Contacts of the strand formed by residues 198 - 207 (chain B) in PDB entry 4BEI


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 ALA 198 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164B  LEU*     4.3    20.4    -      -       +      -
    192B  ASN*     3.4    21.3    -      -       +      +
    194B  ARG*     3.5    27.1    -      -       -      +
    197B  GLU*     1.3    74.4    -      -       -      +
    199B  ASN*     1.3    63.1    +      -       -      +
    200B  VAL*     3.9     2.5    +      -       +      +
    222B  TRP      3.5     2.1    -      -       -      +
    223B  VAL*     3.6     1.7    -      -       -      -
    224B  ILE*     2.9    36.5    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 199 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    194B  ARG*     4.8     2.2    -      -       -      +
    197B  GLU*     3.9    22.3    +      -       -      +
    198B  ALA*     1.3    73.3    -      -       -      +
    200B  VAL*     1.3    65.0    +      -       -      +
    222B  TRP      3.4     3.3    -      -       -      +
    223B  VAL*     3.3    29.2    -      -       -      +
    255B  ASP*     3.5     7.4    +      -       -      +
    256B  ILE*     2.9    44.8    +      -       +      -
    257B  VAL*     4.7    18.7    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 200 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161B  LEU*     4.6     0.2    -      -       +      -
    164B  LEU*     3.3    31.9    -      -       +      -
    190B  LEU*     4.5     9.9    -      -       +      -
    198B  ALA*     4.7     2.7    -      -       +      +
    199B  ASN*     1.3    82.6    -      -       -      +
    201B  GLU*     1.3    60.1    +      -       -      +
    202B  PHE*     5.2     2.0    -      -       +      -
    220B  GLU      3.9     0.3    -      -       -      +
    221B  LYS*     3.5     2.6    -      -       -      -
    222B  TRP*     2.8    57.6    +      -       +      +
    224B  ILE*     4.1    16.8    -      -       +      -
    253B  VAL*     3.8    16.6    -      -       +      -
    254B  VAL      3.1    12.8    -      -       -      +
    255B  ASP*     4.3     8.1    -      -       +      -
    256B  ILE*     3.5     8.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 201 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  ALA*     5.5     1.9    -      -       -      +
    121A  PRO*     4.1     3.7    -      -       -      +
    123A  TYR*     2.6    44.8    +      -       +      +
    124A  MET*     3.8     7.3    -      -       -      +
    200B  VAL*     1.3    74.7    -      -       -      +
    202B  PHE*     1.3    64.9    +      -       -      +
    203B  TRP*     3.7    22.2    -      -       +      -
    219B  ARG*     3.8    29.6    +      -       +      +
    220B  GLU      3.2    13.9    -      -       -      +
    221B  LYS*     4.0    15.5    +      -       +      +
    252B  GLN      4.1     0.2    -      -       -      +
    253B  VAL*     3.4     4.5    -      -       -      +
    254B  VAL*     2.8    34.8    +      -       +      +
    256B  ILE*     3.8     8.4    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 202 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168B  ILE*     4.5     4.5    -      -       +      -
    188B  VAL*     4.0    24.0    -      -       +      -
    190B  LEU*     4.4    15.0    -      -       +      -
    200B  VAL*     5.2     2.9    -      -       +      -
    201B  GLU*     1.3    77.7    -      -       -      +
    203B  TRP*     1.3    70.7    +      -       -      +
    204B  MET*     3.8    38.1    -      -       +      -
    217B  ASN*     3.6    27.4    -      -       -      -
    218B  ALA      3.4     2.3    -      -       -      +
    219B  ARG*     3.5     0.7    -      -       -      -
    220B  GLU*     2.8    44.2    +      -       +      +
    222B  TRP*     5.2     3.1    -      -       +      -
    230B  TYR*     4.3    24.0    -      +       -      -
    232B  LYS*     4.6     2.7    -      -       -      -
    251B  ALA*     4.5     8.1    -      -       +      -
    252B  GLN      3.4    13.2    -      -       -      +
    253B  VAL*     3.8    17.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 203 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  ILE*     4.8     1.1    -      -       +      -
     87A  TYR      2.9    27.0    +      -       -      -
     88A  PHE*     3.5    20.2    -      +       +      +
     89A  PRO*     4.1     3.8    -      -       +      -
    124A  MET*     3.5    26.5    -      -       +      -
    201B  GLU*     3.7    24.7    -      -       +      -
    202B  PHE*     1.3    88.1    -      -       -      +
    204B  MET*     1.3    74.0    +      -       -      +
    205B  THR      5.1     0.2    -      -       -      -
    217B  ASN*     3.5    14.4    -      -       -      +
    218B  ALA      4.0     1.3    -      -       -      +
    219B  ARG*     3.6    31.0    -      -       +      -
    250B  ASN      5.5     0.4    -      -       -      -
    252B  GLN*     2.8    67.5    +      -       +      +
    254B  VAL*     3.3    31.6    -      -       +      -
    261B  ARG*     4.5     2.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 204 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89A  PRO*     4.1     0.9    -      -       -      +
    168B  ILE*     4.3    15.7    -      -       +      -
    186B  PHE*     4.5    13.7    -      -       +      -
    188B  VAL*     4.2    13.5    -      -       -      -
    202B  PHE*     3.8    22.7    -      -       +      -
    203B  TRP*     1.3    83.5    -      -       -      +
    205B  THR*     1.3    68.8    +      -       -      +
    215B  PRO*     4.0     0.9    -      -       -      +
    216B  VAL*     2.9    21.7    +      -       +      -
    217B  ASN*     2.9    44.9    +      -       +      +
    234B  ARG*     4.5     7.4    -      -       -      +
    249B  ILE*     4.0    25.6    -      -       +      -
    250B  ASN      3.2     5.6    -      -       -      +
    251B  ALA*     3.7    23.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 205 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  SER*     5.7     0.2    -      -       -      +
     87A  TYR*     3.7    34.3    -      -       -      +
     88A  PHE*     4.1     1.6    -      -       -      -
     89A  PRO*     4.0    21.3    -      -       +      -
    203B  TRP*     4.8     0.6    -      -       +      -
    204B  MET*     1.3    80.2    -      -       -      +
    206B  ALA*     1.3    56.9    +      -       -      +
    207B  VAL*     3.9     9.6    -      -       -      +
    213B  ILE*     4.0    23.8    -      -       +      -
    214B  ILE      3.3    10.8    -      -       -      +
    215B  PRO*     4.7     2.2    -      -       +      -
    216B  VAL*     3.7     7.2    -      -       -      +
    248B  THR      3.7     0.2    -      -       -      +
    249B  ILE*     3.6     3.1    -      -       -      +
    250B  ASN*     2.7    43.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 206 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205B  THR*     1.3    71.8    -      -       -      +
    207B  VAL*     1.3    64.3    +      -       -      +
    208B  GLY*     3.6     2.6    +      -       -      -
    212B  LEU      3.7     0.2    -      -       -      +
    213B  ILE*     3.7     1.1    -      -       -      -
    214B  ILE*     2.7    45.2    +      -       +      +
    216B  VAL*     3.7    11.0    -      -       +      -
    236B  ILE*     4.0    12.1    -      -       +      -
    247B  TYR*     4.5    10.9    -      -       +      -
    248B  THR      3.5     4.9    -      -       -      +
    249B  ILE*     3.5    26.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 207 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87A  TYR*     3.6    48.9    -      -       +      -
   1272A  O4B      3.9    18.2    -      -       -      -
    205B  THR*     3.9    12.1    -      -       -      +
    206B  ALA*     1.3    72.1    -      -       -      +
    208B  GLY*     1.3    60.6    +      -       -      +
    212B  LEU      3.5     8.3    -      -       -      +
    213B  ILE*     4.5     4.7    -      -       +      +
    246B  GLU      3.8     1.4    -      -       -      +
    247B  TYR*     3.5     0.6    -      -       -      -
    248B  THR*     2.7    44.8    +      -       -      +
    250B  ASN*     4.9     1.6    -      -       +      -
   1272B  O4B      3.6    33.5    -      -       -      +
----------------------------------------------------------
 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