Contacts of the strand formed by residues 105 - 112 (chain B) in PDB entry 2FYU


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 MET 105 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49B  LEU      3.8     1.2    -      -       -      +
     50B  PHE*     3.6     1.4    -      -       -      -
     51B  ILE*     2.7    41.6    +      -       +      +
     53B  ALA*     3.2    39.5    -      -       +      +
     54B  GLY*     3.8     2.2    -      -       -      +
     66B  SER*     3.8    19.5    -      -       -      +
     69B  LEU*     3.5    33.0    -      -       +      -
     70B  ARG      4.9     0.7    -      -       -      -
     98B  VAL*     4.7     5.4    -      -       +      -
     99B  THR      3.4     5.6    -      -       -      +
    100B  SER*     3.9    18.2    -      -       -      +
    104B  ASN*     1.3    76.2    -      -       -      +
    106B  ALA*     1.3    60.0    +      -       -      +
    107B  TYR*     4.1    21.3    -      -       +      -
    194B  TYR*     3.7     8.3    -      -       +      -
    199B  PHE*     3.9     7.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 106 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49B  LEU      3.5     4.7    -      -       -      -
     50B  PHE*     3.7    35.7    -      -       +      +
     97B  SER      3.5     2.3    -      -       -      +
     98B  VAL*     3.3     4.6    -      -       -      +
     99B  THR*     2.7    50.6    +      -       +      +
    104B  ASN*     5.7     1.6    -      -       +      -
    105B  MET*     1.3    75.4    -      -       -      +
    107B  TYR*     1.3    63.3    +      -       -      +
    108B  THR*     3.6     7.9    +      -       +      +
    380B  ASP*     5.6     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 107 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48B  GLY*     3.2     1.6    -      -       -      -
     49B  LEU*     2.8    41.5    +      -       +      +
     51B  ILE*     3.6    20.0    -      -       +      -
     69B  LEU*     3.5    25.1    +      -       -      +
     73B  SER*     4.1     5.4    -      -       -      -
     96B  LEU*     4.8     5.6    -      -       +      -
     97B  SER      3.4     5.8    -      -       -      -
     98B  VAL*     4.0    35.7    -      -       +      -
    105B  MET*     4.1    10.6    -      -       +      -
    106B  ALA*     1.3    72.6    -      -       -      +
    108B  THR*     1.3    60.9    +      -       -      +
    123B  LEU*     3.7    22.1    -      -       +      +
    126B  VAL*     3.6    28.6    +      -       +      -
    127B  THR*     3.7    17.7    -      -       +      -
    199B  PHE*     3.4    35.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with THR 108 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46B  ARG*     5.2     6.7    -      -       -      -
     47B  ILE      3.3     4.0    -      -       -      -
     48B  GLY*     3.9     4.7    -      -       -      -
     50B  PHE*     4.7     9.0    -      -       +      -
     95B  LYS      3.9     0.5    -      -       -      +
     96B  LEU*     3.4     5.9    -      -       -      +
     97B  SER*     2.8    56.6    +      -       -      +
     99B  THR*     5.1     5.1    +      -       -      +
    106B  ALA*     3.6    11.2    +      -       +      +
    107B  TYR*     1.3    78.6    -      -       -      +
    109B  VAL*     1.3    64.5    +      -       -      +
    110B  GLU*     4.4     0.7    +      -       -      -
    379B  LEU*     3.8    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 109 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  SER      4.0     0.2    -      -       -      +
     46B  ARG*     3.4     7.4    -      -       -      +
     47B  ILE*     2.9    56.9    +      -       +      +
     89B  ILE*     5.3     2.0    -      -       +      -
     95B  LYS      3.3     7.0    -      -       -      +
     96B  LEU*     3.9    20.2    -      -       +      -
    108B  THR*     1.3    78.3    -      -       -      +
    110B  GLU*     1.3    59.6    +      -       -      +
    111B  CYS*     5.4     1.3    -      -       -      -
    119B  LEU*     3.7    55.9    -      -       +      +
    120B  MET*     5.3     0.2    -      -       -      -
    122B  PHE*     5.8     0.4    -      -       +      -
    123B  LEU*     4.2    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 110 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363A  ASN*     4.6     3.6    -      -       -      +
    367A  SER*     2.9    28.1    +      -       -      -
     44B  ALA*     5.9     3.1    -      -       +      -
     45B  SER      3.5    10.5    -      -       -      +
     46B  ARG*     3.3    35.5    +      -       +      +
     94B  GLY*     3.2     6.4    -      -       -      -
     95B  LYS*     3.0    70.8    +      -       +      +
     97B  SER*     5.4     2.4    +      -       -      -
    108B  THR*     4.4     0.4    +      -       -      -
    109B  VAL*     1.3    74.5    -      -       -      +
    111B  CYS*     1.3    62.1    +      -       -      +
    119B  LEU*     4.0     3.2    -      -       -      +
    376B  GLU*     4.8     5.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 111 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363A  ASN*     3.4    15.0    +      -       -      -
     44B  ALA*     3.4     5.5    -      -       -      +
     45B  SER      2.8    35.3    +      -       -      +
     47B  ILE*     6.2     1.3    -      -       -      -
     92B  VAL*     4.8     3.8    -      -       +      +
     94B  GLY*     4.6     4.0    -      -       -      +
    109B  VAL*     5.4     2.2    -      -       -      -
    110B  GLU*     1.3    75.7    -      -       -      +
    112B  LEU*     1.3    69.0    +      -       -      +
    115B  ASP*     3.6    27.4    -      -       +      -
    116B  VAL*     3.7    14.8    -      -       -      -
    119B  LEU*     3.7    30.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 112 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  TYR*     3.7    36.6    -      -       +      -
    359A  ASN*     4.7     8.5    -      -       -      +
    362A  ARG*     3.8    49.1    -      -       +      +
    363A  ASN*     3.3    28.3    +      -       -      +
    366A  VAL*     4.8     6.5    -      -       +      -
     43B  PRO      3.5     9.4    -      -       -      +
     44B  ALA*     4.1     2.2    -      -       +      +
     45B  SER*     4.7     0.2    -      -       -      -
     92B  VAL      4.9     0.7    -      -       -      +
    111B  CYS*     1.3    86.0    -      -       -      +
    113B  ARG*     1.3    67.9    +      -       -      +
    114B  ASP*     3.2     4.7    -      -       +      +
    115B  ASP*     3.0    28.7    +      -       -      +
    116B  VAL*     4.5     0.2    -      -       -      +
----------------------------------------------------------
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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