Contacts of the strand formed by residues 103 - 107 (chain B) 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 LYS 103 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79B  LYS      3.0     5.1    +      -       -      +
     80B  ARG*     3.2    32.1    -      -       +      +
     81B  VAL      2.8    30.3    +      -       -      +
    101B  VAL*     3.9     2.0    -      -       -      -
    102B  GLU*     1.3    81.9    -      -       +      +
    104B  ALA*     1.3    55.6    +      -       -      +
    105B  VAL*     4.1    12.4    +      -       +      +
    133B  ARG*     3.6     7.6    -      -       -      +
    135B  VAL*     3.6    28.0    -      -       +      +
    150B  GLU*     2.9    33.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 104 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81B  VAL*     3.3    14.1    -      -       +      +
     83B  ILE*     4.9     2.0    -      -       +      -
     92B  LEU*     4.4    10.3    -      -       +      +
     95B  VAL*     4.1    25.6    -      -       +      -
     96B  LEU*     4.2    16.4    -      -       +      -
    101B  VAL*     4.5     3.3    -      -       +      +
    102B  GLU      4.3     0.2    -      -       -      -
    103B  LYS*     1.3    72.6    -      -       -      +
    105B  VAL*     1.3    63.7    +      -       -      +
    106B  MET      3.5     2.2    +      -       -      -
    133B  ARG      3.0    10.2    +      -       -      +
    134B  ALA*     3.4     6.3    -      -       -      +
    135B  VAL*     3.0    21.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 105 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81B  VAL      3.0     8.2    +      -       -      +
     82B  LEU*     3.4     8.8    -      -       +      +
     83B  ILE*     3.0    25.4    +      -       -      +
    103B  LYS*     4.1     7.4    -      -       +      +
    104B  ALA*     1.3    71.8    -      -       -      +
    106B  MET*     1.3    61.3    +      -       -      +
    107B  VAL*     5.1     1.1    -      -       +      +
    135B  VAL*     3.7    24.9    -      -       +      +
    137B  VAL*     3.6    31.6    -      -       +      -
    144B  TYR*     3.7    18.8    -      -       +      +
    150B  GLU*     3.7    14.6    -      -       -      +
    152B  TYR*     3.7    26.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 106 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83B  ILE*     3.3    15.5    -      -       +      +
     85B  GLY      3.8    16.4    -      -       -      +
     86B  GLY      3.9    19.3    -      -       -      +
     87B  GLY*     4.7     2.5    -      -       -      +
     89B  GLY*     3.8     6.3    -      -       -      -
     91B  THR*     6.0     0.2    -      -       -      -
     92B  LEU*     3.5    44.4    -      -       +      +
    104B  ALA      3.5     4.2    +      -       -      +
    105B  VAL*     1.3    72.9    -      -       -      +
    107B  VAL*     1.3    63.7    +      -       -      +
    108B  ASP*     4.1     5.3    +      -       +      -
    114B  VAL*     5.5     1.3    -      -       -      -
    129B  PHE*     3.3    37.7    -      -       +      -
    134B  ALA*     6.1     0.7    -      -       +      -
    135B  VAL      3.2     9.6    +      -       -      +
    136B  LEU*     3.9    11.7    -      -       +      +
    137B  VAL*     2.8    30.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 107 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82B  LEU*     3.6    28.7    -      -       +      -
     83B  ILE      2.7    15.1    +      -       -      +
     84B  VAL*     3.8     5.8    -      -       +      -
     85B  GLY      3.0    20.1    +      -       -      -
    105B  VAL*     5.1     1.8    -      -       +      -
    106B  MET*     1.3    75.3    -      -       -      +
    108B  ASP*     1.3    62.8    +      -       -      +
    137B  VAL*     3.8    18.6    -      -       +      -
    139B  ASP      3.7    14.4    -      -       -      +
    141B  ALA*     3.4    29.4    -      -       +      -
    144B  TYR*     4.0    23.3    -      -       +      -
    145B  LEU*     5.8     0.2    -      -       +      -
    315B  MTA      3.6     5.2    -      -       -      -
----------------------------------------------------------
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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