Contacts of the strand formed by residues 42 - 46 (chain b) 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 ILE 42 (chain b).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22b  ILE*     4.4    15.7    -      -       +      +
     24b  ALA*     4.3    24.0    -      -       +      +
     25b  ASP      5.9     0.2    -      -       -      +
     26b  MET*     6.0     1.1    -      -       +      -
     40b  SER*     3.5     5.3    -      -       -      -
     41b  ARG*     1.3    86.7    -      -       -      +
     43b  MET*     1.4    67.8    +      -       -      +
     44b  ARG*     3.8     1.4    +      -       -      +
     50b  MET*     4.3    10.5    -      -       -      -
     51b  LEU      3.5    10.8    -      -       -      +
     52b  GLY*     4.1     2.5    -      -       -      -
     60b  PHE*     4.5     0.4    -      -       -      -
     64b  LYS*     5.2     2.1    +      -       -      -
    188b  GLN*     3.3    47.3    -      -       +      +
    190b  ALA*     3.8    29.8    -      -       +      -
    199b  ILE*     4.3    15.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 43 (chain b). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41b  ARG      3.6     3.2    +      -       -      -
     42b  ILE*     1.4    75.5    -      -       -      +
     44b  ARG*     1.4    58.7    +      -       -      +
     45b  VAL*     3.7    21.1    -      -       +      -
     50b  MET*     3.1     7.6    -      -       -      +
     51b  LEU*     2.8    71.3    +      -       +      +
     60b  PHE*     3.6    28.4    -      -       +      -
     63b  LEU      4.0     7.9    -      -       -      +
     64b  LYS*     3.8    60.1    -      -       +      +
     67b  LEU*     4.1     9.6    -      -       +      -
    110b  MET*     4.3     4.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 44 (chain b). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42b  ILE*     3.8     1.1    +      -       +      +
     43b  MET*     1.4    71.2    -      -       -      +
     45b  VAL*     1.3    64.3    +      -       -      +
     46b  ASN      3.7     1.6    -      -       -      -
     49b  THR      3.9     0.4    -      -       -      -
     50b  MET*     4.1     8.3    -      -       +      -
     64b  LYS*     5.5     0.8    -      -       -      +
    197b  VAL*     3.7    35.6    -      -       +      +
    199b  ILE*     4.3    24.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 45 (chain b). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43b  MET*     3.7    12.6    -      -       +      -
     44b  ARG*     1.3    74.5    -      -       -      +
     46b  ASN*     1.3    80.7    +      -       -      +
     49b  THR*     3.0    20.1    +      -       -      +
     50b  MET*     3.8     7.2    -      -       -      +
     51b  LEU*     3.4    32.8    -      -       +      +
     67b  LEU*     3.4    29.4    -      -       +      -
     71b  VAL*     3.7    14.8    -      -       +      +
     88b  ILE*     4.6     7.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 46 (chain b). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44b  ARG      3.7     0.2    -      -       -      -
     45b  VAL*     1.3   100.4    +      -       -      +
     47b  ASN*     1.3    60.5    -      -       -      +
     48b  SER*     1.9    26.5    +      -       -      +
     49b  THR*     3.3    19.8    +      -       +      +
     71b  VAL*     3.2    27.3    -      -       -      +
     74b  GLU*     5.6     1.0    +      -       -      -
     75b  GLU*     3.8    18.8    +      -       -      -
     84b  SER      6.2     1.6    -      -       -      -
     88b  ILE*     5.1     2.9    -      -       -      +
    197b  VAL*     2.7    15.7    -      -       -      +
----------------------------------------------------------
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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