Contacts of the strand formed by residues 80 - 85 (chain A) in PDB entry 3ANX


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 80 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  LYS*     1.3    78.2    -      -       +      +
     81A  VAL*     1.3    64.1    +      -       -      +
    102A  GLU*     5.4     7.6    +      -       +      +
    103A  LYS*     3.2    42.6    -      -       +      +
    150A  GLU*     3.5    31.2    +      -       -      -
    151A  ARG      3.1    29.4    +      -       -      +
    152A  TYR*     3.5    10.4    -      -       +      -
    153A  ASP*     2.6    42.1    +      -       -      +
    154A  VAL      3.5     5.0    +      -       -      -
    186A  ASN*     5.1     5.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 81 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  MET*     3.9    28.9    -      -       +      -
     78A  PRO*     4.9     6.7    -      -       +      -
     80A  ARG*     1.3    82.2    -      -       -      +
     82A  LEU*     1.3    75.4    +      -       -      +
     83A  ILE*     4.0    12.1    -      -       +      -
     95A  VAL*     3.7    28.3    -      -       +      -
    101A  VAL*     5.0     4.5    -      -       +      -
    103A  LYS      2.8    11.0    +      -       -      +
    104A  ALA*     3.2     4.7    -      -       -      -
    105A  VAL*     3.0    25.5    +      -       -      +
    152A  TYR*     3.6     7.5    -      -       -      -
    154A  VAL*     3.3    16.4    -      -       +      +
    156A  ILE*     4.9     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 82 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81A  VAL*     1.3    75.4    -      -       -      +
     83A  ILE*     1.3    63.6    +      -       -      +
     84A  VAL*     4.0    12.6    -      -       +      -
    105A  VAL*     3.4    15.0    -      -       +      +
    107A  VAL*     3.4    32.3    -      -       +      -
    144A  TYR*     4.1    12.6    -      -       +      -
    145A  LEU*     3.8    29.4    -      -       +      -
    152A  TYR*     3.7    32.3    -      -       +      +
    154A  VAL      3.0     6.9    +      -       -      -
    155A  VAL*     3.2    20.8    -      -       +      -
    156A  ILE      2.7    32.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 83 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81A  VAL*     4.0    11.7    -      -       +      -
     82A  LEU*     1.3    79.7    -      -       -      +
     84A  VAL*     1.3    62.1    +      -       -      +
     85A  GLY      3.6    16.8    +      -       -      +
     86A  GLY*     4.9     0.7    -      -       -      -
     91A  THR*     3.9    23.6    -      -       +      -
     92A  LEU*     3.6    42.0    -      -       +      +
     95A  VAL*     3.8    20.6    -      -       +      -
    104A  ALA*     5.4     1.6    -      -       +      -
    105A  VAL      2.9    13.8    +      -       -      +
    106A  MET*     3.7    12.5    -      -       +      +
    107A  VAL*     3.0    25.5    +      -       -      +
    156A  ILE*     3.4     9.0    -      -       +      +
    158A  ASP*     5.4     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 84 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82A  LEU*     4.1    24.9    -      -       +      -
     83A  ILE*     1.3    71.9    -      -       -      +
     85A  GLY*     1.3    65.8    +      -       -      +
    107A  VAL*     4.2     5.2    -      -       +      -
    141A  ALA*     3.8    29.6    -      -       +      -
    145A  LEU*     4.5     9.0    -      -       +      -
    155A  VAL*     4.2     8.1    -      -       +      -
    156A  ILE      2.7    16.2    +      -       -      +
    157A  ILE*     4.2    16.2    -      -       +      -
    158A  ASP*     2.9    26.3    +      -       -      +
    159A  LEU*     3.6    28.5    -      -       +      -
    177A  PHE*     4.7     1.3    -      -       +      -
    181A  VAL*     5.4     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 85 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83A  ILE*     3.6    14.7    -      -       -      +
     84A  VAL*     1.3    80.2    -      -       -      +
     86A  GLY*     1.3    64.0    +      -       -      -
     87A  GLY      3.6     2.0    +      -       -      -
    106A  MET*     4.0     4.2    -      -       -      +
    107A  VAL      3.0    21.8    +      -       -      +
    108A  ASP*     3.7     4.2    -      -       -      +
    158A  ASP      3.4     3.4    -      -       -      -
    159A  LEU*     3.9     2.5    -      -       -      -
    315A  MTA      3.3    28.3    +      -       -      -
----------------------------------------------------------
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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