Contacts of the strand formed by residues 60 - 70 (chain B) in PDB entry 6FF8


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 VAL 60 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  LEU*     3.9    30.4    +      -       +      +
     57B  THR*     4.1     5.1    -      -       -      +
     58B  ILE      3.1     7.0    +      -       -      +
     59B  GLY*     1.3    79.1    -      -       -      +
     61B  ASP*     1.3    73.1    +      -       -      +
     62B  PHE*     3.7    26.8    -      -       +      -
     80B  TRP*     4.0     7.0    -      -       +      -
     81B  ASP      3.3    13.2    -      -       -      +
     82B  ILE*     3.9    16.2    -      -       +      -
     95B  TYR*     3.5    45.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 61 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  PHE*     4.1    15.4    -      -       -      +
     63A  ALA*     5.2     1.9    +      -       -      -
     39B  THR*     4.6    10.9    -      -       -      +
     57B  THR*     3.9    12.6    +      -       +      +
     60B  VAL*     1.3    78.8    -      -       -      +
     62B  PHE*     1.3    86.0    +      -       -      +
     81B  ASP*     2.9    54.2    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 62 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  LEU*     5.7     2.2    -      -       +      -
     61A  ASP*     5.6     0.9    -      -       -      +
     62A  PHE*     3.1    46.3    -      +       +      +
     63A  ALA      4.4     8.7    -      -       -      -
     64A  LEU*     4.3    17.9    -      -       +      -
     78A  GLN*     2.9    48.2    -      -       +      +
     42B  ILE*     5.4     1.6    -      -       -      -
     60B  VAL*     3.7    32.8    -      -       +      -
     61B  ASP*     1.3    92.3    +      -       -      +
     63B  ALA*     1.3    65.0    +      -       -      +
     79B  LEU      3.1     8.5    -      -       -      +
     80B  TRP*     3.6    41.3    -      +       +      -
     81B  ASP*     6.0     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 63 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  PHE*     3.7    11.2    -      -       -      -
     42B  ILE*     3.5    31.0    -      -       +      -
     46B  VAL*     4.2    19.1    -      -       +      -
     47B  HIS*     5.3     7.2    -      -       +      -
     62B  PHE*     1.3    77.8    -      -       -      +
     64B  LEU*     1.3    58.9    +      -       -      +
     65B  LYS      4.2     0.2    -      -       -      -
     78B  GLN*     3.7     3.1    -      -       -      -
     79B  LEU*     2.8    35.7    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 64 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60A  VAL*     5.5     5.6    +      -       +      +
     62A  PHE*     3.9    14.6    -      -       +      -
     80A  TRP*     4.9     7.9    -      -       +      -
     91A  MET*     4.0    15.3    -      -       +      -
     94A  VAL*     5.2     3.4    -      -       +      -
     95A  TYR*     3.8    32.3    -      -       +      +
     25B  LEU*     4.4     9.9    -      -       +      -
     46B  VAL*     3.5    19.0    -      -       -      +
     63B  ALA*     1.3    74.6    -      -       -      +
     65B  LYS*     1.3    64.8    +      -       -      +
     66B  VAL*     4.1     7.6    +      -       +      +
     76B  ARG*     4.5     8.1    -      -       +      -
     77B  LEU      3.2     9.2    -      -       -      +
     78B  GLN*     3.5    35.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 65 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  TYR*     2.9    72.2    +      -       +      +
     46B  VAL*     4.0    21.2    +      -       +      +
     63B  ALA      4.2     0.6    -      -       -      -
     64B  LEU*     1.3    73.9    -      -       -      +
     66B  VAL*     1.3    79.0    +      -       -      +
     67B  LEU*     4.0    11.3    +      -       +      +
     76B  ARG*     3.3     5.5    -      -       -      +
     77B  LEU*     2.8    44.2    +      -       +      +
     79B  LEU*     4.3     6.4    -      -       +      +
    182B  GLU*     4.5     7.4    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 66 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  MET*     4.0    33.7    -      -       +      -
     64B  LEU*     4.1     9.4    +      -       +      +
     65B  LYS*     1.3    88.4    -      -       -      +
     67B  LEU*     1.3    61.9    +      -       -      +
     68B  ASN*     4.2     5.0    +      -       -      +
     74B  LEU*     4.3    26.7    -      -       +      -
     75B  VAL      3.7     4.7    -      -       -      +
     76B  ARG*     4.4     9.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 67 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45B  TYR*     2.9    27.8    -      -       +      +
     65B  LYS*     3.9     9.8    -      -       +      -
     66B  VAL*     1.3    75.4    -      -       -      +
     68B  ASN*     1.3    64.8    +      -       -      +
     69B  TRP*     3.1    44.2    +      -       +      -
     74B  LEU*     3.6     4.7    -      -       -      +
     75B  VAL*     2.7    57.0    +      -       +      +
     77B  LEU*     4.3    10.5    -      -       +      -
    185B  ALA*     5.0     2.5    -      -       +      +
    186B  ARG*     4.4    12.6    -      -       +      +
    189B  VAL*     4.0    22.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 68 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66B  VAL*     4.2     5.2    +      -       -      +
     67B  LEU*     1.3    70.5    -      -       -      +
     69B  TRP*     1.3    67.5    +      -       -      +
     70B  ASP*     3.4     9.3    +      -       -      +
     73B  THR      4.1     4.2    +      -       -      -
     74B  LEU*     3.2    27.3    -      -       -      +
    186B  ARG*     3.9     8.0    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 69 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67B  LEU*     3.1    14.7    +      -       +      -
     68B  ASN*     1.3    74.7    -      -       -      +
     70B  ASP*     1.3    82.9    +      -       -      +
     73B  THR*     3.0    30.7    +      -       +      +
     75B  VAL*     4.0    13.9    -      -       +      -
    186B  ARG*     3.0    90.0    +      -       +      +
    189B  VAL*     3.6    22.9    -      -       +      -
    190B  GLU*     3.7    34.5    -      -       +      -
    193B  LEU*     3.7    20.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 70 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68B  ASN*     4.4     9.1    +      -       -      +
     69B  TRP*     1.3    95.3    +      -       +      +
     71B  SER*     1.3    64.1    +      -       -      +
     72B  ARG*     2.8    13.2    +      -       -      +
     73B  THR*     2.7    41.2    +      -       -      +
    186B  ARG*     5.4     0.4    -      -       -      +
----------------------------------------------------------
 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