Contacts of the strand formed by residues 135 - 140 (chain E) in PDB entry 1AXC


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 CYS 135 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133E  TYR*     3.9     0.3    -      -       -      +
    134E  SER*     1.3    78.7    -      -       -      +
    136E  VAL*     1.3    65.5    +      -       -      +
    137E  VAL*     5.2     0.2    -      -       -      -
    162E  CYS*     3.3    46.2    -      -       +      -
    198E  GLU      3.3     2.9    -      -       -      -
    199E  MET*     3.4    26.2    -      -       -      -
    201E  GLU      3.5    10.8    -      -       -      -
    203E  VAL*     3.8    11.7    -      -       +      -
    227E  LEU      3.5     1.5    -      -       -      +
    228E  SER*     3.1     5.0    -      -       -      -
    229E  MET*     2.8    44.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 136 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133E  TYR*     4.5    14.6    -      -       +      +
    135E  CYS*     1.3    80.9    -      -       -      +
    137E  VAL*     1.3    63.9    +      -       -      +
    138E  LYS*     4.1     1.5    +      -       +      +
    196E  THR      3.9     0.3    -      -       -      +
    197E  ILE*     3.3     4.5    -      -       -      +
    198E  GLU*     2.7    54.7    +      -       +      +
    226E  THR*     4.6    15.7    -      -       +      -
    227E  LEU      3.1     5.6    -      -       -      +
    228E  SER*     3.7    23.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 137 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136E  VAL*     1.3    77.4    -      -       -      +
    138E  LYS*     1.3    68.9    +      -       -      +
    139E  MET*     3.8    26.4    -      -       +      +
    162E  CYS*     4.2    17.9    -      -       -      -
    167E  VAL*     3.9    23.8    -      -       +      -
    195E  VAL*     4.3     9.0    -      -       +      -
    196E  THR      3.6     6.1    -      -       -      +
    197E  ILE*     4.6     4.9    -      -       +      +
    225E  VAL      3.6     1.4    -      -       -      +
    226E  THR*     3.0     6.1    -      -       -      -
    227E  LEU*     2.8    38.9    +      -       +      +
    229E  MET*     4.0    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 138 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136E  VAL*     4.1     2.8    -      -       +      +
    137E  VAL*     1.3    74.2    -      -       -      +
    139E  MET*     1.3    68.5    +      -       -      +
    191E  GLU      3.6    22.0    +      -       -      -
    194E  ALA*     4.1    18.5    +      -       -      +
    195E  VAL*     3.3     2.4    -      -       -      -
    196E  THR*     2.8    55.8    +      -       -      +
    224E  THR*     4.2    25.6    -      -       +      +
    225E  VAL      3.7     2.7    -      -       -      -
    226E  THR*     3.8    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 139 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137E  VAL*     3.8    19.1    -      -       +      -
    138E  LYS*     1.3    78.3    -      -       -      +
    140E  PRO*     1.3    70.0    -      -       +      +
    143E  GLU*     4.9     1.3    -      -       -      -
    144E  PHE*     4.1    26.5    -      -       +      -
    147E  ILE*     5.1     0.4    -      -       -      -
    167E  VAL*     4.8     0.2    -      -       +      -
    169E  PHE*     3.5    28.5    -      -       +      -
    182E  LEU*     3.8    22.0    -      -       +      -
    194E  ALA      3.5     6.7    -      -       -      +
    195E  VAL*     4.4     9.9    -      -       +      -
    224E  THR*     3.2     8.2    -      -       -      -
    225E  VAL*     2.8    48.9    +      -       +      +
    227E  LEU*     3.7    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 140 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139E  MET*     1.3    90.1    -      -       +      +
    141E  SER*     1.3    60.9    +      -       -      +
    142E  GLY*     4.3     1.8    -      -       -      +
    143E  GLU*     3.0    24.8    +      -       +      +
    144E  PHE*     3.0    25.6    +      -       -      +
    192E  GLU      3.0    22.2    -      -       -      +
    193E  GLU*     4.1    13.7    -      -       -      +
    194E  ALA      3.4    11.7    -      -       -      +
    195E  VAL*     4.4     6.7    -      -       +      -
    223E  SER      3.6     9.6    -      -       -      +
    225E  VAL*     4.1     0.2    -      -       -      -
----------------------------------------------------------
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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