Contacts of the strand formed by residues 84 - 87 (chain N) in PDB entry 5X6E


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 ASN 84 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27N  LEU*     3.6    28.1    -      -       +      +
     29N  PHE      3.4     3.6    -      -       -      -
     30N  ASN*     3.1     1.1    -      -       -      -
     31N  GLN*     2.5    51.0    +      -       -      +
     32N  TRP*     4.0     7.9    -      -       -      -
     47N  LYS      3.4     1.6    -      -       -      +
     48N  LEU*     3.4     8.3    -      -       -      +
     49N  THR*     2.8    58.9    +      -       -      +
     51N  ILE*     3.9    20.4    -      -       -      +
     83N  TYR*     1.3    74.9    -      -       -      +
     85N  LEU*     1.3    58.9    -      -       -      +
     86N  GLU      3.4     0.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 85 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27N  LEU*     3.5     1.9    -      -       -      -
     28N  ILE*     3.0    49.5    +      -       +      +
     29N  PHE*     3.2    45.6    +      -       +      -
     39N  ILE*     4.1    10.8    -      -       +      -
     41N  LEU*     5.5     0.4    -      -       +      -
     46N  THR*     3.3    29.8    -      -       +      +
     47N  LYS      3.4    12.8    -      -       -      +
     48N  LEU*     4.3    11.4    -      -       +      -
     63N  TYR*     4.3    12.3    -      -       +      -
     69N  ILE*     4.1    23.3    -      -       +      -
     84N  ASN*     1.3    69.2    -      -       -      +
     86N  GLU*     1.3    61.9    +      -       -      +
     87N  VAL      3.8     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 86 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25N  LYS*     3.9    26.9    -      -       -      +
     26N  GLU      3.8     5.4    -      -       -      -
     27N  LEU*     4.4    17.7    -      -       +      +
     46N  THR*     2.6    19.6    +      -       -      -
     47N  LYS*     2.6    63.7    +      -       +      +
     49N  THR*     4.8    10.6    +      -       -      +
     84N  ASN      3.4     1.8    +      -       -      -
     85N  LEU*     1.3    71.2    -      -       -      +
     87N  VAL*     1.3    64.3    +      -       -      +
     88N  ILE*     5.6     1.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 87 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22N  PHE*     4.9     6.7    -      -       +      -
     23N  HIS      3.0    27.6    -      -       -      +
     24N  LYS*     4.0     1.0    -      -       -      +
     25N  LYS      3.6    17.0    +      -       -      +
     26N  GLU*     3.3    17.8    +      -       +      +
     28N  ILE*     5.4     6.3    -      -       +      -
     41N  LEU*     6.3     0.2    -      -       +      -
     45N  ILE      3.2    15.0    -      -       -      +
     46N  THR*     3.5    11.9    -      -       -      +
     85N  LEU      3.8     1.7    +      -       -      +
     86N  GLU*     1.3    76.7    -      -       -      +
     88N  ILE*     1.3    61.9    +      -       -      +
     89N  SER*     3.2    21.3    -      -       -      +
     91N  GLN      3.7    13.2    -      -       -      +
     92N  ALA*     3.9    13.0    -      -       +      -
----------------------------------------------------------
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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