Contacts of the strand formed by residues 37 - 41 (chain E) in PDB entry 5A0Q


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 ALA 37 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35E  SER      4.3     2.5    -      -       -      +
     36E  THR*     1.3    78.4    +      -       -      +
     38E  ILE*     1.3    62.0    +      -       -      +
     39E  GLY      3.9     0.2    +      -       -      -
     49E  ALA      3.4    15.3    -      -       -      +
     50E  VAL*     4.2    11.4    -      -       +      +
     77E  ALA*     5.1     2.9    -      -       +      -
     78E  MET      5.0     4.5    -      -       -      +
    142E  LEU*     4.1     6.8    -      -       +      +
    169E  ALA*     2.8     4.6    -      -       -      -
    170E  ILE*     2.4    66.8    +      -       +      +
    202E  LEU*     5.3     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 38 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36E  THR*     5.3     2.0    -      -       -      +
     37E  ALA*     1.3    73.1    -      -       -      +
     39E  GLY*     1.3    63.0    +      -       -      +
     40E  ILE*     3.5    31.8    +      -       +      +
     48E  LEU      4.0     0.2    -      -       -      -
     49E  ALA*     2.9    40.1    +      -       +      +
    142E  LEU*     4.0     4.4    -      -       -      +
    169E  ALA*     3.7    11.0    -      -       +      -
    177E  ALA*     5.0     2.7    -      -       +      -
    181E  LEU*     4.2    20.6    -      -       +      -
    198E  SER*     3.6    25.1    -      -       -      +
    201E  ILE*     3.6    38.1    -      -       +      -
    202E  LEU*     3.9    20.1    -      -       +      +
    205E  VAL*     5.9     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 39 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37E  ALA      3.9     0.2    +      -       -      -
     38E  ILE*     1.3    73.3    -      -       -      +
     40E  ILE*     1.3    66.1    +      -       -      +
     41E  GLN      3.5     1.7    +      -       -      -
     47E  CYS      4.6     0.2    -      -       -      -
     48E  LEU*     4.2     4.0    -      -       -      -
    142E  LEU*     3.7    15.5    -      -       -      -
    153E  LEU*     3.4    28.7    -      -       -      +
    167E  ALA*     3.7    10.3    -      -       -      -
    168E  ARG      2.8    23.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 40 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38E  ILE*     3.5    26.7    -      -       +      -
     39E  GLY*     1.3    75.4    -      -       -      +
     41E  GLN*     1.4    63.5    +      -       -      +
     42E  THR*     3.9     5.8    -      -       +      +
     46E  VAL*     4.2     0.5    -      -       -      -
     47E  CYS*     3.3    40.5    +      -       +      +
    153E  LEU*     3.3    13.2    -      -       -      +
    166E  ASP      4.5     0.9    -      -       -      -
    167E  ALA*     5.0     4.3    -      -       +      -
    181E  LEU*     4.0    19.3    -      -       +      -
    189E  MET*     4.8     7.6    -      -       +      -
    194E  ALA*     3.5    47.6    -      -       +      +
    197E  SER*     4.2    12.3    -      -       -      +
    198E  SER*     3.9    11.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 41 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40E  ILE*     1.4    73.6    -      -       -      +
     42E  THR*     1.3    72.9    +      -       -      +
     43E  SER*     4.2     6.4    +      -       -      +
     45E  GLY      4.4     2.2    -      -       -      +
     46E  VAL*     5.1     2.5    -      -       +      +
    151E  PRO*     3.1    42.5    +      -       +      +
    152E  GLN*     4.3     4.2    -      -       -      +
    153E  LEU*     4.0    18.6    +      -       +      +
    164E  GLN*     5.7     1.3    +      -       -      +
    165E  CYS      2.9    25.8    -      -       -      +
    166E  ASP*     3.1    33.0    +      -       -      +
    167E  ALA*     5.1     0.4    -      -       -      +
    185E  TYR*     4.4     9.5    +      -       -      -
    188E  SER      5.0     2.1    -      -       -      +
    189E  MET*     4.3    12.1    -      -       -      +
----------------------------------------------------------
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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