Contacts of the strand formed by residues 8 - 18 (chain B) in PDB entry 1FYT


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 LEU 8 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  PHE*     3.9    26.5    -      -       +      -
     13A  TYR      3.5    15.0    -      -       -      +
     14A  LEU*     3.9    15.7    -      -       +      -
     70A  LEU*     4.0     3.1    -      -       -      +
     82A  ILE*     3.8    15.3    -      -       +      -
    113A  THR*     3.6    23.6    -      -       -      +
    115A  PRO*     3.7    17.7    -      -       +      -
    145A  PHE*     4.1     4.9    -      -       +      -
      7B  PHE*     1.3    75.1    -      -       -      +
      9B  TRP*     1.3    64.1    +      -       -      +
     10B  GLN*     3.8    25.1    -      -       +      +
     31B  ILE      3.7     0.6    -      -       -      +
     32B  TYR*     3.4     9.6    -      -       -      -
     33B  ASN*     2.8    42.0    +      -       -      +
     34B  GLN*     5.1     2.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 9 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  PHE*     3.0     7.8    -      -       -      +
     13A  TYR*     2.9    35.4    +      -       +      +
     66A  ASP*     3.1    47.4    +      -       +      +
     69A  ASN*     3.9    22.9    -      -       +      +
     70A  LEU*     3.8    23.3    -      -       +      -
     73A  MET*     3.5    43.7    -      -       +      -
      8B  LEU*     1.3    74.2    -      -       -      +
     10B  GLN*     1.3    67.7    +      -       -      +
     11B  LEU*     4.3    13.7    -      -       +      +
     30B  CYS*     3.5    40.8    -      -       +      -
     31B  ILE      3.5    15.0    -      -       -      -
     32B  TYR*     4.6     3.8    -      +       +      -
     37B  SER*     4.8     0.2    -      -       -      -
     38B  VAL*     5.9     0.2    -      -       +      -
    314C  LEU      5.5     0.4    -      -       -      -
    316C  LEU*     3.6    19.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 10 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  GLU      3.4     4.7    -      -       -      +
     12A  PHE*     3.7    19.3    -      -       +      -
    139A  PRO*     6.2     0.8    -      -       -      +
    143A  HIS*     3.2    31.8    +      -       -      +
    144A  LEU      5.0     0.2    +      -       -      -
    145A  PHE*     2.9    33.0    -      -       +      -
      8B  LEU*     3.8    17.4    -      -       +      +
      9B  TRP*     1.3    79.1    -      -       -      +
     11B  LEU*     1.3    62.2    +      -       -      +
     12B  LYS*     4.5    14.4    -      -       +      +
     30B  CYS*     3.6     2.1    -      -       -      -
     31B  ILE*     2.7    68.2    +      -       +      +
     34B  GLN*     4.2     5.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 11 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  GLN      3.6     1.5    -      -       -      +
     10A  ALA*     3.5     3.3    -      -       -      -
     11A  GLU*     2.9    45.5    +      -       +      +
     66A  ASP*     3.9     4.5    -      -       -      +
     69A  ASN*     6.0     0.2    -      -       -      +
      9B  TRP*     4.3    13.9    -      -       +      +
     10B  GLN*     1.3    76.0    -      -       -      +
     12B  LYS*     1.3    63.0    +      -       -      +
     13B  PHE*     3.8    24.9    -      -       +      -
     28B  GLU*     4.9     4.9    -      -       +      +
     29B  ARG      3.0    26.2    -      -       -      +
     30B  CYS*     3.4    28.7    -      -       -      -
    313C  THR*     3.3    45.5    -      -       +      -
    314C  LEU      5.0     1.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 12 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  ILE*     4.4    16.5    -      -       +      +
      9A  GLN      3.3     4.9    -      -       -      +
     10A  ALA*     4.5     7.2    -      -       +      -
    139A  PRO*     4.2    17.3    -      -       +      +
    140A  ARG      2.6    37.0    +      -       -      +
    141A  GLU*     4.7     1.0    -      -       -      +
    143A  HIS*     3.2    32.8    +      -       +      +
     10B  GLN*     4.5    17.0    -      -       +      +
     11B  LEU*     1.3    80.7    -      -       -      +
     13B  PHE*     1.3    64.2    +      -       -      +
     14B  GLU*     3.9    21.9    +      -       +      +
     27B  LEU      3.5     1.4    -      -       -      +
     28B  GLU*     3.4     2.8    -      -       -      +
     29B  ARG*     2.7    48.5    +      -       +      +
     31B  ILE*     4.6     8.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 13 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  ILE      3.6     1.9    -      -       -      +
      8A  ILE*     3.4     2.8    -      -       -      -
      9A  GLN*     2.9    62.1    +      -       +      +
     11A  GLU*     4.2     1.8    -      -       -      -
     11B  LEU*     3.8    29.4    -      -       +      -
     12B  LYS*     1.3    73.7    -      -       -      +
     14B  GLU*     1.3    61.6    +      -       -      +
     15B  CYS      4.0     0.2    +      -       -      -
     26B  LEU*     4.7     7.6    -      -       +      -
     27B  LEU      3.5     2.9    -      -       -      -
     28B  GLU*     3.1    44.4    -      -       +      -
     71B  ARG*     4.1     0.7    -      -       -      -
     78B  TYR*     3.4    25.6    +      +       +      +
    311C  GLN*     3.3    32.3    -      -       +      -
    312C  ASN      3.7    20.0    -      -       -      -
    313C  THR*     4.5     0.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 14 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  VAL*     4.9     0.4    -      -       +      -
      7A  ILE      3.6     4.0    -      -       -      -
      8A  ILE*     3.7    32.6    -      -       +      +
    141A  GLU*     6.0     1.4    -      -       -      +
     12B  LYS*     4.1    16.2    +      -       +      +
     13B  PHE*     1.3    75.0    -      -       -      +
     15B  CYS*     1.3    61.3    +      -       -      +
     16B  HIS*     3.1    31.1    +      -       +      +
     25B  ARG      3.4     2.3    -      -       -      +
     26B  LEU*     3.4     6.8    -      -       -      +
     27B  LEU*     2.8    49.5    +      -       +      +
     29B  ARG*     2.7    43.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 15 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  VAL*     3.3     5.8    -      -       -      -
      7A  ILE*     2.8    42.3    +      -       +      +
     14B  GLU*     1.3    72.2    -      -       -      +
     16B  HIS*     1.3    60.6    +      -       -      +
     17B  PHE*     3.5    22.7    -      -       +      -
     24B  VAL*     5.1     0.2    -      -       +      -
     25B  ARG      3.6     4.3    -      -       -      -
     26B  LEU*     3.8     1.6    -      -       -      -
     78B  TYR*     3.5    24.9    -      -       -      -
     79B  CYS*     2.1    52.7    -      -       +      -
     82B  ASN*     5.9     1.1    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 16 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3A  GLU*     5.8     4.0    -      -       -      +
      5A  HIS      3.6     4.3    -      -       -      +
      6A  VAL*     3.4    27.7    -      -       +      +
     14B  GLU*     3.1    39.4    +      -       +      +
     15B  CYS*     1.3    75.0    -      -       -      +
     17B  PHE*     1.3    60.5    +      -       -      +
     18B  PHE*     3.7    26.7    -      +       +      -
     24B  VAL*     3.3     7.3    -      -       -      +
     25B  ARG*     2.8    66.8    +      -       +      +
     27B  LEU*     4.6     8.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 17 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  GLU*     3.3    10.1    +      -       -      +
      5A  HIS*     3.0    42.5    +      -       +      +
      7A  ILE*     3.7    23.8    -      -       +      -
     15B  CYS*     3.5    37.0    -      -       +      -
     16B  HIS*     1.3    73.7    -      -       -      +
     18B  PHE*     1.3    61.5    +      -       -      +
     19B  ASN      4.1     0.7    -      -       -      -
     20B  GLY      3.2    20.0    -      -       -      +
     21B  THR*     3.8    10.5    -      -       +      -
     23B  ARG      3.6     3.4    -      -       -      -
     24B  VAL*     4.0    11.7    -      -       +      -
     79B  CYS*     3.6    25.8    -      -       +      -
     80B  ARG      4.2     1.3    -      -       -      -
     83B  TYR*     3.3    51.6    -      +       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 18 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2A  LYS*     2.8    30.7    -      -       +      +
      3A  GLU*     3.3    39.7    -      -       +      -
      4A  GLU*     4.2     3.4    -      -       -      -
      5A  HIS      6.0     0.2    -      -       -      -
     16B  HIS*     3.7    36.1    -      +       +      -
     17B  PHE*     1.3    72.8    -      -       -      +
     19B  ASN*     1.3    76.1    +      -       +      +
     20B  GLY      4.0     0.2    +      -       -      -
     22B  GLU*     3.5    12.5    +      -       -      +
     23B  ARG*     3.0    68.5    +      -       +      +
     25B  ARG*     4.6     8.1    -      -       +      -
----------------------------------------------------------
 Back to top of page


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