Contacts of the strand formed by residues 91 - 96 (chain O) in PDB entry 2AXT


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 PHE 91 (chain O).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77O  LEU*     3.6    33.0    -      -       +      +
     79O  LYS*     3.5    37.0    -      -       +      +
     89O  ALA      5.2     2.9    -      -       -      -
     90O  GLU*     1.3    78.9    -      -       -      +
     92O  VAL*     1.3    62.8    +      -       -      +
     93O  PRO*     4.2     1.6    -      -       -      +
    244O  GLU*     3.5    28.0    -      -       -      -
    258O  GLU*     4.3    10.8    -      -       +      -
    259O  VAL      4.2    11.0    -      -       -      -
    260O  LYS*     3.7    48.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 92 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77O  LEU*     3.1     6.9    -      -       -      -
     78O  VAL      2.9    30.5    +      -       -      +
     80O  GLU*     4.5    15.7    -      -       +      -
     90O  GLU*     3.6    15.8    +      -       +      +
     91O  PHE*     1.3    76.3    -      -       -      +
     93O  PRO*     1.3    94.9    -      -       +      +
     94O  THR*     3.9     2.1    -      -       +      +
    136O  MET*     6.1     5.2    -      -       +      -
    137O  ALA*     4.6    13.7    -      -       +      -
   5084b  THR*     3.8    30.1    -      -       +      -
   5085b  GLY      4.9     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 93 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75O  THR*     5.6     5.8    -      -       +      -
     76O  PHE      3.9     7.0    -      -       -      +
     77O  LEU*     4.5     7.4    -      -       +      -
     91O  PHE      4.5     2.2    -      -       -      +
     92O  VAL*     1.3   106.2    -      -       +      +
     94O  THR*     1.3    61.7    +      -       -      +
    136O  MET*     5.0     0.2    -      -       -      +
    137O  ALA*     4.6     9.0    +      -       -      +
   5084b  THR*     4.0    18.6    -      -       +      +
   5085b  GLY*     4.6    11.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 94 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76O  PHE*     3.2    24.1    +      -       -      +
     78O  VAL*     3.8    21.3    -      -       +      -
     92O  VAL      3.9     7.0    -      -       -      +
     93O  PRO*     1.3    81.7    -      -       -      +
     95O  LYS*     1.3    61.6    +      -       -      +
     96O  LEU      3.9     1.2    +      -       -      -
    134O  VAL*     3.4    25.2    -      -       +      +
    135O  GLN      3.6     9.9    -      -       -      -
    136O  MET*     3.5    28.5    -      -       +      +
    137O  ALA      5.1     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 95 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A  SER*     5.2    10.8    -      -       -      +
    103A  ASP*     5.3    10.5    -      -       +      +
     94O  THR*     1.3    72.2    -      -       -      +
     96O  LEU*     1.3    60.0    +      -       -      +
     97O  VAL      3.2     1.7    +      -       -      -
    134O  VAL*     3.2     4.1    -      -       -      -
    135O  GLN*     2.7    50.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 96 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100A  ALA*     5.3     3.5    -      -       -      +
    101A  SER*     4.8     4.7    +      -       -      -
    104A  GLU*     4.3     9.9    -      -       -      +
     76O  PHE*     5.1    10.8    -      -       +      -
     94O  THR      3.9     2.4    +      -       -      -
     95O  LYS*     1.3    68.8    -      -       -      +
     97O  VAL*     1.3    61.2    +      -       -      +
     98O  THR*     3.4    27.3    -      -       -      +
     99O  ARG      3.1    25.4    -      -       -      +
    100O  GLU*     5.3     1.3    -      -       +      -
    102O  THR*     4.1    14.8    -      -       +      -
    132O  VAL*     3.9    22.2    -      -       +      -
    133O  THR      3.6     9.6    -      -       -      +
    134O  VAL*     4.1     9.4    -      -       +      +
----------------------------------------------------------
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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