Contacts of the strand formed by residues 34 - 40 (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 GLY 34 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29E  ASP      4.0     0.5    -      -       -      +
     30E  ILE*     3.8     1.2    -      -       -      -
     31E  SER*     3.0    30.4    +      -       -      -
     32E  SER      3.3     0.4    -      -       -      -
     33E  SER*     1.3    81.6    +      -       -      +
     35E  VAL*     1.3    60.5    +      -       -      -
     36E  ASN*     4.2     5.7    +      -       -      -
     52E  LEU      3.3    10.5    -      -       -      -
     53E  ARG*     4.4     0.2    -      -       -      -
     54E  SER      3.7     6.3    -      -       -      -
     60E  TYR*     3.1    20.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 35 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2E  PHE*     4.5    11.0    -      -       +      -
     28E  TRP*     3.3    39.5    -      -       +      -
     29E  ASP      3.6     4.3    -      -       -      +
     30E  ILE*     3.4    25.8    -      -       +      -
     34E  GLY*     1.3    74.2    -      -       -      -
     36E  ASN*     1.3    69.5    +      -       -      +
     50E  LEU*     3.9     2.7    -      -       +      +
     51E  THR*     3.6     1.2    -      -       -      -
     52E  LEU*     2.9    47.4    +      -       +      +
     57E  PHE*     4.4    17.9    -      -       +      -
     60E  TYR*     4.2     7.2    -      -       +      +
     90E  LEU*     5.7     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 36 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27E  CYS      3.9     0.9    -      -       -      +
     28E  TRP*     3.9     2.1    -      -       -      -
     29E  ASP*     3.0    47.9    +      -       +      +
     31E  SER*     5.5     3.4    -      -       -      -
     33E  SER*     4.3    16.4    +      -       -      -
     34E  GLY      4.5     6.1    +      -       -      -
     35E  VAL*     1.3    82.9    -      -       -      +
     37E  LEU*     1.3    62.2    +      -       -      +
     49E  GLN*     4.8     4.0    -      -       -      +
     50E  LEU*     3.2     4.9    -      -       -      +
     51E  THR*     2.9    32.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 37 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19E  LEU*     4.5     7.9    -      -       +      -
     23E  ILE*     3.9    20.4    -      -       +      -
     26E  ALA*     3.7    23.1    -      -       +      -
     27E  CYS      3.9    11.7    -      -       -      +
     28E  TRP*     3.7    37.7    -      -       +      +
     29E  ASP*     5.4     1.6    -      -       -      -
     36E  ASN*     1.3    76.2    -      -       -      +
     38E  GLN*     1.3    70.7    +      -       -      +
     39E  SER*     4.4     0.2    -      -       -      -
     48E  VAL*     4.3    12.3    -      -       +      +
     49E  GLN*     3.1     7.3    +      -       -      -
     50E  LEU*     2.7    57.7    +      -       +      +
     72E  LEU*     4.3     7.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 38 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27E  CYS      4.5     5.8    +      -       -      +
     29E  ASP*     5.5     1.4    +      -       -      -
     37E  LEU*     1.3    75.5    -      -       -      +
     39E  SER*     1.3    65.8    +      -       -      +
     47E  LEU*     3.9    21.9    -      -       +      +
     48E  VAL      3.2    13.2    -      -       -      +
     49E  GLN*     4.2    14.8    -      -       +      +
    123E  VAL*     4.8     2.9    -      -       -      +
    124E  GLU      4.8     0.2    -      -       -      +
    125E  GLN*     3.3    44.4    +      -       -      +
    126E  LEU      3.0    45.0    +      -       -      -
    128E  ILE*     4.3    15.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 39 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23E  ILE*     3.8    28.9    -      -       -      +
     25E  GLU      3.7    17.5    +      -       -      -
     26E  ALA*     4.0    12.2    -      -       -      -
     37E  LEU*     4.4     0.9    -      -       -      -
     38E  GLN*     1.3    81.2    -      -       -      +
     40E  MET*     1.3    72.6    +      -       -      +
     41E  ASP      4.3     0.2    +      -       -      -
     47E  LEU*     3.4     3.4    -      -       -      -
     48E  VAL*     2.9    33.9    +      -       -      +
    123E  VAL*     5.9     3.0    -      -       -      +
    124E  GLU      5.8     2.9    -      -       -      -
    125E  GLN*     5.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 40 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23E  ILE*     3.9     5.0    -      -       -      +
     39E  SER*     1.3    84.7    +      -       -      +
     41E  ASP*     1.3    64.3    +      -       -      +
     44E  HIS*     3.3    65.2    -      -       +      +
     46E  SER      3.5     9.0    -      -       -      +
     47E  LEU*     3.6    21.5    -      -       +      -
    124E  GLU*     4.6    18.4    +      -       -      +
    126E  LEU*     4.3    10.3    -      -       +      -
    147F  MET*     3.3    20.2    -      -       +      -
    148F  THR*     3.5    26.9    -      -       +      +
----------------------------------------------------------
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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