Contacts of the strand formed by residues 57 - 64 (chain B) 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 ILE 57 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  ILE*     5.5     3.3    -      -       -      +
     49B  THR*     4.5    17.3    -      -       +      -
     50B  SER      3.3     9.0    -      -       -      +
     51B  ILE*     4.2    22.2    -      -       +      -
     55B  GLY      3.6    13.9    -      -       -      +
     56B  THR*     1.3    74.7    -      -       -      +
     58B  MET*     1.3    63.3    +      -       -      +
     59B  ASN*     4.3     6.5    -      -       -      +
    176B  TYR*     3.3    53.4    -      -       +      +
    180B  ILE      5.7     0.3    -      -       -      +
    181B  ALA*     6.0     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 58 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131A  PHE*     3.5    26.9    -      -       +      -
    132A  ASN*     3.3    35.2    -      -       -      +
    135A  SER*     3.4    32.8    -      -       -      +
    136A  ILE*     4.5    15.7    -      -       +      -
     49B  THR*     3.4     4.0    -      -       -      -
     50B  SER      3.0    30.4    +      -       -      +
     56B  THR      5.7     0.2    -      -       -      +
     57B  ILE*     1.3    76.5    -      -       -      +
     59B  ASN*     1.3    67.2    +      -       -      +
     60B  LEU*     3.2    17.1    +      -       +      +
    176B  TYR*     3.8     6.7    -      -       -      +
    177B  SER      3.9     1.6    -      -       -      +
    178B  SER      3.2    28.3    -      -       -      +
    179B  GLY*     4.8     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 59 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47B  LYS*     3.6    10.2    +      -       +      +
     48B  LEU      3.9     5.4    -      -       -      +
     49B  THR*     3.2    21.5    -      -       -      +
     57B  ILE*     4.3     2.4    -      -       -      +
     58B  MET*     1.3    72.2    -      -       -      +
     60B  LEU*     1.3    65.5    +      -       -      +
     61B  GLN      3.5     2.7    -      -       -      +
     62B  TYR*     3.8     7.8    +      -       +      +
    130B  LYS*     4.8     0.2    +      -       -      -
    173B  GLU*     2.8    44.4    +      -       -      +
    176B  TYR*     2.8    38.1    +      -       -      +
    177B  SER*     3.3    32.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 60 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  LEU*     4.1    27.4    -      -       +      +
    131A  PHE*     3.7    25.9    -      -       +      -
    132A  ASN*     3.7    32.3    -      -       +      +
     48B  LEU*     3.1    30.7    +      -       +      +
     50B  SER*     5.0     1.6    -      -       -      -
     58B  MET*     3.2    16.3    +      -       +      +
     59B  ASN*     1.3    72.4    -      -       -      +
     61B  GLN*     1.3    58.1    +      -       +      +
     83B  TYR*     3.5    38.6    -      -       +      -
    130B  LYS*     2.7    31.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 61 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  LEU*     4.0    14.6    -      -       +      +
     47B  LYS*     3.6     1.7    -      -       -      +
     48B  LEU*     2.9    29.5    +      -       +      +
     59B  ASN*     3.5     3.2    -      -       -      +
     60B  LEU*     1.3    85.0    -      -       +      +
     62B  TYR*     1.3    75.3    +      -       -      +
     63B  TYR*     3.0    33.2    +      -       +      -
    123B  GLN*     3.3    25.9    +      -       -      +
    126B  TYR*     3.7    24.0    -      -       +      -
    127B  SER*     4.5     1.4    +      -       -      -
    130B  LYS*     4.1     2.7    -      -       -      +
    301B  GSH      3.1    36.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 62 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  ILE*     4.7     2.2    -      -       +      -
     46B  THR      3.4    16.4    -      -       -      +
     47B  LYS*     3.8    26.5    -      -       +      -
     59B  ASN*     3.8     6.4    +      -       +      -
     61B  GLN*     1.3    89.4    -      -       -      +
     63B  TYR*     1.3    63.1    +      -       -      +
     88B  ILE*     4.5    11.5    -      -       +      +
    146B  GLN*     4.2     9.9    -      -       -      -
    150B  LEU*     3.9    25.6    -      -       +      -
    154B  TYR*     3.2    23.1    -      +       -      +
    166B  LEU*     5.1    11.4    -      -       +      +
    168B  ASN*     6.2     0.4    -      -       -      -
    169B  LEU*     4.9     7.5    -      -       +      +
    173B  GLU*     3.7    25.1    +      -       -      +
    174B  LEU*     5.9     0.2    -      -       -      -
    177B  SER*     3.7    16.8    +      -       -      -
    301B  GSH      2.7    46.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 63 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  LEU*     4.6     0.7    -      -       -      +
     41B  LEU*     4.2     4.7    -      -       +      +
     44B  GLY      3.9     0.9    -      -       -      +
     45B  ILE*     3.1     3.5    -      -       -      +
     46B  THR*     2.6    57.8    +      -       +      +
     48B  LEU*     4.2    30.3    -      -       +      +
     61B  GLN*     3.0    39.9    +      -       +      -
     62B  TYR*     1.3    75.9    -      -       -      +
     64B  LYS*     1.3    59.8    +      -       -      +
     67B  PHE*     3.4    43.3    -      +       +      -
     69B  ILE*     3.6    33.8    -      -       +      +
     85B  LEU*     5.0     2.0    -      -       +      -
    123B  GLN*     2.9    28.6    +      -       -      -
    154B  TYR*     4.3     0.2    -      -       -      -
    301B  GSH      3.3     7.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 64 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44B  GLY      3.3     5.2    -      -       -      -
     45B  ILE*     3.7    25.8    -      -       +      -
     63B  TYR*     1.3    74.4    -      -       -      +
     65B  GLY*     1.3    73.1    +      -       -      +
     67B  PHE*     4.4     0.9    -      -       -      +
    153B  VAL*     3.7    38.9    +      -       +      +
    154B  TYR*     3.7    18.6    +      -       +      +
    156B  LYS*     5.2     7.3    -      -       -      +
    301B  GSH      3.1    40.2    +      -       +      +
----------------------------------------------------------
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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