Contacts of the strand formed by residues 239 - 244 (chain A) in PDB entry 1W7L


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 THR 239 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    210A  CYS*     3.3    10.9    -      -       +      +
    212A  THR*     3.7    21.5    -      -       +      -
    229A  ILE*     3.8    10.3    -      -       +      +
    230A  ALA*     3.7    27.9    -      -       +      -
    235A  MET*     2.8    42.9    +      -       -      +
    236A  TRP*     3.5     4.0    +      -       -      +
    238A  ARG*     1.3    80.6    +      -       -      +
    240A  LEU*     1.3    66.7    +      -       -      +
    241A  THR*     3.8     2.0    -      -       -      +
    260A  LEU      4.0     0.2    -      -       -      +
    261A  GLY*     3.8     4.0    -      -       -      -
    262A  PRO*     3.4    23.7    -      -       -      +
    265A  ILE*     4.4     1.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 240 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107A  ALA*     4.0    16.6    -      -       +      -
    111A  LEU*     3.8    22.7    -      -       +      -
    209A  VAL*     4.5     6.9    -      -       +      +
    210A  CYS      2.9     8.9    +      -       -      +
    211A  ILE*     3.7    11.3    -      -       +      +
    212A  THR*     2.8    34.4    +      -       -      +
    239A  THR*     1.3    80.0    -      -       -      +
    241A  THR*     1.3    59.1    +      -       -      +
    242A  ILE*     4.8     2.1    -      -       +      +
    259A  VAL*     3.8    10.8    -      -       +      -
    260A  LEU      3.5     1.6    -      -       -      -
    261A  GLY*     4.2     5.8    -      -       -      -
    265A  ILE*     3.7    23.6    -      -       +      -
    266A  MET*     3.8    28.0    -      -       -      -
    269A  LEU*     3.7    24.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 241 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80A  PHE*     6.5     0.4    -      -       +      -
     84A  LEU*     4.9     9.5    -      -       +      +
    212A  THR*     3.4    13.6    -      -       +      +
    214A  GLU*     3.6    35.2    -      -       +      +
    217A  GLN*     5.9     0.9    -      -       -      +
    228A  SER*     5.1     2.0    -      -       -      +
    230A  ALA*     3.5    23.6    -      -       -      +
    236A  TRP*     5.6     0.5    -      -       -      -
    239A  THR*     3.8     0.3    -      -       -      +
    240A  LEU*     1.3    73.5    -      -       -      +
    242A  ILE*     1.3    66.2    +      -       -      +
    243A  GLY      4.2     0.3    +      -       -      -
    258A  TRP*     3.7     1.0    -      -       -      +
    259A  VAL*     3.2     3.8    -      -       -      -
    260A  LEU*     2.8    63.6    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 242 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100A  GLY*     4.0    14.6    -      -       -      +
    103A  ALA*     3.9    22.2    -      -       +      +
    104A  LEU*     3.7    40.2    -      -       +      +
    107A  ALA*     4.8     3.6    -      -       +      -
    211A  ILE*     3.9    18.8    -      -       +      -
    212A  THR      2.8    16.6    +      -       -      +
    213A  ASP*     4.3     7.0    -      -       -      +
    214A  GLU*     3.0    32.4    +      -       -      +
    215A  VAL*     4.4     7.9    -      -       +      -
    240A  LEU*     4.9     2.2    -      -       +      +
    241A  THR*     1.3    80.9    -      -       -      +
    243A  GLY*     1.3    68.2    +      -       -      +
    258A  TRP*     3.4     2.9    -      -       -      -
    259A  VAL*     3.9    22.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 243 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100A  GLY*     4.0     2.3    -      -       -      -
    214A  GLU      4.8     1.8    -      -       -      -
    215A  VAL*     4.0    10.5    -      -       -      -
    242A  ILE*     1.3    80.7    -      -       -      +
    244A  SER*     1.3    61.7    +      -       -      -
    257A  GLY*     3.2     3.5    -      -       -      -
    258A  TRP*     3.1    54.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 244 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100A  GLY      4.1     1.3    -      -       -      -
    215A  VAL*     3.6    28.7    -      -       -      +
    243A  GLY*     1.3    75.6    -      -       -      -
    245A  ALA*     1.3    61.8    +      -       -      +
    246A  GLY*     3.3    11.3    +      -       -      -
    247A  LYS*     3.4    14.0    +      -       -      +
    248A  THR*     2.8    26.8    +      -       -      -
    256A  VAL      3.7     4.7    -      -       -      -
    257A  GLY*     4.1     0.4    -      -       -      -
    258A  TRP*     3.7     6.8    -      -       -      -
   1247A  PLP      2.6    29.8    +      -       -      -
----------------------------------------------------------
 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