Contacts of the strand formed by residues 198 - 208 (chain D) in PDB entry 4O2E


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 GLU 198 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194D  ILE*     3.1    39.3    +      -       +      +
    195D  SER*     3.1    21.7    +      -       -      +
    196D  ASP      3.6     0.6    -      -       -      -
    197D  HIS*     1.3   108.4    +      -       +      +
    199D  ALA*     1.3    62.5    +      -       -      +
    248D  VAL*     3.5    21.3    -      -       +      +
    249D  VAL      3.3    17.5    -      -       -      +
    250D  PRO*     4.4     2.2    -      -       +      -
    251D  SER*     3.7     4.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 199 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191D  HIS*     3.4    38.4    -      -       +      +
    192D  HIS      3.5    10.3    -      -       -      +
    193D  PRO*     3.5     6.1    -      -       +      -
    194D  ILE*     3.7     7.9    -      -       -      +
    198D  GLU*     1.3    77.4    -      -       -      +
    200D  THR*     1.3    61.3    +      -       -      +
    201D  LEU*     5.5     0.9    -      -       +      -
    248D  VAL*     3.5     1.2    -      -       -      -
    249D  VAL*     2.7    43.0    +      -       +      +
    251D  SER*     4.8     1.8    -      -       -      +
    254D  GLU*     5.1     3.4    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 200 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190D  THR      3.6     1.0    -      -       -      +
    191D  HIS*     3.5     4.9    -      -       -      -
    192D  HIS*     2.7    50.6    +      -       +      -
    194D  ILE*     3.5    21.5    -      -       -      +
    199D  ALA*     1.3    72.1    -      -       -      +
    201D  LEU*     1.3    68.4    +      -       -      +
    202D  ARG*     4.1    20.6    -      -       +      +
    246D  ALA*     3.8    27.8    -      -       +      -
    247D  VAL      3.5     8.1    -      -       -      +
    248D  VAL*     4.2     6.1    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 201 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189D  VAL*     4.4     2.0    -      -       +      -
    190D  THR      3.5     8.5    -      -       -      +
    191D  HIS*     3.6    32.1    -      -       +      -
    199D  ALA*     3.8     0.9    +      -       +      +
    200D  THR*     1.3    75.7    -      -       -      +
    202D  ARG*     1.3    59.7    +      -       -      +
    217D  TRP*     3.8    24.8    +      -       +      -
    246D  ALA*     3.2     3.3    -      -       -      -
    247D  VAL*     3.0    38.6    +      -       +      +
    249D  VAL*     3.8    26.0    -      -       +      -
    254D  GLU*     4.3    19.3    -      -       +      +
    257D  TYR*     4.2    18.2    -      -       +      +
    274D  TRP*     4.0    23.1    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 202 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189D  VAL*     3.3     4.4    -      -       -      +
    190D  THR*     2.9    44.3    +      -       -      +
    192D  HIS*     3.4    32.2    +      -       +      -
    200D  THR*     4.0    16.2    -      -       +      +
    201D  LEU*     1.3    73.7    -      -       -      +
    203D  CYS*     1.3    60.9    +      -       -      +
    204D  TRP*     3.4    35.9    -      -       +      +
    217D  TRP*     4.1     2.9    -      -       -      -
    229D  GLU*     5.0     3.0    +      -       -      -
    244D  TRP*     3.2    59.2    -      -       +      -
    245D  ALA      3.4     2.5    -      -       -      -
    246D  ALA*     4.2     5.1    -      -       +      +
     98E  ASP*     3.3    17.5    +      -       -      +
     99E  MET*     4.1    16.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 203 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188D  HIS      3.7     3.1    -      -       -      -
    189D  VAL*     4.4     3.6    -      -       -      -
    202D  ARG*     1.3    71.4    -      -       -      +
    204D  TRP*     1.3    65.2    +      -       -      +
    215D  LEU*     4.1    11.4    -      -       +      +
    217D  TRP*     3.6    17.6    -      -       +      +
    244D  TRP*     3.1     7.4    -      -       -      +
    245D  ALA*     2.7    39.8    +      -       +      +
    259D  CYS*     2.0    48.9    -      -       -      -
    261D  VAL*     4.4     3.1    -      -       -      -
    272D  LEU*     4.4    18.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 204 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186D  LYS      4.2     0.7    -      -       -      -
    187D  THR*     3.1    30.8    -      -       -      +
    188D  HIS*     2.9    51.0    +      +       +      +
    190D  THR*     3.2    22.7    +      -       -      +
    192D  HIS*     5.8     0.4    -      +       -      -
    202D  ARG*     3.4    30.9    -      -       +      +
    203D  CYS*     1.3    76.0    -      -       -      +
    205D  ALA*     1.3    59.8    +      -       -      +
    206D  LEU*     3.8    29.8    -      -       +      -
    215D  LEU*     5.0     0.7    -      -       -      -
    234D  ARG*     3.9    13.7    -      -       -      -
    242D  GLN*     6.1     0.2    -      -       +      -
    243D  LYS      3.9     3.1    -      -       -      -
    244D  TRP*     3.5    29.2    -      +       +      -
     97E  ARG      5.0     3.6    -      -       -      -
     98E  ASP*     3.2    26.5    -      -       -      -
     99E  MET*     3.7    20.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 205 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185D  PRO*     3.9     9.6    -      -       +      -
    186D  LYS      3.6     2.7    -      -       -      -
    187D  THR*     4.2     3.4    -      -       +      -
    204D  TRP*     1.3    72.8    -      -       -      +
    206D  LEU*     1.3    63.6    +      -       -      +
    208D  PHE*     3.3    10.7    -      -       +      -
    213D  ILE*     3.8    29.6    -      -       +      -
    215D  LEU*     4.0    15.7    -      -       +      +
    242D  GLN*     3.3     1.6    -      -       -      -
    243D  LYS      2.8    38.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 206 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185D  PRO*     3.5     0.5    -      -       -      +
    186D  LYS*     2.8    55.5    +      -       +      +
    188D  HIS*     4.3    20.6    -      -       +      +
    204D  TRP*     3.8    29.6    -      -       +      -
    205D  ALA*     1.3    82.2    -      -       -      +
    207D  GLY*     1.3    64.6    +      -       -      +
    208D  PHE*     3.3     4.3    +      -       -      -
    241D  PHE      4.0     0.9    -      -       -      -
    242D  GLN*     3.6    32.3    -      -       +      +
    243D  LYS      4.9     0.2    -      -       -      +
     12E  ARG      6.1     0.2    -      -       -      +
     14E  PRO*     4.2    29.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 207 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183D  ASP*     3.6    19.4    -      -       -      +
    184D  PRO      4.0     5.1    -      -       -      +
    186D  LYS*     4.9    13.0    +      -       -      -
    206D  LEU*     1.3    74.9    -      -       -      +
    208D  PHE*     1.3    60.8    +      -       -      +
    236D  ALA*     5.7     0.9    -      -       -      -
    240D  THR*     3.3    27.0    -      -       -      +
    241D  PHE      3.0     9.0    +      -       -      -
    242D  GLN*     4.5     3.8    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 208 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183D  ASP      3.4    13.2    -      -       -      +
    185D  PRO*     3.6    30.1    -      -       +      -
    205D  ALA*     3.3    34.5    -      -       +      -
    207D  GLY*     1.3    79.6    -      -       -      +
    209D  TYR*     1.3    62.7    +      -       -      +
    210D  PRO      3.3    19.1    -      -       -      -
    211D  ALA      3.3    23.1    -      -       -      -
    213D  ILE*     3.9    20.4    -      -       +      -
    233D  THR*     4.1     2.9    -      -       +      -
    240D  THR*     3.5     0.9    -      -       -      -
    241D  PHE*     2.8    49.1    +      -       +      -
    242D  GLN*     3.6    19.3    -      -       -      -
    243D  LYS*     3.8     2.9    -      -       +      -
    263D  HIS*     3.7    13.0    -      +       -      +
----------------------------------------------------------
 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