Contacts of the strand formed by residues 48 - 52 (chain A) 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 48 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  VAL      3.5     8.1    -      -       -      +
     43A  ARG*     4.6     0.4    -      -       -      +
     47A  CYS*     1.3    75.6    -      -       -      +
     49A  VAL*     1.3    66.0    +      -       -      +
    141A  ILE*     3.1    39.1    -      -       +      +
    142A  GLY      4.8     2.9    -      -       -      +
    149A  PRO*     3.9    19.7    -      -       +      -
    150A  GLN      4.5     5.2    -      -       -      +
    151A  VAL*     5.0     2.7    -      -       +      -
    218A  GLY      3.5     2.6    -      -       -      +
    219A  VAL*     4.7     0.2    -      -       -      -
    220A  VAL*     3.9    24.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 49 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  ALA*     3.1     7.0    -      -       -      +
     42A  VAL*     3.0    31.5    +      -       +      +
     47A  CYS*     4.9     1.6    -      -       -      -
     48A  ALA*     1.3    74.9    -      -       -      +
     50A  ILE*     1.4    62.4    +      -       -      +
     51A  VAL*     4.9     0.2    -      -       +      -
    141A  ILE*     4.5     0.3    -      -       -      +
    194A  THR*     3.2    35.2    -      -       -      +
    195A  VAL*     3.6    28.5    -      -       +      +
    198A  ALA*     4.1    21.3    -      -       +      -
    217A  VAL*     3.6    27.1    -      -       +      -
    218A  GLY      3.4     5.6    -      -       -      +
    219A  VAL*     4.1     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 50 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  SER*     5.6     1.1    -      -       -      -
     40A  VAL      3.5    12.6    -      -       -      +
     41A  ALA*     4.0     6.3    -      -       +      -
     49A  VAL*     1.4    74.0    -      -       -      +
     51A  VAL*     1.3    70.1    +      -       -      +
     69A  LEU*     4.2    13.5    -      -       +      -
     78A  CYS      4.5     0.9    -      -       -      -
     79A  VAL*     3.6    24.9    -      -       +      +
    139A  ILE*     3.3    41.7    -      -       +      +
    141A  ILE*     3.4    32.8    -      -       +      -
    217A  VAL*     3.3     4.3    -      -       -      +
    218A  GLY*     2.9    41.6    +      -       -      +
    227A  PHE*     4.9     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 51 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  SER*     3.2     6.1    -      -       -      -
     40A  VAL      2.9    39.5    +      -       -      +
     49A  VAL*     4.9     0.2    -      -       +      -
     50A  ILE*     1.3    79.2    -      -       -      +
     52A  THR*     1.4    68.2    +      -       -      +
     69A  LEU*     5.1     0.4    -      -       -      -
    198A  ALA*     3.6    22.7    -      -       +      +
    199A  ILE*     4.8     7.0    -      -       +      -
    202A  LEU*     3.4    38.8    -      -       +      -
    215A  ILE*     3.9    16.6    -      -       +      -
    216A  GLU      3.2    15.3    -      -       -      +
    217A  VAL*     4.0    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 52 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  LEU*     4.3    19.7    -      -       +      -
     38A  THR      4.5     5.2    -      -       -      +
     39A  SER*     3.5    24.0    -      -       -      +
     51A  VAL*     1.4    77.9    +      -       -      +
     68A  HIS*     4.1    22.6    -      -       +      +
     69A  LEU*     3.8     6.4    -      -       -      +
     79A  VAL*     3.5    29.1    -      -       +      +
     80A  MET      5.3     0.2    -      -       -      +
    202A  LEU*     4.3    15.5    -      -       -      -
    214A  GLU      3.1    25.0    -      -       -      +
    215A  ILE*     3.5     2.4    -      -       -      -
    216A  GLU*     3.1    34.9    +      -       -      +
----------------------------------------------------------
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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