
    319F  ALA*     3.9    11.9    -      -       +      -
    321F  ILE*     3.7    33.9    -      -       +      -
    332F  TYR*     3.6    31.9    -      -       +      -
    342F  GLU*     4.5     4.3    -      -       +      -
    343F  LEU      2.9    20.7    +      -       -      +
    344F  HIS*     3.9    32.3    -      -       +      +
    345F  LEU*     3.1    16.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 178 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176F  ILE*     4.6     4.5    -      -       +      +
    177F  VAL*     1.3    80.6    -      -       -      +
    179F  PRO*     1.3    76.3    -      -       +      +
    182F  ALA*     4.2     2.2    -      -       +      -
    184F  LYS*     3.7    30.7    -      -       +      +
    319F  ALA      3.6    16.0    +      -       -      +
    320F  LEU*     4.1     2.8    -      -       -      +
    321F  ILE*     3.8    14.0    +      -       -      -
    345F  LEU*     3.7    23.1    -      -       +      -
----------------------------------------------------------
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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