Contacts of the strand formed by residues 200 - 208 (chain A) in PDB entry 1SDW


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 200 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  PRO*     6.2     0.2    -      -       +      -
    152A  LYS      5.0     4.7    -      -       -      +
    153A  GLY      3.1    16.3    +      -       -      +
    154A  VAL*     3.8    24.5    -      -       +      -
    155A  GLY      3.1    20.4    +      -       -      -
    198A  GLN*     3.6     6.8    -      -       -      +
    199A  PRO*     1.3    92.0    -      -       +      +
    201A  ILE*     1.3    63.3    +      -       -      +
    322A  TYR*     3.9    33.4    -      -       +      -
    323A  MET      3.4     7.0    -      -       -      +
    324A  GLU*     3.7    29.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 201 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  PHE*     3.8    30.7    -      -       +      -
    155A  GLY      3.3    11.0    -      -       -      +
    157A  ARG*     3.8    33.2    -      -       +      +
    198A  GLN*     3.9    12.6    -      -       +      +
    200A  LEU*     1.3    81.0    -      -       -      +
    202A  ALA*     1.3    74.3    +      -       -      +
    203A  GLY      4.0     0.3    +      -       -      -
    321A  TYR*     4.7     1.4    -      -       -      -
    322A  TYR*     3.2     3.5    -      -       -      -
    323A  MET*     2.9    32.3    +      -       -      +
    325A  ALA*     3.8    24.2    -      -       +      +
    328A  ALA*     3.6    20.8    -      -       +      +
    329A  LEU      5.5     0.6    -      -       -      +
    330A  SER*     4.4     5.8    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 202 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150A  LEU*     4.7     0.4    -      -       +      -
    154A  VAL*     3.6    23.8    -      -       +      +
    155A  GLY      2.9    12.3    +      -       -      +
    156A  PHE*     3.6    42.8    -      -       +      -
    201A  ILE*     1.3    84.4    -      -       -      +
    203A  GLY*     1.3    59.4    +      -       -      +
    237A  PHE*     4.4     8.3    -      -       +      -
    321A  TYR*     3.1    11.0    -      -       -      +
    329A  LEU      5.4     0.2    -      -       -      -
    330A  SER*     4.5     3.0    +      -       -      -
    365A  GOL      4.2     4.9    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 203 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156A  PHE*     4.4     6.7    -      -       -      -
    202A  ALA*     1.3    74.3    -      -       -      +
    204A  MET*     1.3    60.7    +      -       -      -
    320A  MET*     3.5    10.9    -      -       -      +
    321A  TYR*     2.8    49.2    +      -       -      +
    330A  SER*     3.1    16.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 204 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  ASN*     6.0     0.4    -      -       +      -
    137A  ILE*     3.7    20.4    -      -       +      +
    156A  PHE*     4.8     3.8    -      -       +      -
    203A  GLY*     1.3    74.1    -      -       -      +
    205A  TYR*     1.3    63.7    +      -       -      +
    206A  LEU      3.9     0.2    -      -       -      -
    274A  PHE*     3.8     9.2    -      -       +      -
    318A  TYR*     3.8    28.9    -      -       +      -
    319A  ILE      3.5    17.5    -      -       -      +
    320A  MET*     3.6    40.4    -      -       +      -
    321A  TYR*     3.3     6.1    -      -       -      -
    330A  SER      3.0     8.2    +      -       -      +
    331A  PHE*     3.3     1.7    -      -       -      -
    332A  MET      3.0    22.9    +      -       -      -
    368A  GOL      3.2    42.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 205 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204A  MET*     1.3    74.5    -      -       -      +
    206A  LEU*     1.3    59.6    +      -       -      +
    207A  MET*     3.7    26.0    -      -       +      -
    227A  CYS*     3.6     7.6    -      -       -      +
    229A  TYR*     4.0     4.0    -      +       -      -
    234A  MET*     4.1     8.1    -      -       +      -
    289A  LEU*     3.4    33.2    -      -       +      +
    317A  LEU      3.6     2.8    -      -       -      +
    319A  ILE*     2.8    52.7    +      -       +      +
    321A  TYR*     3.6    10.7    -      -       +      -
    332A  MET*     3.4    42.0    -      -       +      -
    333A  THR      4.3     0.4    -      -       -      -
    334A  CYS*     3.6    22.2    -      -       +      +
    366A  GOL      2.6    41.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 206 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204A  MET      3.9     0.8    -      -       -      -
    205A  TYR*     1.3    73.2    -      -       -      +
    207A  MET*     1.3    77.9    +      -       -      +
    208A  MET*     3.9    19.1    -      -       +      -
    316A  ASN*     4.1    10.3    -      -       +      -
    317A  LEU      3.7     7.2    -      -       -      +
    318A  TYR*     3.8    27.4    -      -       +      +
    332A  MET      2.9    10.2    +      -       -      +
    333A  THR*     3.2    11.2    -      -       +      +
    334A  CYS      2.8    25.6    +      -       -      -
    368A  GOL      3.8    30.1    -      -       -      -
    701A  IYT      3.8    36.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 207 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205A  TYR*     3.7    21.1    -      -       +      -
    206A  LEU*     1.3    72.2    -      -       -      +
    208A  MET*     1.3    62.3    +      -       -      +
    225A  ILE*     3.7    39.5    -      -       +      +
    226A  SER*     4.3     1.8    -      -       -      -
    252A  GLY*     5.6     0.2    -      -       -      -
    253A  TYR      5.7     0.2    -      -       -      +
    263A  ILE*     6.2     0.4    -      -       -      -
    289A  LEU*     3.5    44.4    -      -       +      +
    290A  ALA      4.6     2.0    -      -       -      -
    291A  ALA*     3.7    19.3    -      -       +      +
    315A  CYS      3.7     0.5    -      -       -      +
    316A  ASN*     3.4     2.8    -      -       -      -
    317A  LEU*     2.9    45.4    +      -       +      +
    319A  ILE*     4.0    21.3    -      -       +      -
    334A  CYS*     3.5    11.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 208 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206A  LEU*     3.9    25.8    -      -       +      -
    207A  MET*     1.3    75.1    -      -       -      +
    209A  SER*     1.3    71.4    +      -       -      +
    210A  VAL*     4.0    14.4    -      -       +      -
    225A  ILE*     3.5    11.9    -      -       -      +
    315A  CYS      3.2     5.6    -      -       -      -
    316A  ASN*     3.5    16.2    -      -       -      +
    333A  THR*     4.5     2.9    -      -       +      -
    334A  CYS      3.0     9.4    +      -       -      +
    335A  THR*     3.4    47.5    -      -       +      -
    701A  IYT      3.3    54.5    -      -       +      +
----------------------------------------------------------
 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