Contacts of the strand formed by residues 44 - 47 (chain I) in PDB entry 5A31


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 VAL 44 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36I  ALA*     5.1     4.3    -      -       +      -
     37I  LEU      3.4    12.1    -      -       -      +
     38I  ALA*     4.4     1.3    -      -       +      +
     42I  GLY      5.0     1.1    -      -       -      +
     43I  GLU*     1.3    74.4    -      -       -      +
     45I  LEU*     1.3    63.4    +      -       -      +
     56I  TRP*     3.6    14.2    -      -       +      -
     58I  PHE*     3.0    39.3    +      -       +      +
     68I  VAL*     4.1    22.2    -      -       +      -
     71I  LEU*     4.1    25.1    -      -       +      -
     80I  LEU*     5.6     4.0    -      -       +      -
     82I  PHE*     4.1    39.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 45 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36I  ALA*     3.5     3.6    -      -       -      +
     37I  LEU*     2.8    48.9    +      -       +      +
     39I  ASN*     4.6     5.8    -      -       -      +
     43I  GLU*     3.5    47.6    -      -       +      +
     44I  VAL*     1.3    81.2    -      -       -      +
     46I  LEU*     1.3    61.1    +      -       -      +
     47I  HIS*     3.9     0.7    -      -       +      -
     54I  ARG*     2.8    46.0    -      -       -      +
     56I  TRP*     3.5     3.6    -      -       -      +
     57I  SER*     3.5    29.2    -      -       -      -
     58I  PHE      4.2     3.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 46 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34I  LEU*     3.4    32.8    -      -       +      -
     35I  ILE      3.3    15.0    -      -       -      +
     36I  ALA*     4.0     2.7    -      -       +      -
     44I  VAL      4.2     0.2    +      -       -      -
     45I  LEU*     1.3    74.3    -      -       -      +
     47I  HIS*     1.3    59.4    +      -       -      +
     54I  ARG*     3.5     2.3    -      -       -      -
     55I  VAL*     2.5    43.3    +      -       +      -
     56I  TRP*     2.9    61.4    +      -       +      +
     73I  TRP*     3.6    32.5    -      -       +      -
     80I  LEU*     3.9    12.3    -      -       +      -
     95I  VAL*     4.9     2.0    -      -       +      -
    389N  PRO*     5.8     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 47 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19I  LEU*     4.1     6.4    -      -       +      +
     34I  LEU*     3.2     2.9    -      -       -      -
     35I  ILE*     2.8    52.5    +      -       +      +
     37I  LEU*     3.3    33.3    -      -       +      +
     45I  LEU*     3.9     4.7    -      -       +      -
     46I  LEU*     1.3    74.5    -      -       -      +
     48I  ARG*     1.3    61.9    +      -       -      +
     52I  PHE*     3.1    46.2    -      +       +      +
     53I  HIS      3.6     5.6    -      -       -      +
     54I  ARG*     3.0    56.7    +      -       +      +
     55I  VAL*     3.6     6.3    -      -       -      +
----------------------------------------------------------
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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