Contacts of the strand formed by residues 368 - 371 (chain A) in PDB entry 5XA0


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 PHE 368 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303A  PHE*     2.8    30.3    +      -       -      +
    305A  PHE*     3.2    28.3    -      +       +      -
    314A  LEU*     3.9    13.9    -      -       +      -
    316A  ALA*     2.8    40.8    -      -       +      -
    355A  LEU*     4.1     1.6    -      -       +      -
    366A  SER      3.4    12.8    +      -       -      -
    367A  ILE*     1.3    94.4    -      -       -      +
    369A  GLU*     1.3    57.5    +      -       -      +
    390A  LEU*     3.8     6.5    -      -       +      -
    391A  ARG*     2.7    25.6    -      -       -      +
    392A  HIS*     3.0    33.2    -      +       +      -
    393A  LEU*     2.8    14.8    -      -       -      +
    399A  VAL*     3.3    26.9    -      -       +      -
    420A  THR*     5.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 369 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299A  TRP*     6.0     3.4    -      -       +      -
    300A  ASN*     5.2    13.4    +      -       -      +
    302A  LEU*     4.2     9.2    -      -       +      +
    303A  PHE*     4.7     2.5    -      -       -      -
    368A  PHE*     1.3    71.2    -      -       -      +
    370A  LEU*     1.3    76.3    +      -       -      +
    371A  ASP      3.6     0.7    +      -       -      -
    390A  LEU*     2.9    11.2    -      -       -      +
    391A  ARG*     3.0    14.3    +      -       -      +
    393A  LEU*     2.8    31.0    -      -       +      +
    398A  TRP*     5.6     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 370 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299A  TRP*     3.3    38.4    -      -       +      -
    303A  PHE*     3.0    60.1    -      -       +      -
    369A  GLU*     1.3    89.9    -      -       -      +
    371A  ASP*     1.3    71.7    +      -       -      +
    372A  PRO*     5.2     0.2    -      -       +      -
    382A  VAL*     4.0    22.7    -      -       +      -
    388A  VAL*     5.4     8.7    -      -       +      -
    389A  ARG      3.4     3.6    -      -       -      +
    390A  LEU*     3.1    19.1    -      -       +      +
    398A  TRP*     5.1     1.2    -      -       -      -
    432A  ILE*     6.5     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 371 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299A  TRP*     4.2     4.3    -      -       -      -
    369A  GLU      3.6     1.6    +      -       -      -
    370A  LEU*     1.3    79.0    -      -       -      +
    372A  PRO*     1.3    69.8    -      -       -      +
    388A  VAL*     4.1     0.3    -      -       -      -
    389A  ARG*     2.5    41.0    +      -       +      +
    390A  LEU*     4.1     0.6    -      -       -      +
    398A  TRP*     2.9    47.1    -      -       +      -
    424A  LYS      4.9     4.3    -      -       -      +
----------------------------------------------------------
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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